SI Appendix

S upporting Information Corrected November 7, 2011 Materials and Methods

Bioinformatics. Using the 454 next generation sequencing platforms, we previously sequenced a small RNA library prepared using pooled adult mouse testes (testes from 3 individual adult mice). A total of ~half million reads were obtained. We developed an in-house computer program to identify endo-siRNAs. A flow chart illustrating the identification process is shown in SI Appendix, Fig. S1. Briefly, three criteria were used in the initial screening: 1) the length of small RNAs ranged from 19-23-nt; 2) sequences of small RNAs were matched to the mouse genome; 3) sequences of small RNAs were completely complementary to known transcripts. Transcript libraries used in this study included cDNA from Ensembl, refMrna from UCSC Genome Browser (1), LTR retrotransposon, Endogenous Retrovirus and Non-LTR retrotransposon from Genetic Information Research Institute (2), piRNA from RNAdb (3), miRNA from miRBase (4), tRNA from Genomic tRNA Database (5), snoRNA from RNAdb (3), and rRNA from Ensembl. Small RNAs that fulfilled all the three criteria were defined as candidate endo-siRNAs. All candidate endo-siRNAs then went through further analyses of the inherent stem-loop structure using Mfold (6). Candidate endo-siRNAs that cannot form the short stem-loop structure were included in the final list as endo-siRNAs (SI Appendix, Table S1). Sequences of endo-siRNAs were then subject to forward and reverse complementary (RC) matching against the sequences of all known transcripts collected in the libraries described above. If the forward- and RC-matched sequences were complementary to each other, then these two sequences were defined as two strands of a potential dsRNA precursor for the endo-siRNA(s). If two sequences were from two different transcripts, than the dsRNA precursor was defined as an intermolecular dsRNA. If two sequences came from one single transcript, than the dsRNA precursor was defined as intramolecular dsRNA. The length and percentage of complementarity of the two strands of the dsRNA precursor were calculated (SI Appendix, Dataset 1). For intermolecular dsRNA precursors, the top two potential dsRNA precursors with the greatest length and percentage of complementarity were chosen as the most likely precursors. Since some dsRNA precursors contained multiple endo-siRNAs, a total of 60 intermolecular dsRNA precursors were analyzed in this study that could generate 42 endo-siRNAs (SI Appendix, Dataset 1).

Quantitative analyses of endo-siRNAs, miRNAs and other transcripts. Small RNA isolation, small RNA cDNA synthesis, and small RNA semi-quantitative PCR were performed following our published protocols (7). For TaqMan-based small RNA quantitative real-time PCR (qPCR), a TaqMan probe (5’FAM-CTCGGATCCACTAGTC-MGB3’) was used (Applied Biosystems) and U6 snoRNA was used as endogenous control. Total RNA of human testis was purchased from Zyagen. Small RNAs were further isolated using the method described previously (7). For sequencing, the products from small RNA semi-quantitative PCR were cloned into pCR4-TOPO vector (Invitrogen) and sequenced by M13 forward or reverse primer. Semi-quantitative PCR for other transcripts including mRNAs, transcripts of pseudogenes, retrotransposons, and large non- coding RNAs was performed as described previously (8). Primer sequences for quantitative analyses of endo-siRNAs, miRNAs and other transcripts can be found in SI Appendix, Table S3. Image J (NIH) was used to determine the band density in the semi-qPCR gels, and an in-house computer program was created to convert densitometric values into a heat map.

Luciferase Assay. The 3’UTR sequences containing the predicted targeting sites for endo- siRNAs were inserted into the XbaI-FesI site immediately downstream of the stop codon in the pGL4.13 firefly luciferase vector (Promega). The endo-siRNAs were chemically synthesized double-stranded RNAs, which can mimic endo-siRNAs after transfection into cells (QIAGEN). Details of construction are available upon request. The NIH/3T3 cells were cultured in 10% fetal calf serum (Hyclone) in DMEM (Invitrogen). On the day before transfection, growing cells were trypsinized and plated into 12- well plates at a density of 1 × 105 cells/well in an antibiotic-free medium. The next day, cells were co-transfected using the Attractene Transfection Reagent (QIAGEN) with 20ng of pGL4.13 constructs, 480ng of pRL-TK control vector (Renilla luciferase vector, Promega), and 1pmol of endo-siRNA mimics in a final volume of 1.0 ml. 24 hours after transfection, firefly and Renilla luciferase activities were measured using the Dual-Luciferase Reporter Assay System (Promega). The luciferase activity was expressed as the ratio of firefly/Renilla luciferase activities. For quantitative analyses of firefly and Renilla mRNAs, total RNA was isolated from each sample and cDNAs were then synthesized followed by SYBR Green-based quantitative real-time PCR. Primer sequences used can be found in SI Appendix, Table S3. This protocol was modified from Luciferase Assay method in the previous report (9).

Generation of male germ cell-specific Dicer or Drosha knockout mice with EGFP expression in Cre-expressing cells. Four lines of mice (Stra8-iCre, Dicerlox/lox, Droshalox/lox and Rosa26mTmGtg/tg) were used to generate the compound male postnatal germ cell-specific Dicer or Drosha knockout mice (Stra8-iCre-Dicerlox/lox-Rosa26mTmG+/tg and Stra8-iCre-Droshalox/lox- Rosa26mTmG+/tg). Stra8-iCre, Dicer-loxp and Rosa26mTmG mice were previously characterized (10-12) and were purchased from the Jackson Laboratory. Drosha-loxp mice were generated as described (13).

Purification of spermatogenic cells using the STA-PUT method. We purified pachytene spermatocytes from control (Stra8-iCre-Rosa26mTmG+/tg) and knockout (Stra8-iCre-Dicerlox/lox- Rosa26mTmG+/tg and Stra8-iCre-Droshalox/lox-Rosa26mTmG+/tg) testes (SI Appendix, Fig. S4A) at the age of postnatal day 25 (P25) using the STA-PUT system (Proscience) as described (14). Briefly, the gradient of 2%-4% BSA was formed under the suspension of germ cells in the sedimentation chamber. After 3 hours, the 2%-4% BSA gradient was unloaded from bottom of the sedimentation chamber. According to unit gravity, the initial fractions from bottom gradients were cells with larger radius like pachytene spermatocytes, and the later fractions from top gradients were cells with smaller radius like round spermatids. Since all Cre-expressing cells were green (EGFP-positive) and non-Cre-expressing cells were red, the cell types and purity collected from each fraction were monitored directly using phase and fluorescent microscopy (Carl Zeiss, Axioplan2). A representative result of purified Dicer-null or Drosha-null spermatocytes is shown in SI Appendix, Fig. S4B. In addition to morphological evaluation of the cell types and purity in each of the fractions collected, we also performed quantitative real-time PCR (qPCR) analyses to more accurately determine the purity of the cells in each fraction by examining levels of marker mRNAs for all major types of testicular cells (SI Appendix, Fig. S5). Small RNAs and mRNAs were isolated from first four fractions (No.2-No.5), and we generated small RNA cDNAs and mRNAs cDNAs, respectively. SYBR Green-based qPCR was used to quantify levels of marker genes among four fractions of purified cells and P25 whole testis. These marker genes included Cyp17a1 for Leydig cells (15), Gata4 for Sertoli cells (16), Sohlh1 for spermatogonia (17), Sycp2 for spermatocytes (18), and Catsper3 for spermatids (8). The fractions with the highest levels of Sycp2 and the lowest levels of other marker genes were chosen for quantitative analyses of Drosha and Dicer mRNAs, endo-siRNAs and miRNAs. Primer sequences for all qPCR analyses can be found in SI Appendix, Table S3.

References

1. Fujita PA, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39(Database issue):D876-882. 2. Jurka J, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110(1-4):462-467. 3. Pang KC, et al. (2005) RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res 33(Database issue):D125-130. 4. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, & Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue):D140-144. 5. Chan PP & Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37(Database issue):D93-97. 6. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406-3415. 7. Ro S, Park C, Jin J, Sanders KM, & Yan W (2006) A PCR-based method for detection and quantification of small RNAs. Biochem Biophys Res Commun 351(3):756-763. 8. Jin JL, et al. (2005) Catsper3 and catsper4 encode two cation channel-like proteins exclusively expressed in the testis. Biol Reprod 73(6):1235-1242. 9. Yu Z, Raabe T, & Hecht NB (2005) MicroRNA Mirn122a reduces expression of the posttranscriptionally regulated germ cell transition protein 2 (Tnp2) messenger RNA (mRNA) by mRNA cleavage. Biol Reprod 73(3):427-433. 10. Sadate-Ngatchou PI, Payne CJ, Dearth AT, & Braun RE (2008) Cre recombinase activity specific to postnatal, premeiotic male germ cells in transgenic mice. Genesis 46(12):738- 742. 11. Harfe BD, McManus MT, Mansfield JH, Hornstein E, & Tabin CJ (2005) The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. Proc Natl Acad Sci U S A 102(31):10898-10903. 12. Muzumdar MD, Tasic B, Miyamichi K, Li L, & Luo L (2007) A global double-fluorescent Cre reporter mouse. Genesis 45(9):593-605. 13. Chong MM, Rasmussen JP, Rudensky AY, & Littman DR (2008) The RNAseIII enzyme Drosha is critical in T cells for preventing lethal inflammatory disease. J Exp Med 205(9):2005-2017. 14. Bellve AR (1993) Purification, culture, and fractionation of spermatogenic cells. Methods Enzymol 225:84-113. 15. Bridges PJ, et al. (2008) Generation of Cyp17iCre transgenic mice and their application to conditionally delete estrogen receptor alpha (Esr1) from the ovary and testis. Genesis 46(9):499-505. 16. Mazaud Guittot S, et al. (2007) The proximal Gata4 promoter directs reporter gene expression to sertoli cells during mouse gonadal development. Biol Reprod 76(1):85-95. 17. Ballow D, Meistrich ML, Matzuk M, & Rajkovic A (2006) Sohlh1 is essential for spermatogonial differentiation. Dev Biol 294(1):161-167. 18. Yang F, et al. (2006) Mouse SYCP2 is required for synaptonemal complex assembly and chromosomal synapsis during male meiosis. J Cell Biol 173(4):497-507.

SI Figures

Fig. S1. The flowchart used to identify mouse testicular endo-siRNAs.

Fig. S2. Chromosome mapping of mouse testicular endo-siRNAs. (A) Number of chromosome hits of five representative endo-siRNAs (endo-siRNAs-T8, T3, T40, T6 and T19). (B) Number of chromosomes with endo-siRNA hits. Majority of the 73 endo-siRNAs have hits on all 21 chromosomes in mice.

Fig. S3. Expressions of transcripts that were predicted to form dsRNA precursors for testicular endo-siRNAs in developing testes of mice. (A) Expression profiles of transcripts predicted to form intermolecular dsRNA precursors during testicular development. (B) Expression profiles of transcripts predicted to form intramolecular dsRNA precursors during testicular development. P, postnatal day; NTC, non-template control. Gapdh was used as a loading control.

Fig. S4. Purification of pachytene spermatocytes from testes of control (Stra8-iCre-Rosa26mTmG+/tg) and knockout (Stra8-iCre-Dicerlox/lox-Rosa26mTmG+/tg and Stra8-iCre-Droshalox/lox-Rosa26mTmG+/tg) mice at P25 using the STA-PUT method. (A) Representative cross sections of the seminiferous tubules of control, Drosha, and Dicer knockout testes at postnatal day 25 (P25) (600×). eGFP-positive cells are the spermatogenic cells with Cre expression and Cre-mediated Dicer or Drosha inactivation. (B) Representative fluorescent and phase-contrast images of purified Drosha-null or Dicer-null pachytene spermatocytes (200×). Green cells are the Cre-expressing pachytene spermatocytes, whereas the rare red cells represent non-Cre-expressing spermatogonia or somatic cells (i.e. Sertoli or Leydig cells).

Fig. S5. Quantitative real-time PCR analyses of levels of Cyp17a1 (Leydig cell marker), Gata4 (Sertoli cell marker), Sohlh1 (Spermatogonia marker), Sycp2 (Spermatocytes marker), and Catsper3 (Spermatids marker) in top four fractions (No.2-No.5) of cells collected from the STA-PUT sedimentation chamber. Whole testes at P25 were used as calibration sample. Fractions No.4 in controls, No.4 in Drosha KO samples, and No. 5 in Dicer KO samples contained mostly spermatocytes (~85%). In addition these three samples displayed similar proportions of contamination from other four types of testicular cells.

Fig. S6. Levels of Dicer, Drosha and miRNAs in pachytene spermatocytes purified from control (Stra8- iCre-Rosa26mTmG+/tg) and knockout (Stra8-iCre-Dicerlox/lox-Rosa26mTmG+/tg and Stra8-iCre-Droshalox/lox- Rosa26mTmG+/tg) mice at P25. (A) Levels of Dicer in pachytene spermatocytes purified from control, Dicer or Drosha KO mice using SYBR Green-based real-time PCR. (B) Levels of Drosha in pachytene spermatocytes purified from control, Dicer or Drosha KO mice using SYBR Green-based real-time PCR. (C) Levels of 12 testicular miRNAs in pachytene spermatocytes purified from control, Dicer or Drosha KO mice using TaqMan-based real-time PCR.

Fig. S7. Levels of 58 endo- siRNAs in pachytene spermatocytes purified from control (Stra8-iCre- Rosa26mTmG+/tg) and knockout (Stra8-iCre- Dicerlox/lox-Rosa26mTmG+/tg and Stra8-iCre-Droshalox/lox- Rosa26mTmG+/tg) mice at P25 using TaqMan-based real-time PCR.

Fig. S8. Endo-siRNA expression in human testes. Mouse testes severed as a positive control and the negative control was reactions without templates (non- template control, NTC). Endo-siRNAs marked with asterisks (*) were confirmed by sequencing, which showed sequences identical to those of moue endo- siRNAs. The bands with arrow pointed are primer dimers.

Fig. S9. Effects of endo-siRNAs on the translations of their target mRNAs revealed by a luciferase-based reporter assay. (A) Expression profiles of 5 mRNAs (Frmpd1, Lrrc2, Kif17, Spata1, and Syt11) predicted to be targeted by the three endo-siRNAs (endo-siRNAs-T6, T40 and T19) tested in developing mouse testes. Gapdh served as a loading control. P, postnatal day. NTC, non-template controls. (B) Expressions of three endo-siRNAs (endo-siRNAs-T6, T40 and T19) in the NIH 3T3 cells and wild-type (WT) mouse testes. snoRNA U6 served as a loading control. NTC, non-template controls. (C) Expressions of 5 mRNAs predicted to be targeted by the three endo-siRNAs at their 3’UTRs in mouse NIH 3T3 cells and wild-type (WT) mouse testes. Gapdh severed as a loading control. NTC, non-template controls. (D) Luciferase-based reporter assays to examine effects of endo-siRNAs on the translations of their target mRNAs. NIH 3T3 cells were transfected using firefly luciferase plasmids bearing the 3’UTR of Frmpd1, Lrrc2, Kif17, Spata1 or Syt11, and its corresponding targeting endo-siRNAs (T6, T40 and T19). Three types of controls included transfection without corresponding endo-siRNAs (open bars), the native firefly luciferase plasmid (None) and the firefly luciferase plasmid bearing Klhl10 3’UTR which did not contain any targeting sites for three endo-siRNAs tested. Experiments were performed in triplicates and values of luciferase activity were calibrated against the negative controls with no endo-siRNA transfection. Table S1. Detailed information on all 73 endo-siRNAs including endo-siRNA ID, sequence, length, predicted targets, targeting sites in predicted targets, and accession numbers for predicted targets

ID Sequence Length Taget Transcripts Target Sites Accession Number endo-siRNA-T1 ACAGTGTACTCACATATAT 19 AC158921.17 3'UTR, Known protein coding ENSMUST00000100773 endo-siRNA-T2 GCAGGCTGGCCTCGAACTC 19 Cd22 3'UTR ENSMUST00000108123, ENSMUST00000108125, ENSMUST00000019248, NM_001043317 2, NM_009845 3 mmu-miR-1195 (23 bp) tgagttcgaggccagcctgctca MIMAT0005856 piR-140680 (22 bp) tgagttcgaggccagcctgcta PIR234006 endo-siRNA-T3 TCAGGTCCCTGTTCGGGCGCC 21 Endogenous Retrovirus 2 MMERVK9E_I endo-siRNA-T4 GCTCTTCCGAAGGTCCAGAGT 21 AC134329.2 3'UTR, Known protein coding ENSMUST00000116231 Gas2l3 3'UTR ENSMUST00000105298, NM_001033331 2, ENSMUST00000099374, NM_001079876 1 Nmnat1 3'UTR ENSMUST00000119921 Prkcbp1 3'UTR ENSMUST00000109262 RP23-159H8.4 Known processed pseudogene ENSMUST00000120163 Zfp397os Exon4 ENSMUST00000070583 endo-siRNA-T5 CTCGAACTCAGAAATCTACCTG 22 AC124987.9-1 3'UTR, Known protein coding ENSMUST00000098523 Csf3r 3'UTR ENSMUST00000106162, ENSMUST00000030673, ENSMUST00000106163, NM_007782 2 Heatr6 3'UTR ENSMUST00000001002, NM_145432 3 Thap6 3'UTR ENSMUST00000094611, NR_028429 1 endo-siRNA-T6 CTGTGTAGCCTTGGCTGTCCTG 22 9630025I21Rik 3' UTR NM_001076791 2 A130010J15Rik 3' UTR NM_001160359 1, NM_181048 3, NM_001160360 1 B4galt6 3'UTR ENSMUST00000070080 Dclre1b 3'UTR ENSMUST00000106832 Ewsr1 3'UTR ENSMUST00000063232 Frmpd1 3'UTR ENSMUST00000044773 Gabpb2 3'UTR ENSMUST00000107209, NM_172512 2, NM_029885 1, ENSMUST00000098873 Lrrc2 3'UTR ENSMUST00000035076, NM_028838 2 Mettl13 3'UTR ENSMUST00000028017, NM_144877 1 Pik3c2a 3' UTR NM_011083 2 Rnasel 3' UTR NM_011882 2 Samd8 3'UTR ENSMUST00000022292, NM_026283 2, ENSMUST00000119430 Tmem20 3‘UTR ENSMUST00000054098, NM_175507 3 endo-siRNA-T7 CTCTGTAGAGCAGGCTGGCCTTG 23 1200011I18Rik 3'UTR ENSMUST00000022585, NM_026177 3 Top3b 3'UTR ENSMUST00000118424 endo-siRNA-T8 AAGTCATGTTCATTGTTTGAGTT 23 C230052I12Rik 3' UTR NM_178643 5 endo-siRNA-T9 GTTCCCGGGTTTCGGCACC 19 Endogenous Retrovirus 2 IAPEY5_I endo-siRNA-T10 TCTCCTGCTTTTTTACCAC 19 Slc38a6 3‘UTR ENSMUST00000058139 endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT 19 1810030O07Rik 3'UTR ENSMUST00000060108, NM_175141 5 endo-siRNA-T12 CCCGGGTTTCGGCACCAAC 19 AC121960.3 3'UTR, Known protein coding ENSMUST00000100355 endo-siRNA-T13 TAGCCTGGTCTACAGAGTG 19 0610010E21Rik 5'UTR ENSMUST00000098585 4933407H18Rik 3'UTR ENSMUST00000045520, ENSMUST00000087864 9830001H06Rik 3' UTR NM_001164663 1 A230107C01Rik 3'UTR ENSMUST00000069861 AC138737.10 3'UTR, Known protein coding ENSMUST00000115135 AL844204.3 3'UTR, Known protein coding ENSMUST00000099399 C130079G13Rik 5'UTR ENSMUST00000049476, NM_177661 3 C230078M08Rik 5'UTR ENSMUST00000059100, NM_001081656 2 Ces1 3'UTR ENSMUST00000044602, NM_021456 3 D330041H03Rik 5'UTR ENSMUST00000084725 Dynll1 3' UTR NM_019682 4 Exoc8 3' UTR NM_198103 2 Hdgfrp3 3'UTR ENSMUST00000107305, NM_013886 4, ENSMUST00000107306 Ints7 3'UTR ENSMUST00000045450 Ldlrad2 3'UTR ENSMUST00000088339 Tmbim1 5'UTR ENSMUST00000113796 Xkr8 3' UTR NM_201368 1 Zfp11 3'UTR ENSMUST00000049778, NM_172462 4 endo-siRNA-T14 TATTCCTGGTTGTCAACTT 19 Prkcq 3'UTR ENSMUST00000114853 Rhbdd2 3'UTR ENSMUST00000043707, NM_146002 2 piR-100709 (29 bp) tagtcaagttgacaaccaggaatagccac PIR194035 piR-111806 (31 bp) tagtcaagttgacaaccaggaatagccacta PIR205132 piR-117177 (30 bp) tagtcaagttgacaaccaggaatagccact PIR210503 piR-122954 (30 bp) taatcaagttgacaaccaggaatagccact PIR216280 piR-128381 (26 bp) tagtcaagttgacaaccaggaatagc PIR221707 piR-134232 (28 bp) tagtcaagttgacaaccaggaatagcca PIR227558 piR-27294 (28 bp) tngtcaagttgacaaccaggaatagcca PIR21293 piR-27295 (29 bp) tngtcaagttgacaaccaggaatagccac PIR21294 piR-27296 (31 bp) tngtcaagttgacaaccaggaatagccacta PIR21295 piR-7540 (29 bp) tagtcaagttgacaaccaggaatagccac PIR28563 piR-7541 (30 bp) tagtcaagttgacaaccaggaatagccact PIR28564 piR-7542 (31 bp) tagtcaagttgacaaccaggaatagccactt PIR28565 piR-7543 (29 bp) tagtcaagttgacaaccaggaatagccat PIR28566 piR-7544 (27 bp) tagtcaagttgacaaccaggaatagct PIR28567 endo-siRNA-T15 CCAGGACAGCCAGGGCAAT 19 Dync1li2 3' UTR NM_001013380 2 endo-siRNA-T16 GCCCTGGCTGTCCTGGAACG 20 Atpbd4 3'UTR ENSMUST00000102542, ENSMUST00000055144, ENSMUST00000028640, NM_025675 4 endo-siRNA-T17 TAACAAGATACCAGAACTAC 20 Acnat1 3' UTR NM_001164565 1 endo-siRNA-T18 CACAGAGAAACCCTGTCTTG 20 1110059G10Rik 3' UTR NM_025419 4 1700052K11Rik 3' UTR NR_027956 1 2410129H14Rik 3' UTR NM_175245 4 3000002C10Rik 3'UTR ENSMUST00000093782 4930455C21Rik 3'UTR ENSMUST00000114734, NM_024273 2, ENSMUST00000002925 AC134329.2 3'UTR, Known protein coding ENSMUST00000116231 AC163640.5-1 3'UTR, Known protein coding ENSMUST00000100178 Arntl2 3'UTR ENSMUST00000111639 Bpnt1 3'UTR ENSMUST00000027916, NM_011794 3 C030027K23Rik 3'UTR ENSMUST00000040409 Ccdc127 3'UTR ENSMUST00000022063 Cfhr1 3'UTR ENSMUST00000023965, NM_015780 2 D230037D09Rik 3'UTR ENSMUST00000057416 Dhrs7b 3'UTR ENSMUST00000108718 Dhx37 3'UTR ENSMUST00000031443 Gfpt1 3'UTR ENSMUST00000113658, NM_013528 3 Hist1h2bm Exon2 ENSMUST00000110476 Kif23 3'UTR ENSMUST00000055275 Lrrn4cl 3'UTR ENSMUST00000096257, NM_001013019 2 Med18 3'UTR ENSMUST00000102567, NM_026039 3 Mina 3'UTR ENSMUST00000120667 Mkl2 3' UTR NM_001122667 2, NM_153588 3 Mmachc 3'UTR ENSMUST00000030453, NM_025962 3 Mmgt1 3'UTR ENSMUST00000059899, NM_146234 3 Nxnl1 3'UTR ENSMUST00000048243, NM_145598 2 Oscp1 3'UTR ENSMUST00000035497, NM_172701 2 Parp4 3' UTR NM_001145978 2 Pik3c2b 3'UTR ENSMUST00000077730, NM_001099276 2 Polr1b 3'UTR ENSMUST00000103205, NM_009086 2 Ppm1k 3'UTR ENSMUST00000042766, NM_175523 4 Rbm11 3'UTR ENSMUST00000114249, NM_198302 2, ENSMUST00000114253 Rbms2 3'UTR ENSMUST00000092033, NM_019711 2, NM_001039080 1, ENSMUST00000099139, ENSMUST00000105247, ENSMUST00000076233 Rfxank 3' UTR NM_011266 2, NM_001025589 1 Sc5d 3'UTR ENSMUST00000052725, NM_172769 2 Sgms2 3' UTR NM_028943 5 Siglece 3'UTR ENSMUST00000032667, NM_031181 2 Slc6a20b 3'UTR ENSMUST00000026273, NM_011731 3 Strbp 3' UTR NM_009261 3 Tbc1d24 3'UTR ENSMUST00000097376, ENSMUST00000040474, NM_001163847 1, NM_001163848 1, NM_173186 4, NM_001163850 1, NM_001163852 1, NM_001163853 1, NM_001163849 1, NM_001163851 1 Trp53rk 3' UTR NM_023815 4 Ttyh1 3' UTR NM_021324 5, NM_001001454 3, NM_001109765 1 Ube2j2 3'UTR ENSMUST00000024056, NM_021402 5, NM_001039157 1, NM_001039158 1, NM_001039159 1 Wdr25 3'UTR ENSMUST00000047115, NM_177602 3 Wipf2 3' UTR NM_197940 2 Zbtb44 3' UTR NM_172765 3, NM_001115130 1 endo-siRNA-T19 TCACTTTGTAGACCAGGCTG 20 1700037C18Rik 3'UTR ENSMUST00000115859 2010109I03Rik 3'UTR ENSMUST00000077004, NM_025929 2 2210404J11Rik 3'UTR ENSMUST00000081476 2810408P10Rik 3'UTR ENSMUST00000105718, NM_198619 2 5430411K18Rik 3'UTR ENSMUST00000044622 5730460C07Rik Exon3 ENSMUST00000081193 6820431F20Rik 5' UTR NR_028428 1 A130042E20Rik 3'UTR ENSMUST00000049185, NM_172550 4 A630033H20Rik 3'UTR ENSMUST00000067249, NM_001122595 1, NM_175442 4, NM_001122596 1 AB041806 3'UTR ENSMUST00000062902 AC121914.3 Novel pseudogene ENSMUST00000079884 AC151477.1 3'UTR, Known protein coding ENSMUST00000070021 Agtrap 3' UTR NM_009642 4 AL669855.20-2 5'UTR, Known protein coding ENSMUST00000076255 AL669969.14 3'UTR, Known protein coding ENSMUST00000105047 Ash2l 3'UTR ENSMUST00000068892 BC011426 3'UTR ENSMUST00000054780, NM_145490 4 BC055004 3'UTR ENSMUST00000110928 C030039L03Rik 3'UTR ENSMUST00000120004, NM_198417 2, NM_001112731 1, ENSMUST00000076421 Cand2 3' UTR NM_025958 2 Car5b 3'UTR ENSMUST00000033739, NM_181315 4 Ccdc125 3'UTR ENSMUST00000057325, NM_183115 4, NM_001168386 1 Cdan1 3'UTR ENSMUST00000085840 Cdnf 3'UTR ENSMUST00000036350, NM_177647 4 Cebpg 3' UTR NM_009884 3 Cntn2 3'UTR ENSMUST00000086521, NM_177129 5 CR974462.5-1 Exon5 + 3'UTR ENSMUST00000087244 Csf2rb 3'UTR ENSMUST00000096355, NM_007780 4 Csf3r 3'UTR ENSMUST00000106162, NM_007782 2, ENSMUST00000030673, ENSMUST00000106163 D730040F13Rik 3'UTR ENSMUST00000068792, ENSMUST00000107609 Ddx11 3'UTR ENSMUST00000038387, NM_001003919 1 Dffa 3'UTR ENSMUST00000103216 Dido1 5'UTR ENSMUST00000037764 Erich1 3'UTR ENSMUST00000063593, NM_001034862 2, ENSMUST00000110813 Fam116a 3'UTR ENSMUST00000037585 Fam86 3'UTR ENSMUST00000064635, NM_027446 2 Fbxl3 3'UTR ENSMUST00000022720, NM_015822 2 Fcer2a 3' UTR NM_013517 4 Fktn 3' UTR NM_139309 4 Ftsj1 3'UTR ENSMUST00000033513, NM_133991 2 Gad2 3'UTR ENSMUST00000028123, NM_008078 2 Gprc5c 3'UTR ENSMUST00000053361, NM_001110337 1 Haus2 3'UTR (2) ENSMUST00000110706, NM_025475 2 Ikbip 3'UTR ENSMUST00000020149, NM_026166 2 Kcnn1 3'UTR ENSMUST00000110078, NM_032397 2, ENSMUST00000110080, ENSMUST00000110081, ENSMUST00000002987 Kctd14 3'UTR ENSMUST00000121987, NM_001012434 3, NM_001010826 3, ENSMUST00000050732, NM_001136235 1 Kif5b 3'UTR ENSMUST00000025083, NM_008448 2 Klhl32 3'UTR ENSMUST00000108214 Kremen2 3'UTR ENSMUST00000046525, NM_028416 2 Lgr5 3'UTR ENSMUST00000020350, NM_010195 2 Lrrc14b 3'UTR ENSMUST00000022064, NM_001033042 3 Lrrc8e 3'UTR ENSMUST00000053035, NM_028175 2 Lsm11 3' UTR NM_028185 2 Med16 3'UTR ENSMUST00000045844, NM_001163276 1, NM_198107 2, ENSMUST00000105378 Mettl2 3' UTR NM_172567 3 Mobkl3 3' UTR NM_025283 3 Mrpl19 3'UTR ENSMUST00000032124, NM_026490 2 Mtif2 3'UTR ENSMUST00000020749, NM_133767 2, ENSMUST00000101423, ENSMUST00000093239 Myo1e 3'UTR ENSMUST00000034745, NM_181072 3 Mysm1 3'UTR ENSMUST00000075872, NM_177239 2 Nek7 3'UTR ENSMUST00000027642, NM_021605 3 Npy1r 3'UTR ENSMUST00000039303, NM_010934 4 Nt5dc3 3'UTR ENSMUST00000099396, NM_175331 3 Nwd1 3' UTR NM_001159403 1 Pclo 3' UTR NM_011995 4 Prox2 3'UTR ENSMUST00000110249, NM_175198 4 Ptpn7 3'UTR ENSMUST00000049449, NM_177081 3 Rangap1 3'UTR ENSMUST00000052374, NM_001146174 1, NM_011241 4 Rhbdl2 3'UTR ENSMUST00000053202, NM_183163 2, ENSMUST00000106204 Rint1 3'UTR ENSMUST00000115113, NM_177323 3, ENSMUST00000030852 RP23-360L8.1 Known processed pseudogene ENSMUST00000122293 RP23-58C21.2 Known processed pseudogene ENSMUST00000119460 Slc17a8 3'UTR ENSMUST00000020102, NM_182959 3 Slc5a4b 3'UTR ENSMUST00000120757, ENSMUST00000099573 Smyd4 3'UTR ENSMUST00000044530, NM_001102611 1 Spata1 3'UTR ENSMUST00000093951 Spin1 5' UTR NR_029463 1 Syt11 3'UTR ENSMUST00000107503, ENSMUST00000107505, NM_018804 3, ENSMUST00000090945 Tbc1d24 3'UTR ENSMUST00000097376, ENSMUST00000040474, NM_001163847 1, NM_001163848 1, NM_173186 4, NM_001163850 1, NM_001163852 1, NM_001163853 1, NM_001163849 1, NM_001163851 1 Tmc2 5'UTR ENSMUST00000077988, NM_138655 1 Tmed5 3'UTR ENSMUST00000002837, NM_028876 2, ENSMUST00000119437 Tmem20 3'UTR ENSMUST00000054098, NM_175507 3 Tmem50a 3'UTR ENSMUST00000030626, NM_027935 2 Trim39 3'UTR ENSMUST00000113706, NM_024468 2, NM_178281 1, ENSMUST00000042717, ENSMUST00000097327 Trove2 3'UTR ENSMUST00000018343, NM_013835 2 Ttbk2 3'UTR ENSMUST00000028740, NM_001024856 2, NM_001024857 2, NM_080788 3, ENSMUST00000057135 Ttc38 3'UTR ENSMUST00000088960, NM_001033337 4 Txnl4a 3' UTR NM_025299 3 Ubxn4 3'UTR ENSMUST00000027592, NM_026390 2 Yeats2 3'UTR ENSMUST00000090052, NM_001145930 1, ENSMUST00000115560, NM_001033237 2, ENSMUST00000041176 Zfp397 3'UTR ENSMUST00000060762, NM_027007 2 Zfp459 3'UTR ENSMUST00000056470, NM_177811 3 Zfp704 3'UTR ENSMUST00000041124, NM_133218 2 Zfyve27 3'UTR ENSMUST00000018964, NM_177319 3, NM_001164531 1 Zxda 3' UTR NR_003292 1 endo-siRNA-T20 TCGGCACCAATTGTTATTAG 20 AL845308.11 5'UTR, Known protein coding ENSMUST00000087474 piR-12185 (29 bp) tctaataacaattggtgccgaattccggg PIR5184 endo-siRNA-T21 GTTCAGCATCCTTAATCATC 20 Zfp277 Exon2 ENSMUST00000069692, NM_172575 3 endo-siRNA-T22 TCTGAGTTCAAGGCCAGCCT 20 2310010M20Rik 3'UTR ENSMUST00000054267, NM_183283 2, ENSMUST00000093183 2410129H14Rik 3' UTR NM_175245 4 2810021J22Rik 3'UTR ENSMUST00000073924, ENSMUST00000108820, NM_172403 2 5630401D24Rik 3'UTR ENSMUST00000097501 6030422M02Rik 3'UTR ENSMUST00000052843 9530003J23Rik 3'UTR ENSMUST00000020392, NM_029906 3 AC113329.7-1 5'UTR, Known protein coding ENSMUST00000078427 AC140291.2 3'UTR, Known protein coding ENSMUST00000100939 AC140300.3 3'UTR, Known protein coding ENSMUST00000097433 AC159372.1-1 3'UTR, Known protein coding ENSMUST00000098355 Acer1 3' UTR NM_175731 3 Aco1 3'UTR ENSMUST00000102973, NM_007386 2, ENSMUST00000030112 Asxl2 3'UTR ENSMUST00000092003 B230340J04Rik 3'UTR ENSMUST00000056152 Bpnt1 3'UTR ENSMUST00000027916, NM_011794 3 Car9 3'UTR ENSMUST00000107917, NM_139305 2, ENSMUST00000030183 Ccdc49 3'UTR ENSMUST00000018685, NM_026186 4 Cramp1l 3'UTR ENSMUST00000073337, NM_020608 3 Efr3b 3'UTR ENSMUST00000077156, NM_001082483 1, ENSMUST00000111178 Eif6 3'UTR ENSMUST00000109638 Elovl7 3' UTR NM_029001 5 Fadd 3' UTR NM_010175 5 Fam96a 3'UTR ENSMUST00000034945, NM_026635 3 Fnbp1 3'UTR ENSMUST00000073879 Galns 3'UTR ENSMUST00000015171, NM_016722 3, ENSMUST00000093060 Gen1 3'UTR ENSMUST00000052581 Gls 3' UTR NM_001081081 2 Glt8d1 3' UTR NM_029626 2, NM_001165930 1 Hist1h4i 3'UTR ENSMUST00000102977, NM_175656 2 Hnrnpab 3'UTR ENSMUST00000074669, NM_001048061 1, NM_010448 3, ENSMUST00000109103 Hsd17b7 3' UTR NM_010476 3 I0C0044D17Rik 3'UTR ENSMUST00000097964 Jub 3'UTR ENSMUST00000054487, NM_010590 4 Kcnk6 3'UTR ENSMUST00000085818, NM_001033525 3 Lix1 3'UTR ENSMUST00000115576, NM_025681 2, ENSMUST00000097389 Macf1 3'UTR ENSMUST00000068523 Mcart1 3'UTR ENSMUST00000107796, NM_001009949 2, ENSMUST00000084630 Mdc1 3'UTR ENSMUST00000082337, NM_001010833 2 Mfn1 3' UTR NM_024200 4 Nkiras1 3' UTR NM_023526 3 Nup214 3'UTR ENSMUST00000065398, NM_172268 2 Osbpl8 3'UTR ENSMUST00000095310, NM_175489 3, ENSMUST00000040683, NM_001003717 1, ENSMUST00000105275 P2rx7 3'UTR ENSMUST00000121489, NM_011027 2, NM_001038839 1, ENSMUST00000100737 Pigv 3'UTR ENSMUST00000062118, NM_001145955 1, NM_001145956 1, NM_178698 5, ENSMUST00000067902 Plin3 3'UTR ENSMUST00000019726, NM_025836 3 Ppm1k 3'UTR ENSMUST00000042766, NM_175523 4 Rdh1 3'UTR ENSMUST00000073639, NM_080436 3 Sgms2 3' UTR NM_028943 5 Slc24a6 3'UTR ENSMUST00000076051, NM_133221 2, ENSMUST00000068326, ENSMUST00000111890 Slc28a3 3'UTR ENSMUST00000022036, NM_022317 3 Smpd4 3'UTR ENSMUST00000090159, NM_029945 3, NM_001164609 1, NM_001164610 1, NM_001164611 1, ENSMUST00000006053 Smtnl2 3'UTR ENSMUST00000108500, NM_177776 3, ENSMUST00000050226, ENSMUST00000054338 Stx17 3'UTR ENSMUST00000107720 Supt7l 3'UTR ENSMUST00000117642, ENSMUST00000065388, NM_028150 2 Syt15 3'UTR ENSMUST00000035351, NM_181529 4 Tigd3 3'UTR ENSMUST00000055911, NM_198634 1 Trim36 3'UTR ENSMUST00000037011, NM_178872 3 Ubac1 3' UTR NM_133835 2 Zbtb11 5'UTR ENSMUST00000114448 Zdhhc3 3' UTR NM_026917 5 Zfp446 3'UTR ENSMUST00000108535, NM_175558 4, NM_001168561 1, NM_001168562 1, ENSMUST00000108538, ENSMUST00000108537, ENSMUST00000045810, ENSMUST00000108536 endo-siRNA-T23 TGGTATCGGCTTCTGGAACAC 21 RP23-139H14.3 Known processed pseudogene ENSMUST00000120188 RP23-161B3.4 Known processed pseudogene ENSMUST00000117856 RP23-235P16.1 Known processed pseudogene ENSMUST00000121035 RP23-260P9.1 Known processed pseudogene ENSMUST00000120687 RP23-302D20.1 Known processed pseudogene ENSMUST00000121675 RP23-303A21.2 Known processed pseudogene ENSMUST00000120708 RP23-66O9.1 Known processed pseudogene ENSMUST00000118329 RP23-74L11.2 Known processed pseudogene ENSMUST00000118418 endo-siRNA-T24 TATCACAGAGAAAGGAGCTTC 21 AC161410.3 5'UTR, Known protein coding ENSMUST00000098652 Cdc14b 3' UTR NM_172587 3, NM_001122989 1 Colec12 3'UTR ENSMUST00000040069, NM_130449 2 Crx 3'UTR ENSMUST00000044434, NM_001113330 1, NM_007770 4 D730040F13Rik 3'UTR ENSMUST00000068792, ENSMUST00000107609 Hmmr 3'UTR ENSMUST00000109302, NM_013552 2, ENSMUST00000020579, ENSMUST00000109303 Utp23 3' UTR NM_030132 5 endo-siRNA-T25 TCTGTGTTCATCTGACGAATT 21 Endogenous Retrovirus ERVB7_1-I_MM Endogenous Retrovirus 2 ETNERV endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG 21 1810012P15Rik 3'UTR ENSMUST00000100748 2210404J11Rik 3'UTR ENSMUST00000081476 2310003C23Rik 5'UTR ENSMUST00000078687, NM_029607 1 2310010M20Rik 3'UTR ENSMUST00000093183, ENSMUST00000054267, NM_183283 2 2410002O22Rik 3' UTR NM_001093759 1, NM_001093760 1, NM_025879 2 2600006K01Rik 3'UTR ENSMUST00000047607 2810006K23Rik 3'UTR ENSMUST00000077376, NM_001134717 1 4930594C11Rik Non-coding RNA NR_024017 1 4933432B09Rik 3' UTR NM_029407 1 6030458C11Rik 3'UTR ENSMUST00000057256, ENSMUST00000022804, NM_029998 3 A4galt 3'UTR ENSMUST00000049530, NM_001004150 3, NM_001170954 1 A530082C11Rik 3'UTR (2) ENSMUST00000105608, NM_177186 4 AC016522.1 Known processed pseudogene ENSMUST00000120986 AC016522.2 Known processed pseudogene ENSMUST00000121335 AC091523.23 3'UTR, Known protein coding ENSMUST00000097466 AC129188.3-1 Novel pseudogene ENSMUST00000048874 AC134329.2 3'UTR, Known protein coding ENSMUST00000116231 AC140047.8-2 3'UTR, Known protein coding ENSMUST00000115023 AC171318.3 3'UTR, Known protein coding ENSMUST00000067768 AI597468 3'UTR ENSMUST00000095383, NM_001013028 2 AL606521.24 Exon2, Known protein coding ENSMUST00000109941 AL670169.9-2 Exon2, Known protein coding ENSMUST00000085330 AL772249.6 Exon1, Known protein coding ENSMUST00000074761 AL831793.4 Novel pseudogene ENSMUST00000116247 AL928924.12-1 Novel pseudogene ENSMUST00000091477 AL928924.12-2 Exon1, Known protein coding ENSMUST00000100443 Arhgap19 3'UTR ENSMUST00000026150, NM_027667 3, NM_001163495 1 Atad2 3'UTR ENSMUST00000038194, ENSMUST00000022988, NM_027435 2 B4galnt2 3'UTR ENSMUST00000103158, ENSMUST00000038343, NM_008081 3 B4galt7 3'UTR ENSMUST00000064701, ENSMUST00000100764 Bbs1 3‘UTR ENSMUST00000053506, NM_001033128 3 BC019943 5'UTR ENSMUST00000033982, ENSMUST00000098842, NM_144927 3, NM_001112729 1 BC024139 3'UTR ENSMUST00000089654, ENSMUST00000068344, ENSMUST00000054022, NM_001142968 1 C230096C10Rik 3' UTR NM_146157 3, NM_001039200 1 Car5b 3'UTR ENSMUST00000033739, NM_181315 4 Car8 3'UTR ENSMUST00000098290, NM_007592 3 Ccdc127 3'UTR ENSMUST00000022063, NM_024201 3, NM_001168659 1 Cd93 3'UTR ENSMUST00000099269, NM_010740 3 Cep97 3' UTR NM_028815 4 Ctcfl 3'UTR ENSMUST00000094287, ENSMUST00000109117, NM_001081387 2 Cybrd1 3'UTR ENSMUST00000112154, ENSMUST00000028403, NM_028593 2 D14Abb1e 3' UTR NM_028945 1, NM_001114879 1 D330050I16Rik 3'UTR ENSMUST00000093445, NR_033224 1 Dhx37 3'UTR ENSMUST00000031443, NM_203319 1 Dnase2a 3'UTR ENSMUST00000109744, NM_010062 3, ENSMUST00000003910 Fam65b 3'UTR ENSMUST00000110384, ENSMUST00000058009, ENSMUST00000110383, NM_029679 1 Ftsjd2 3'UTR ENSMUST00000087910 Gaa 3' UTR NM_008064 3, NM_001159324 1 Gdf3 3' UTR NM_008108 4 Gjc3 3'UTR ENSMUST00000077119, NM_080450 4 Gm4925 3' UTR NM_001037166 2 Gng2 3' UTR NM_010315 4, NM_001038637 1 Gngt1 3'UTR ENSMUST00000031673, NM_010314 2 Gnl3l 3'UTR ENSMUST00000112691, NM_198110 2, NM_001168600 1 Gpr157 3'UTR ENSMUST00000094451, NM_177366 3 Gpr77 3‘UTR ENSMUST00000098792, NM_176912 4, NM_001146005 1 Hn1l 3'UTR ENSMUST00000024981 Ifnar1 3' UTR NM_010508 2 Il1rl1 3'UTR ENSMUST00000053043, ENSMUST00000097772, NM_001025602 2 Irak2 3'UTR ENSMUST00000089023, NM_001113553 1, ENSMUST00000089022, NM_172161 4, ENSMUST00000059286 Iws1 3' UTR NM_173441 3 Kbtbd10 3'UTR ENSMUST00000100050, NM_001081087 1 Kbtbd2 3'UTR ENSMUST00000114323, NM_145958 2, ENSMUST00000081115, ENSMUST00000114321 Lilrb3 3'UTR ENSMUST00000049747, ENSMUST00000078451 Lpp 3' UTR NM_001145952 1, NM_178665 5, NM_001145954 1 Lrrc58 3'UTR ENSMUST00000078717, NM_177093 3 Lrrn4cl 3'UTR ENSMUST00000096257, NM_001013019 2 Ltb4r2 3'UTR ENSMUST00000044554 Mcm5 3' UTR NM_008566 2 Mfap1a 3'UTR ENSMUST00000089926, NM_026220 4 Mga 3'UTR ENSMUST00000110774, NM_001164274 1, NM_013720 2, ENSMUST00000110773, ENSMUST00000079934 Mmp25 3'UTR ENSMUST00000024696, NM_001033339 3 Mrgprb1 3' UTR NM_205810 4 Mrpl24 5'UTR ENSMUST00000121048 Mrpl35 3'UTR ENSMUST00000065103, NM_025430 3 N4bp2 3'UTR ENSMUST00000113738 Nip7 3' UTR NM_001164472 1, NM_025391 2, NR_028367 1 Nosip 3' UTR NM_025533 3, NM_001163684 1 Nsl1 3'UTR ENSMUST00000078259, NM_198654 3 Nucks1 3'UTR ENSMUST00000062264, NM_175294 3, NM_001145804 1, ENSMUST00000112381 Ostf1 3' UTR NM_017375 3 Paxip1 3'UTR ENSMUST00000002291, NM_018878 2 Pde4c 3'UTR ENSMUST00000034307, NM_201607 2, ENSMUST00000110095 Peo1 3'UTR ENSMUST00000026227, NM_153796 3 Pfas 3'UTR ENSMUST00000021282, NM_001159519 1, ENSMUST00000108668 Polh 3'UTR ENSMUST00000024749 Ppp1r7 3' UTR NM_023200 2 Rab11b 3'UTR ENSMUST00000057373, NM_008997 3 Rad1 3'UTR ENSMUST00000022856, NM_011232 2 Rad51c 3'UTR ENSMUST00000007790, ENSMUST00000067692 Rbak 3'UTR ENSMUST00000049861, NM_021326 2, NM_001045482 1 Rbm11 3'UTR ENSMUST00000114249, NM_198302 2, ENSMUST00000114253 Rchy1 3' UTR NM_026557 3 Rfxank 3' UTR NM_011266 2, NM_001025589 1 Rg9mtd2 3'UTR ENSMUST00000040321, NM_175389 4 Riok3 3'UTR ENSMUST00000025270, NM_024182 4 RP23-40P1.1 Known processed pseudogene ENSMUST00000118379 RP24-392J24.7 Known processed pseudogene ENSMUST00000121066 Rrp1b 3' UTR NM_028244 2, NM_001163734 1 Rufy3 3'UTR ENSMUST00000101048 S1pr4 5' UTR NM_010102 1 Sco1 3'UTR ENSMUST00000108690, NM_001040026 1, ENSMUST00000092996 Sema3e 3'UTR ENSMUST00000073957, NM_011348 2 Sgsm1 Exon22 ENSMUST00000100876, NR_027936 1, NM_001162965 1 Slc35e1 3'UTR ENSMUST00000043238. NM_177766 3 Slc3a2 3' UTR NM_008577 4, NM_001161413 1 Slfn5 3'UTR ENSMUST00000108158, NM_183201 4, ENSMUST00000067443 Soat1 3'UTR ENSMUST00000051396, NM_009230 3 Sod2 3' UTR NM_013671 3 Stard7 3'UTR ENSMUST00000110374 Tapbp 3'UTR ENSMUST00000114350, NM_001025313 1, NM_009318 2, ENSMUST00000025161 Tbx20 3'UTR ENSMUST00000052946, NM_194263 1 Tln2 3'UTR ENSMUST00000034771, NM_001081242 2, ENSMUST00000039662, ENSMUST00000085405, ENSMUST00000039509, ENSMUST00000040025 Tmem82 5' UTR NM_145987 2 Tnfaip6 3'UTR ENSMUST00000065927, NM_009398 2 Tnfrsf10b 3'UTR ENSMUST00000022663, NM_020275 4 Tor1aip2 3'UTR ENSMUST00000060404, NM_172843 4, ENSMUST00000111757 Tox4 3'UTR ENSMUST00000022766, NM_023434 3, ENSMUST00000071842 Tstd2 3'UTR ENSMUST00000107772, NM_173033 3 Ttc26 3'UTR ENSMUST00000039394, NM_153600 2 Txndc11 3'UTR ENSMUST00000118679 Ube2v2 3' UTR NM_023585 4, NM_001159351 1 Usp45 3'UTR ENSMUST00000040429, NM_152825 2 Wipf2 3' UTR NM_197940 2 Xpo1 3'UTR ENSMUST00000109548, NM_134014 3, NM_001035226 1, ENSMUST00000109551, ENSMUST00000020538, ENSMUST00000102869 Xrcc2 3'UTR ENSMUST00000030773, NM_020570 2 Zbtb44 3' UTR NM_172765 3, NM_001115130 1 Zbtb6 3'UTR ENSMUST00000112932, NM_146253 5 Zc3hav1 3'UTR ENSMUST00000114900 Zfp113 3'UTR ENSMUST00000049393, NM_019747 4 Zfp187 3'UTR ENSMUST00000032820, NM_001013786 2 Zfp345 3'UTR ENSMUST00000109914, NM_001034900 3 Zfp385c 3'UTR ENSMUST00000103119, NM_177790 4, ENSMUST00000014342, ENSMUST00000107370 Zfp780b 3'UTR ENSMUST00000081618, NM_001081021 1 Zfp799 3'UTR ENSMUST00000079404, NM_177359 4 endo-siRNA-T27 AGAGAAAGTACCCAAGGAGCT 21 Gjc3 3'UTR ENSMUST00000077119, NM_080450 4 Olfr614 5'UTR ENSMUST00000106888, NM_147100 3 Tnfrsf10b 3'UTR ENSMUST00000022663, NM_020275 4 Tyms 3'UTR ENSMUST00000026846, NM_021288 3 endo-siRNA-T28 TCACTCTGTAGACCAGGCTAG 21 Hccs 3'UTR ENSMUST00000112115, ENSMUST00000033717, NM_008222 4 Psmd9 3' UTR NM_026000 2 Slfn5 3' UTR NM_183201 4 Tgfbr2 3'UTR ENSMUST00000061101, ENSMUST00000035014 Tnk1 3'UTR ENSMUST00000108626 endo-siRNA-T29 TCTGAGTTCGAGGCCAGCCTT 21 Fam178a Exon6+7 ENSMUST00000087330 Ttyh1 3' UTR NM_021324 5, NM_001001454 3, NM_001109765 1 endo-siRNA-T30 TACACAGAGAAACCCTGTTTC 21 Cog8 3'UTR ENSMUST00000034391 Dgke 3'UTR ENSMUST00000107894 Lrrc58 3'UTR ENSMUST00000078717, NM_177093 3 Ncan 3'UTR ENSMUST00000002412, NM_007789 3 Pdf 3'UTR ENSMUST00000055316, NM_026513 2 Rbak 3'UTR ENSMUST00000049861, NM_021326 2, NM_001045482 1 Trim14 3'UTR ENSMUST00000046897 endo-siRNA-T31 TTACATATAATAAATAAATCTT 22 1810063B07Rik 3'UTR ENSMUST00000059666, NM_026209 1 Ggps1 3' UTR NM_010282 2 Papola 3'UTR ENSMUST00000109901, ENSMUST00000093264, ENSMUST00000101063 endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC 22 1110021J02Rik 3' UTR NM_001163741 1 1110054O05Rik 3'UTR ENSMUST00000095063, NM_001013577 1 2010012O05Rik 3'UTR ENSMUST00000074912, NM_025563 3 2010106G01Rik 3' UTR NM_023220 2 2410091C18Rik 3'UTR ENSMUST00000024887, NM_028611 3 2510002D24Rik 3'UTR ENSMUST00000055413, NM_001033164 2 2510006D16Rik 3'UTR ENSMUST00000102591, NM_029748 2, ENSMUST00000071840 2610029I01Rik 3'UTR ENSMUST00000029915, NM_029840 1 4930579G24Rik 3'UTR ENSMUST00000029388, NM_029482 1 4933407I18Rik 3'UTR ENSMUST00000086982 5830416P10Rik 3' UTR NR_028427 1 9130404D08Rik 3' UTR NM_028993 4, NM_001167939 1 Abcd4 3' UTR NM_008992 2 AC102077.7 Exon3, Known protein coding ENSMUST00000085094 AC113595.11-1 3'UTR, Known protein coding ENSMUST00000100431 AC116718.1 3'UTR, Known protein coding ENSMUST00000092720 AC117602.9 5'UTR, Known protein coding ENSMUST00000081114 AC124987.9-1 3'UTR, Known protein coding ENSMUST00000098523 AC131679.2 Known processed pseudogene ENSMUST00000064305 Agphd1 3'UTR ENSMUST00000039742, NM_177351 4 Aldh9a1 3'UTR ENSMUST00000028004, NM_019993 3 Alkbh8 3'UTR ENSMUST00000053407 Anapc7 3'UTR ENSMUST00000119792 Aox3 3'UTR ENSMUST00000040999 Ap4e1 3'UTR ENSMUST00000002063, NM_175550 3 Aph1c 3' UTR NM_026674 3 B3galt6 3'UTR ENSMUST00000052185, NM_080445 4 BC023744 3'UTR ENSMUST00000100833 Bri3bp 3' UTR NM_029752 2 Brp16 3'UTR ENSMUST00000023213, NM_021555 2 Butr1 3'UTR ENSMUST00000069941 C330006K01Rik 3' UTR NM_172725 2 Camk4 3' UTR NM_009793 3 Car5a 3'UTR ENSMUST00000057653, NM_007608 2 Casc5 3'UTR ENSMUST00000028802 Ccdc78 3'UTR ENSMUST00000095500, NM_001165929 1 Cd8b1 3'UTR ENSMUST00000065248, NM_009858 2 Cdan1 3'UTR ENSMUST00000085840 Chek2 3'UTR ENSMUST00000066160, NM_016681 3 Chrnb4 3'UTR ENSMUST00000034854, NM_148944 4 Clmn 3'UTR ENSMUST00000109936, NM_001040682 1, ENSMUST00000109937, NM_053155 2 Dbt 3'UTR ENSMUST00000000349, NM_010022 3 Dci 3'UTR ENSMUST00000024946, NM_010023 4 Dcp2 3' UTR NM_027490 1 Ddx55 3'UTR ENSMUST00000111438 Dhrs7b 3'UTR ENSMUST00000108718 Dkc1 3'UTR ENSMUST00000033776, NM_001030307 2 Dlgap5 3'UTR ENSMUST00000043296, NM_144553 2 Dnalc1 3' UTR NM_028821 3 Dtx3l 3'UTR ENSMUST00000081933, NM_001013371 2 Elf1 3'UTR ENSMUST00000040131, NM_007920 3, ENSMUST00000088767, ENSMUST00000110835 Faf2 3' UTR NM_178397 3 Farsa 3'UTR ENSMUST00000095222 Fxn 3' UTR NM_008044 2 Gabpb2 3'UTR ENSMUST00000107209, NM_172512 2, NM_029885 1, ENSMUST00000098873 Glrx2 3' UTR NM_023505 2, NM_001038592 1, NM_001038593 1, NM_001038594 1 Gm4951 3'UTR ENSMUST00000031549, NM_001033767 3 Gm5607 3'UTR ENSMUST00000080795, NR_027975 1 Gm6320 3'UTR ENSMUST00000092089, NM_001037914 3 Gnal 3' UTR NM_010307 2, NM_177137 4 Habp4 3'UTR ENSMUST00000021929, NM_019986 3 Heatr5a 3'UTR ENSMUST00000040583, NM_177171 4 Krr1 3' UTR NM_178610 4 Lmbrd1 3'UTR ENSMUST00000095062, NM_026719 2 Lrrc3 3' UTR NM_145152 4 Mfsd4 3'UTR ENSMUST00000112370, NM_172510 4 Mobkl2c 3'UTR ENSMUST00000030477, NM_175308 4 Ms4a15 3'UTR ENSMUST00000087923, NM_001034898 2 Mtrr 3'UTR ENSMUST00000045827, NM_172480 2 Ncor1 3'UTR ENSMUST00000069456 Nol10 3'UTR ENSMUST00000046011, NM_001008421 1 Otud7b 3'UTR ENSMUST00000090785, ENSMUST00000035519, NM_001025613 1, NM_001025614 1, ENSMUST00000098849 Pik3c2a 3' UTR NM_011083 2 Pla2g2d 3'UTR ENSMUST00000030528, NM_011109 2 Polr3f 3'UTR ENSMUST00000028914, NM_029763 3 Ppp1r16b 3' UTR NM_153089 4, NM_001159662 1 Psmb11 3' UTR NM_175204 4 Psmd9 3' UTR NM_026000 2 Pwwp2a 3' UTR NM_001164231 1 Rab27a 3'UTR ENSMUST00000034722, NM_023635 5 Rnasel 3' UTR NM_011882 2 Rnf168 3'UTR ENSMUST00000014218, NM_027355 2 RP23-141C15.2 Known processed pseudogene ENSMUST00000117162 RP23-31A20.2 Known processed pseudogene ENSMUST00000121443 RP23-335C3.2 5'UTR, Known protein coding ENSMUST00000081929 Rp2h 3'UTR ENSMUST00000115387, NM_133669 4, ENSMUST00000033372 Rpl7l1 3' UTR NM_025433 3 Samd8 3'UTR ENSMUST00000022292, NM_026283 2, ENSMUST00000119430 Sass6 3'UTR ENSMUST00000029571, NM_028349 2 Sfxn2 3'UTR ENSMUST00000026011, NM_053196 3 Sgpp2 3'UTR ENSMUST00000036172, NM_001004173 2 Slc6a2 3'UTR ENSMUST00000072939, NM_009209 3 Slc7a2 3'UTR ENSMUST00000057784, NM_007514 3, NM_001044740 1, ENSMUST00000098816, ENSMUST00000117077 Snap23 3'UTR ENSMUST00000110711, ENSMUST00000116437 Snhg11 3'UTR ENSMUST00000109488, NM_175692 3 Sox2ot non-coding RNA NR_015580 1 Spc24 3' UTR NM_026282 5 Tada3l 3'UTR ENSMUST00000113107 Taf1 3'UTR ENSMUST00000118878, NM_001081008 1, ENSMUST00000101341 Tcam1 3'UTR ENSMUST00000044462 Tcea1 3'UTR ENSMUST00000081551, NM_001159750 1, NM_001159751 1, NM_011541 4 Thap6 3'UTR ENSMUST00000094611, NR_028429 1 Timm17b 3' UTR NM_011591 4 Tmod1 3'UTR ENSMUST00000107773, NM_021883 2 Tns4 3'UTR ENSMUST00000017751, NM_172564 3 Tprkb 3'UTR ENSMUST00000113753, NM_176842 3, NM_001170488 1, ENSMUST00000067137 Ttbk2 3'UTR ENSMUST00000028740, NM_001024856 2, NM_001024857 2, ENSMUST00000057135, NM_080788 3 Usp6nl 3'UTR ENSMUST00000114937 Veph1 3'UTR ENSMUST00000029419, NM_145820 2, NM_028357 4 Xcr1 3'UTR ENSMUST00000078755, NM_011798 4 Ybx1 3' UTR NM_011732 2 Zfp111 3' UTR NM_019940 2 Zfp316 3' UTR NM_017467 3 Zfp553 3'UTR ENSMUST00000056232, NM_146201 1, ENSMUST00000106312 Zfp60 3'UTR ENSMUST00000108336 Zfp78 3'UTR ENSMUST00000086323, NM_001025163 1, NM_001112805 1, NM_177888 4 Zyg11b 3' UTR NM_001033634 3 endo-siRNA-T33 TCAGTTCGAGGCCAGCCTGGTC 22 A630018P17Rik 3'UTR ENSMUST00000112188, ENSMUST00000055455, NM_001007577 2 endo-siRNA-T34 TCCCAGCAACCACATGGTGGTT 22 8030423F21Rik 3'UTR ENSMUST00000064097 D730040F13Rik 3'UTR ENSMUST00000068792, ENSMUST00000107609 Flt3 3'UTR ENSMUST00000110549 Ube2j2 3'UTR ENSMUST00000024056, NM_021402 5, NM_001039157 1, NM_001039158 1, NM_001039159 1 endo-siRNA-T35 TTTTAATGGAAACAACTTGACC 22 Prex2 3' UTR NM_001033636 4, NM_029525 1 endo-siRNA-T36 TAGAGCAGGCTGGCCTCGAACT 22 Cd22 3'UTR ENSMUST00000108123, ENSMUST00000108125, ENSMUST00000019248, NM_001043317 2, NM_009845 3 endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC 22 1700001C19Rik 3' UTR NM_029296 1 1700052N19Rik 3'UTR ENSMUST00000118544 2010000I03Rik Non-coding RNA NR_015508 1 2010106G01Rik 3' UTR NM_023220 2 2410129H14Rik 3' UTR NM_175245 4 2810417H13Rik 3' UTR NM_026515 2 4632433K11Rik 5'UTR ENSMUST00000076791 4930455C21Rik 3'UTR ENSMUST00000002925, ENSMUST00000114734, NM_024273 2 4930519G04Rik 3'UTR ENSMUST00000031547, NM_026263 2 4933404O12Rik Non-coding RNA NR_015555 1 6030458C11Rik 3'UTR ENSMUST00000057256, ENSMUST00000022804, NM_029998 3 9930104L06Rik 3'UTR ENSMUST00000094769, NM_177573 3 A4galt 3'UTR ENSMUST00000049530, NM_001004150 3, NM_001170954 1 AA386476 3'UTR ENSMUST00000098781 AC119205.8-1 Novel Pseudogene ENSMUST00000100847 AC134329.2 3'UTR, Known protein coding ENSMUST00000116231 AC141880.3-1 Exon2, Known protein coding ENSMUST00000109581 AC148328.3 3'UTR, Known protein coding ENSMUST00000098854 AC163640.5-1 3'UTR, Known protein coding ENSMUST00000100178 AC164093.2-3 3'UTR, Known protein coding ENSMUST00000063399 Adora3 3'UTR ENSMUST00000000574 AI597468 3'UTR ENSMUST00000095383, NM_001013028 2 Aqp7 3'UTR ENSMUST00000054945, NM_007473 4 Atad2 3'UTR ENSMUST00000038194, ENSMUST00000022988, NM_027435 2 B230340J04Rik Exon1 + 3'UTR ENSMUST00000056152 B4galnt2 3'UTR ENSMUST00000103158, ENSMUST00000038343, NM_008081 3 Bbs1 3'UTR ENSMUST00000053506, NM_001033128 3 Bpnt1 3'UTR ENSMUST00000027916, NM_011794 3 Btbd19 3' UTR NR_024078 1 Car5b 3' UTR NM_181315 4 Casc5 3'UTR ENSMUST00000028802 Cbfa2t2 3'UTR ENSMUST00000109725, NM_009823 1, ENSMUST00000045270, NM_172860 2, ENSMUST00000109720, ENSMUST00000109717 Ccdc114 3'UTR ENSMUST00000120643 Ccl9 3' UTR NM_011338 2 Cdc42ep2 3'UTR ENSMUST00000055458 Cercam 3'UTR ENSMUST00000047521, NM_207298 2 Chmp5 3'UTR ENSMUST00000030128 Ctcfl 3'UTR ENSMUST00000094287, NM_001081387 2 Ctsa 3'UTR ENSMUST00000103092, ENSMUST00000017904, NM_008906 3, NM_001038492 1 D14Abb1e 3' UTR NM_028945 1, NM_001114879 1 Dhrs7b 3'UTR ENSMUST00000108718 Dhx37 3'UTR ENSMUST00000031443, NM_203319 1 Dnajc25 3'UTR ENSMUST00000095070 Dqx1 3'UTR ENSMUST00000077502, NM_033606 3 Dusp3 3'UTR ENSMUST00000107172 Dynll1 3' UTR NM_019682 4 Efcab4a 3'UTR ENSMUST00000053670, NM_001025103 2 Efr3b 3'UTR ENSMUST00000111178, ENSMUST00000077156, NM_001082483 1 Elmo2 3'UTR ENSMUST00000071699, NM_207705 1 Eno2 3'UTR ENSMUST00000112476, NM_013509 2 Exosc4 3' UTR NM_175399 4 F730015K02Rik 3'UTR ENSMUST00000098640 Fam65b 3'UTR ENSMUST00000110384, ENSMUST00000058009, ENSMUST00000110383, NM_029679 1 Fam82b Exon6 + 3'UTR ENSMUST00000108253 Fbxl18 3'UTR ENSMUST00000110766 Fnip2 3'UTR ENSMUST00000076136, NM_001162999 2 Ftsjd2 3'UTR ENSMUST00000087910 Gal3st3 3'UTR ENSMUST00000061169, NM_001024717 2 Gjc3 3'UTR ENSMUST00000077119, NM_080450 4 Gk5 3'UTR ENSMUST00000122383, NM_177352 4 Gls 3' UTR NM_001081081 2 Glt8d1 3' UTR NM_029626 2, NM_001165930 1 Gm14461 5'UTR ENSMUST00000067618, NM_177843 3 Gmeb1 3' UTR NM_001122992 1, NM_020273 2 Gpr77 3'UTR ENSMUST00000098792, NM_176912 4, NM_001146005 1 I0C0044D17Rik 3'UTR ENSMUST00000097964 Irgm2 3'UTR ENSMUST00000094169, NM_019440 3, ENSMUST00000108836, ENSMUST00000058704 Kif23 3'UTR ENSMUST00000055275 Lats1 3' UTR NM_010690 1 Lix1 3'UTR ENSMUST00000097389, ENSMUST00000115576, NM_025681 2 March2 3' UTR NM_145486 4 Mbd4 3' UTR NM_010774 2 Mcart1 3'UTR ENSMUST00000084630, ENSMUST00000107796, NM_001009949 2 Mfap1a 3'UTR ENSMUST00000089926, NM_026220 4 Mina 3'UTR ENSMUST00000120667 Mkl2 3' UTR NM_001122667 2, NM_153588 3 Mlxipl 3'UTR ENSMUST00000005507, ENSMUST00000111201 Mmachc 3'UTR ENSMUST00000030453, NM_025962 3 Mrpl35 3'UTR ENSMUST00000065103, NM_025430 3 Ncan 3'UTR ENSMUST00000002412, NM_007789 3 Ncl 3' UTR NM_010880 3 Neil1 3'UTR ENSMUST00000098692, ENSMUST00000034842 Nkiras1 3' UTR NM_023526 3 Nosip 3' UTR NM_025533 3, NM_001163684 1 Ntf5 3'UTR ENSMUST00000058879, NM_198190 1 Nucks1 3'UTR ENSMUST00000112381, ENSMUST00000062264, NM_175294 3, NM_001145804 1 Osbpl8 3'UTR ENSMUST00000105275, ENSMUST00000040683, ENSMUST00000095310, NM_175489 3, NM_001003717 1 Ostf1 3' UTR NM_017375 3 P2rx4 3'UTR ENSMUST00000031429, ENSMUST00000077457, ENSMUST00000081554 Pctp 3'UTR ENSMUST00000020864, NM_008796 2 Pde4c 3'UTR ENSMUST00000110095, ENSMUST00000034307, NM_201607 2 Pdxk 3' UTR NM_172134 2 Pfas 3'UTR ENSMUST00000108668, ENSMUST00000021282, NM_001159519 1 Polr1b 3'UTR ENSMUST00000103205, NM_009086 2 Polr3gl 3'UTR ENSMUST00000091924, NM_027241 3 Ppm1k 3'UTR ENSMUST00000042766, NM_175523 4 Ppp1r7 3' UTR NM_023200 2 Ralgps1 3'UTR ENSMUST00000113164 Ranbp17 3'UTR ENSMUST00000037522 Rbak 3'UTR ENSMUST00000049861, NM_021326 2, NM_001045482 1 Rinl 3'UTR ENSMUST00000059857, NM_177158 5 S1pr4 5' UTR NM_010102 1 Sc5d 3'UTR ENSMUST00000052725, NM_172769 2 Sema4b 3'UTR ENSMUST00000032754, NM_013659 4 Sgms2 3' UTR NM_028943 5 Sip1 3'UTR ENSMUST00000021379, ENSMUST00000072021 Slc24a6 3'UTR ENSMUST00000111890, ENSMUST00000068326, ENSMUST00000076051, NM_133221 2 Slc6a20b 3'UTR ENSMUST00000026273, NM_011731 3 Stam 3'UTR ENSMUST00000114738, ENSMUST00000102960, NM_011484 2 Stard7 3'UTR ENSMUST00000110374 Strbp 3' UTR NM_009261 3 Supt7l 3'UTR ENSMUST00000065388, ENSMUST00000117642, NM_028150 2 Syt12 3'UTR ENSMUST00000059295, NM_134164 5 Taf3 5'UTR ENSMUST00000114909 Tmbim1 5'UTR ENSMUST00000113796 Tmx4 3'UTR ENSMUST00000038228, NM_029148 1 Tnfrsf10b 3'UTR ENSMUST00000022663, NM_020275 4 Trim14 3'UTR ENSMUST00000046897 Trpm1 3'UTR ENSMUST00000032737, ENSMUST00000107515 Ttyh1 3' UTR NM_021324 5, NM_001001454 3, NM_001109765 1 Usp45 3'UTR ENSMUST00000040429, NM_152825 2 Xkr8 3' UTR NM_201368 1 Xkrx 3'UTR ENSMUST00000033611, NM_183319 2 Xpo1 3'UTR ENSMUST00000102869, ENSMUST00000020538, ENSMUST00000109551, ENSMUST00000109548, NM_134014 3, NM_001035226 1 Zbtb44 3' UTR NM_172765 3, NM_001115130 1 Zcchc4 3'UTR ENSMUST00000031077 Zfp113 3'UTR ENSMUST00000049393, NM_019747 4 Zfp459 3'UTR ENSMUST00000056470, NM_177811 3 Zfp830 3' UTR NM_025884 4 piR-132013 (28 bp) ttgtgtagccctggctgtcctggaactc PIR225339 endo-siRNA-T38 AACTCAGAAATCCACCTGCCTG 22 Ncl 3' UTR NM_010880 3 endo-siRNA-T39 TCTTTACCCCGGCAGGCCGACAT 23 Gadl1 3'UTR ENSMUST00000084841, ENSMUST00000119291 endo-siRNA-T40 TTTCTCTGTGTAGCCCTGGCTAT 23 AC131679.2 Known processed pseudogene ENSMUST00000064305 Casp8 3' UTR NM_009812 2, NM_001080126 1 Crtc3 3'UTR ENSMUST00000122255, NM_173863 2, ENSMUST00000032741 Gpi1 3' UTR NM_008155 3 Kif17 3'UTR ENSMUST00000105820 Opa3 3'UTR ENSMUST00000063976, NM_207525 3 Rab3d 3'UTR ENSMUST00000122211, NM_031874 4 Sfxn2 3'UTR ENSMUST00000026011, NM_053196 3 Uhrf2 3'UTR ENSMUST00000112552 endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG 23 1110021J02Rik 3' UTR NM_001163741 1 1700037C18Rik 3’UTR ENSMUST00000115859 2010000I03Rik Non-coding RNA NR_015508 1 2010109I03Rik 3'UTR ENSMUST00000077004, NM_025929 2 2210404J11Rik 3‘UTR ENSMUST00000081476 2510006D16Rik 3'UTR ENSMUST00000102591, ENSMUST00000071840 2810408P10Rik 3'UTR ENSMUST00000105718, NM_198619 2 4930579G24Rik 3'UTR ENSMUST00000029388, NM_029482 1 4933407H18Rik 3'UTR ENSMUST00000087864, ENSMUST00000045520, NM_001081101 2 4933407I18Rik 3'UTR ENSMUST00000086982 A130042E20Rik 3'UTR ENSMUST00000049185, NM_172550 4 AB041806 3'UTR ENSMUST00000062902 Abcd2 3'UTR ENSMUST00000069511, NM_011994 2 Abl2 3'UTR ENSMUST00000027888, NM_009595 3, NM_001136104 1 AC099702.12 Exon4, Known protein coding ENSMUST00000111793 AC102077.7 Exon3, Known protein coding ENSMUST00000085094 AC113595.11-1 3'UTR, Known protein coding ENSMUST00000100431 AC124717.3-1 Exon1, Known protein coding ENSMUST00000084260 AC159372.1-1 3'UTR, Known protein coding ENSMUST00000098355 AC168060.4-1 3‘UTR, Known protein coding ENSMUST00000115885 Adam28 3'UTR ENSMUST00000111072, NM_001048175 1 Aida 3' UTR NM_181732 4 AL807811.9 5'UTR, Known protein coding ENSMUST00000097827 Alox12 3'UTR ENSMUST00000000329, NM_007440 4 Anapc7 3'UTR ENSMUST00000119792 Ash2l 3'UTR ENSMUST00000068892 B230219D22Rik 3'UTR ENSMUST00000057844, NM_181278 2 Bambi 3’UTR ENSMUST00000025075, NM_026505 2 BC030476 3’UTR ENSMUST00000060894, NM_173421 2 Bri3bp 3' UTR NM_029752 2 Btaf1 3‘UTR ENSMUST00000099494, NM_001080706 1 C030039L03Rik 3'UTR ENSMUST00000120004, NM_001112731 1, ENSMUST00000076421, NM_198417 2 Camk4 3' UTR NM_009793 3 Car5b 3'UTR ENSMUST00000033739, NM_181315 4 Ccdc125 3'UTR ENSMUST00000057325, NM_183115 4, NM_001168386 1 Chrnb4 3'UTR ENSMUST00000034854, NM_148944 4 Ciapin1 3' UTR NM_134141 4 D730040F13Rik 3'UTR ENSMUST00000107609, ENSMUST00000068792, NM_175518 5 Dgke 3'UTR ENSMUST00000000285, ENSMUST00000107894, NM_019505 3 Disc1 3'UTR ENSMUST00000122389 E330033B04Rik Non-coding RNA NR_030690 1 Elk1 3' UTR NM_007922 4 F10 3'UTR ENSMUST00000063820, NM_007972 3 Fam86 3‘UTR ENSMUST00000064635, NM_027446 2 Fcer2a 3' UTR NM_013517 4 Ftsj1 3'UTR ENSMUST00000033513, NM_133991 2 Gad2 3'UTR ENSMUST00000028123, NM_008078 2 Glrx2 3' UTR NM_023505 2, NM_001038592 1, NM_001038593 1, NM_001038594 1 Gm6531 3'UTR ENSMUST00000076896, NM_001037922 3 Gmip 3'UTR ENSMUST00000036074, NM_198101 1 Haus2 3'UTR ENSMUST00000110706, NM_025475 2 Heatr5a 3'UTR ENSMUST00000040583, NM_177171 4 Hyal1 3'UTR ENSMUST00000010195, NM_008317 4 Ikbip 3'UTR ENSMUST00000020149, NM_026166 2 Il11 3'UTR ENSMUST00000094892, NM_008350 3 Iws1 3' UTR NM_173441 3 Jhdm1d 3' UTR NM_001033430 4 Kdsr 3' UTR NM_027534 2 Klhl24 3’UTR ENSMUST00000023509, NM_029436 3 Lmbrd1 3'UTR ENSMUST00000095062, NM_026719 2 Lrrc8e 3'UTR ENSMUST00000053035, NM_028175 2 Lypla1 3'UTR ENSMUST00000027036, NM_008866 2 Malat1 Non-coding RNA NR_002847 2 Med16 3'UTR ENSMUST00000045844, NM_198107 2, ENSMUST00000105378, NM_001163276 1 Mfsd4 3'UTR ENSMUST00000112370, NM_172510 4 Mobkl3 3' UTR NM_025283 3 Myo1e 3'UTR ENSMUST00000034745, NM_181072 3 N4bp2l2 3'UTR ENSMUST00000016274 Otud7b 3'UTR ENSMUST00000090785, ENSMUST00000035519, NM_001025613 1, NM_001025614 1, ENSMUST00000098849 Polr3f 3'UTR ENSMUST00000028914, NM_029763 3 Ppp2r3d 3' UTR NM_011154 2, NM_001163415 1, NR_028110 1 Prss43 3'UTR ENSMUST00000077549, NM_199471 1 Psmb11 3' UTR NM_175204 4 Psmd9 3' UTR NM_026000 2 Pus7 3'UTR ENSMUST00000119946, NM_178403 4, ENSMUST00000072492 Pxmp4 3'UTR ENSMUST00000000896, NM_021534 3 Rab27b 3'UTR ENSMUST00000121693, NM_030554 3, NM_001082553 1 Slc23a1 3‘UTR ENSMUST00000025212, NM_011397 3 Snx30 3'UTR ENSMUST00000030080, NM_172468 2 Stxbp4 3'UTR ENSMUST00000020858, NM_011505 2 Syt11 3'UTR ENSMUST00000107503, ENSMUST00000107505, NM_018804 3, ENSMUST00000090945 Tada3l 3'UTR ENSMUST00000113107 Taf1 3'UTR ENSMUST00000101341, NM_001081008 1 Tcam1 3'UTR ENSMUST00000044462 Tecpr2 3‘UTR ENSMUST00000021703, NM_001081057 2 Tgfbr2 3'UTR ENSMUST00000061101, ENSMUST00000035014 Thap6 3'UTR ENSMUST00000094611, NR_028429 1 Timm17b 3' UTR NM_011591 4 Tirap 3'UTR ENSMUST00000093872 Tmc2 5'UTR ENSMUST00000077988, NM_138655 1 Tnk1 3'UTR ENSMUST00000108626 Tsn 3'UTR ENSMUST00000027623 Ttc9c 3’UTR ENSMUST00000096751, NM_027412 3 Txnl4a 3' UTR NM_025299 3 Ubxn2a 3'UTR ENSMUST00000020962, NM_145441 3 Usp6nl 3'UTR ENSMUST00000114937 Wdfy1 3'UTR ENSMUST00000113514, ENSMUST00000113515, NM_001111279 1, ENSMUST00000113513, ENSMUST00000113512, ENSMUST00000097685 Xcr1 3'UTR ENSMUST00000078755, NM_011798 4 Yeats2 3‘UTR ENSMUST00000041176, ENSMUST00000115560, ENSMUST00000090052, NM_001145930 1, NM_001033237 2 Zdhhc20 3'UTR ENSMUST00000089473, NM_029492 4, ENSMUST00000022541 Zfp111 3' UTR NM_019940 2 Zfp704 3'UTR ENSMUST00000041124, NM_133218 2 Zfyve20 3'UTR ENSMUST00000014694, NM_030081 2 Zfyve28 3'UTR ENSMUST00000114370 Zmym5 3' UTR NM_144842 3 Non-LTR Retrotransposon, SINE B1 endo-siRNA-T42 TAAAAGCAGCACCAGCTCTGGGC 23 RP23-276E19.2 Known processed pseudogene ENSMUST00000118067 endo-siRNA-T43 TGGTTATGCACTAAGCCTCATTT 23 Cd209c 5'UTR ENSMUST00000044060, NM_130903 3 Klhdc7a 3'UTR ENSMUST00000105031 endo-siRNA-T44 CACTTCTGTGTTTGCTAGGCCCT 23 RP23-272G10.2 Known processed pseudogene ENSMUST00000121772 endo-siRNA-T45 CACTTCTGTGTTTGCTAGGCCCC 23 Hsd3b2 3'UTR ENSMUST00000107022 LOC100316870 Dcaf5 pseudogene NR_033146 1 RP23-298M2.10 Known processed pseudogene ENSMUST00000117964 endo-siRNA-T46 CTGTGTAGCTCTGGCTGTCCTAG 23 1810008A18Rik 3'UTR ENSMUST00000099540, ENSMUST00000045454, NM_133998 3 Siglech 3'UTR ENSMUST00000094360, NM_178706 4 endo-siRNA-T47 GGCTCCTCACAACAGGGTC 19 piR-13355 (30 bp) tgaaaggtgtgaccctgttgtgaggagccc PIR6354 piR-139354 (30 bp) tgaaaggtgtgaccctgttgtgaggagccc PIR232680 endo-siRNA-T48 ATGAGCCACCATGTGGTTG 19 1600002H07Rik 3' UTR NM_028056 1 AC165951.3-2 3'UTR, Known protein coding ENSMUST00000097355 Dqx1 3'UTR ENSMUST00000077502, NM_033606 3 Gm10941 3'UTR ENSMUST00000105408, NR_026944 1 Klhl7 3' UTR NM_001161800 1, NM_026448 3 Nus1 3' UTR NM_030250 2 Rabggta 3'UTR ENSMUST00000062861, NM_019519 2 Scd3 3'UTR ENSMUST00000026220, NM_024450 2 Slc17a5 3'UTR ENSMUST00000117645, NM_172773 2, ENSMUST00000052441 endo-siRNA-T49 CCAGCCTGGTCTACAGAGC 19 AL627235.12-2 Exon1, Known protein coding ENSMUST00000100338 AL732538.6 3'UTR, Known protein coding ENSMUST00000095145 Ccdc157 3'UTR ENSMUST00000101626, ENSMUST00000093381, NM_177616 3, NM_001164620 1 Dusp3 3'UTR ENSMUST00000107172 Irak4 3'UTR ENSMUST00000074936, NM_029926 5 Mxra7 3'UTR ENSMUST00000021170, NM_026280 3 Nup214 3'UTR ENSMUST00000065398, NM_172268 2 Pmpca 3'UTR ENSMUST00000114093 Ptplad1 3'UTR ENSMUST00000036615, NM_021345 2 Zfp324 3'UTR ENSMUST00000038701, NM_178732 3 Zfp345 3'UTR ENSMUST00000109914, NM_001034900 3 endo-siRNA-T50 TCTGTAGGCTTCTTGTATG 19 A630089N07Rik 3' UTR NR_015491 1 LOC100316870 Dcaf5 pseudogene NR_033146 1 Zfp353 3' UTR NM_153096 2 Non-LTR Retrotransposon, L1 L1B_MM endo-siRNA-T51 CTGTATTTCAGGGGAATGTT 20 Endogenous Retrovirus 2 IAPEZI Endogenous Retrovirus 2 IAPLTR1a_I_MM endo-siRNA-T52 TACACTTCCATACTGCTGTTCAT 23 Ccdc82 3‘UTR ENSMUST00000110583 Gm8234 Non-coding RNA NR_004433 3 RP23-413M3.2 Known Processed pseudogene ENSMUST00000117166 Trim30 3’UTR ENSMUST00000066673 endo-siRNA-T53 TCCTAGGCGAAGGAGAATT 19 piR-137731 (30 bp) ttaaagagaattctccttcgcctaggacgt PIR231057 endo-siRNA-T54 ACAGCAACCAATCAGTGTG 19 piR-115774 (31 bp) tccacacactgattggttgctgtcttactgg PIR209100 piR-115909 (29 bp) tccacacactgattggttgctgtcttact PIR209235 endo-siRNA-T55 AAATGAGGAAAATACCTAAT 20 1110021L09Rik 3'UTR ENSMUST00000119597, ENSMUST00000092661, NM_183116 2 Angptl7 3'UTR ENSMUST00000030840 Ccdc114 3'UTR ENSMUST00000120643 E130120F12Rik 3'UTR ENSMUST00000081582, NM_001038651 3 Il2ra 3'UTR ENSMUST00000028111, NM_008367 3 Tcfcp2l1 3' UTR NM_023755 2 Tyms 3'UTR ENSMUST00000026846, NM_021288 3 Tyms-ps Tyms pseudogene, non-coding RNA NR_000040 2 Veph1 3'UTR ENSMUST00000029419, NM_145820 2, NM_028357 4 endo-siRNA-T56 TACAGTGTAAGACCACATATC 21 Stox1 3'UTR ENSMUST00000045500, NM_001033260 1 endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT 23 1500035H01Rik 3' UTR NM_023831 3 2810408P10Rik 3'UTR ENSMUST00000105718, NM_198619 2 8030423F21Rik 3'UTR ENSMUST00000064097 A130010J15Rik 3' UTR NM_001160359 1, NM_181048 3, NM_001160360 1 A230067G21Rik 3'UTR ENSMUST00000048349 A230069A22Rik 3' UTR NM_001033394 3 AC107865.7 Exon2, Known protein coding ENSMUST00000069918 AC158921.17 3'UTR, Known protein coding ENSMUST00000100773 Aldh16a1 3'UTR ENSMUST00000007977 Arl5c 3'UTR ENSMUST00000107563 BC106179 3'UTR ENSMUST00000055369 Ccdc114 3'UTR ENSMUST00000120643 Ctns 5'UTR ENSMUST00000108476 Gm5113 3'UTR ENSMUST00000085668, NM_001033540 2 Hnrnph2 5'UTR ENSMUST00000113202 Lrrc48 3'UTR ENSMUST00000070805 Mical2 3'UTR ENSMUST00000106648 Morc4 Exon6 ENSMUST00000113014 Ocrl Exon16 ENSMUST00000115015 Paxip1 3'UTR ENSMUST00000002291, NM_018878 2 Pigv 3'UTR ENSMUST00000062118, NM_001145955 1, NM_001145956 1, ENSMUST00000067902, NM_178698 5 Rbm41 3'UTR ENSMUST00000113007, ENSMUST00000096311, NM_153586 1, ENSMUST00000113011, ENSMUST00000033810 RP23-353B17.2 Known processed pseudogene ENSMUST00000120326 Rsad1 3'UTR ENSMUST00000040487, NM_001013381 2 Tspan7 3'UTR ENSMUST00000115526 Zfp451 3'UTR ENSMUST00000115167 Zfp872 3'UTR ENSMUST00000091508, NM_001033813 4 piR-20177 (28 bp) tggaattgaactcaggacctctggaaca PIR14176 piR-20178 (28 bp) tggaattgaactcaggacctctggaaga PIR14177 piR-21706 (29 bp) tgggaattgaactcaggacctctggaaga PIR15705 piR-21707 (31 bp) tgggaattgaactcaggacctctggaagagc PIR15706 endo-siRNA-T58 GCCCTGGCTGTCTTGGAAC 19 Abcd1 3'UTR ENSMUST00000114461 BC055004 3'UTR ENSMUST00000110930, ENSMUST00000110928 Cpm 3' UTR NM_027468 1 Kif5b 3'UTR ENSMUST00000025083, NM_008448 2 Nav2 3'UTR ENSMUST00000050869, ENSMUST00000064395 Thap4 3'UTR ENSMUST00000112905 endo-siRNA-T59 GGCAGAGGCAGGTGGATTT 19 2310008H09Rik 3'UTR ENSMUST00000063607, NM_023197 3, NM_001168218 1, NM_001168219 1, NM_001168220 1 2310010M20Rik 3'UTR ENSMUST00000054267, NM_183283 2, ENSMUST00000093183 2410129H14Rik 3' UTR NM_175245 4 2600006K01Rik 3'UTR ENSMUST00000047607 4930519G04Rik 3'UTR ENSMUST00000031547, NM_026263 2 Abcc9 3'UTR ENSMUST00000073173, ENSMUST00000087527, ENSMUST00000100827, ENSMUST00000111771, NM_011511 2, NM_021042 2, NM_021041 2, NM_001044720 1 Abi2 3'UTR ENSMUST00000087417, NM_198127 1, ENSMUST00000052332 AC091523.23 3'UTR, Known protein coding ENSMUST00000097466 AC124505.4 Exon1, Known protein coding ENSMUST00000068836 AC129188.3-1 Novel pseudogene ENSMUST00000048874 AC171318.3 3'UTR, Known protein coding ENSMUST00000067768 Aco1 3'UTR ENSMUST00000102973, NM_007386 2, ENSMUST00000030112 AL831793.4 Novel pseudogene ENSMUST00000116247 B230340J04Rik 3'UTR ENSMUST00000056152 B3gnt3 3'UTR ENSMUST00000034260 Cage1 3'UTR ENSMUST00000089840 Car5b 3' UTR NM_181315 4 Ccdc127 3'UTR ENSMUST00000022063, NM_024201 3, NM_001168659 1 Cnnm3 3'UTR ENSMUST00000097776, NM_001039551 1, NM_053186 2, ENSMUST00000001166 Cnpy2 3'UTR ENSMUST00000026446 Cx3cr1 3'UTR ENSMUST00000064165, NM_009987 3 Cyb5d2 3'UTR ENSMUST00000079681, NM_001024926 3, ENSMUST00000087640 D14Abb1e 3' UTR NM_028945 1, NM_001114879 1 Dffa Exon4 ENSMUST00000105697 Dgke 3'UTR ENSMUST00000107894 Dynll1 3' UTR NM_019682 4 Efr3b 3'UTR ENSMUST00000077156, ENSMUST00000111178, NM_001082483 1 Fam116a 3‘UTR ENSMUST00000037585, NM_001134465 1 Fam178a Exon7 ENSMUST00000087330 Fanca 3'UTR ENSMUST00000118395 Fkbp8 5'UTR ENSMUST00000119425 Git2 3'UTR ENSMUST00000102579, NM_001077359 1, NM_001077360 1, NM_019834 3, ENSMUST00000112185, ENSMUST00000043283, ENSMUST00000112183 Gm4925 3' UTR NM_001037166 2 Gngt1 3'UTR ENSMUST00000031673, NM_010314 2 Gpr77 3'UTR ENSMUST00000098792, NM_176912 4, NM_001146005 1 H2-DMb2 3'UTR ENSMUST00000041982 Irgm2 3'UTR ENSMUST00000094169, NM_019440 3, ENSMUST00000108836, ENSMUST00000058704 Itgb1bp3 3'UTR ENSMUST00000005069, NM_027120 2 Kif24 3'UTR ENSMUST00000051409, NM_024241 2, ENSMUST00000030148, ENSMUST00000108055 Lage3 3'UTR ENSMUST00000114153 Mapre1 3' UTR NM_007896 3 Mcart1 3'UTR ENSMUST00000107796, NM_001009949 2, ENSMUST00000084630 Med18 3'UTR ENSMUST00000102567, NM_026039 3 Mmachc 3'UTR ENSMUST00000030453, NM_025962 3 Mrpl24 5'UTR ENSMUST00000121048 Naa16 3'UTR ENSMUST00000022597, NM_025832 2 Nip7 3' UTR NM_001164472 1, NM_025391 2, NR_028367 1 Noc3l 3' UTR NM_021315 2 Ostf1 3' UTR NM_017375 3 Paxip1 3'UTR ENSMUST00000002291, NM_018878 2 Pctp 3'UTR ENSMUST00000020864, NM_008796 2 Pde4c 3'UTR ENSMUST00000034307, NM_201607 2, ENSMUST00000110095 Pfas 3'UTR ENSMUST00000021282, NM_001159519 1, ENSMUST00000108668 Pldn 3'UTR ENSMUST00000005954, NM_019788 3 Plin3 3'UTR ENSMUST00000019726, NM_025836 3 Polr1b 3'UTR ENSMUST00000103205, NM_009086 2 Rab11b 3’UTR ENSMUST00000057373, NM_008997 3 Rad51c 3'UTR ENSMUST00000007790, ENSMUST00000067692 Rbms2 3'UTR ENSMUST00000092033, NM_019711 2, NM_001039080 1, ENSMUST00000099139, ENSMUST00000105247, ENSMUST00000076233 Sfxn2 3‘UTR ENSMUST00000026011, NM_053196 3 Slc27a1 3'UTR ENSMUST00000034267, NM_011977 3 Slc28a3 3'UTR ENSMUST00000022036, NM_022317 3 Slc3a2 3' UTR NM_008577 4, NM_001161413 1 Slc7a2 3'UTR ENSMUST00000117077, ENSMUST00000057784, NM_001044740 1, ENSMUST00000098816, NM_007514 3 Slfn5 3'UTR ENSMUST00000108158, NM_183201 4, ENSMUST00000067443 Soat1 3'UTR ENSMUST00000051396, NM_009230 3 Spib 3'UTR ENSMUST00000098483, ENSMUST00000107921, ENSMUST00000035323, NM_019866 1 Strbp 3' UTR NM_009261 3 Svopl 3'UTR ENSMUST00000096040, NM_177200 4 Tspan31 3'UTR ENSMUST00000060991, NM_025982 4 Ttc26 3'UTR ENSMUST00000039394, NM_153600 2 Ufd1l 3'UTR ENSMUST00000005394, NM_011672 4, NR_028403 1 Zbtb8a 3'UTR ENSMUST00000030610, NM_028603 4 Zfp113 3'UTR ENSMUST00000049393, NM_019747 4 Zfp174 3'UTR ENSMUST00000041778, NM_001081217 1 piR-11711 (30 bp) tcgaactcagaaatccacctgcctctgcct PIR4710 piR-28769 (31 bp) ttgaactcagaaatccacctgcctctgcctc PIR22768 endo-siRNA-T60 TTTCTTTCGAGACAGGGTT 19 Olfr522 Exon3 ENSMUST00000106060 endo-siRNA-T61 TAAAATTTGAGCCTTGATC 19 Wiz Exon4 ENSMUST00000087699 endo-siRNA-T62 AAATAAATAAAATCTTTTT 19 C330024D12Rik 3'UTR ENSMUST00000032770, NM_030101 1 Mical2 3'UTR ENSMUST00000106648 Slc35d2 3' UTR NM_001001321 3 endo-siRNA-T63 TCTCTCCTAGTTTGGGCCTT 20 AC121960.3 3'UTR, Known protein coding ENSMUST00000100355 Endogenous Retrovirus 2 IAPLTR1a_I_MM endo-siRNA-T64 TCCCGGGTTTCGGCACCAAT 20 Endogenous Retrovirus 2 IAPEY5_I endo-siRNA-T65 AAATAAATAAATAAATCTTT 20 A230072E10Rik 3' UTR NR_015600 1 Gm5113 3'UTR ENSMUST00000085668, NM_001033540 2 Ide 3'UTR ENSMUST00000087306 Padi2 3'UTR ENSMUST00000030765, NM_008812 2 Pld2 3'UTR ENSMUST00000108556 Ppp1r16b 3' UTR NM_153089 4, NM_001159662 1 Slc1a7 3'UTR ENSMUST00000009076, NM_146255 1, ENSMUST00000106713 Snhg11 3'UTR ENSMUST00000109488, NM_175692 3 endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT 20 0610040B10Rik 3'UTR ENSMUST00000087782 1500035H01Rik 3' UTR NM_023831 3 2810408P10Rik 3'UTR ENSMUST00000105718, NM_198619 2 3110057O12Rik 3'UTR ENSMUST00000108077 A230067G21Rik 3'UTR ENSMUST00000048349 A230069A22Rik 3' UTR NM_001033394 3 AC107865.7 Exon2, Known protein coding ENSMUST00000069918 AC158921.17 3'UTR, Known protein coding ENSMUST00000100773 Aldh16a1 3'UTR ENSMUST00000007977 Arl5c 3'UTR ENSMUST00000107563 Ccdc114 3'UTR ENSMUST00000120643 Def8 3'UTR ENSMUST00000093049 Fam161b 3'UTR ENSMUST00000021659, NM_172581 2, ENSMUST00000065536 Gm5113 3'UTR ENSMUST00000085668, NM_001033540 2 Homez 3'UTR ENSMUST00000081162, NM_183174 2 Igfbp4 3'UTR ENSMUST00000017637 Lrrc48 3'UTR ENSMUST00000070805 Mical2 3'UTR ENSMUST00000106648 Mllt11 3' UTR NM_019914 4 Morc4 Exon6 ENSMUST00000113014 Ocrl Exon16 ENSMUST00000115015 Paxip1 3'UTR ENSMUST00000002291, NM_018878 2 Pigv 3'UTR ENSMUST00000062118, NM_001145955 1, NM_178698 5, ENSMUST00000067902, NM_001145956 1 Rbm41 3'UTR ENSMUST00000113007, NM_153586 1, ENSMUST00000096311, ENSMUST00000113011, ENSMUST00000033810 Rsad1 3'UTR ENSMUST00000040487, NM_001013381 2 Stx19 3'UTR ENSMUST00000055557 Ube2j2 3'UTR ENSMUST00000024056, NM_021402 5, NM_001039157 1, NM_001039158 1, NM_001039159 1 Vav1 3' UTR NM_011691 4, NM_001163815 1, NM_001163816 1 piR-21707 (31 bp) tgggaattgaactcaggacctctggaagagc PIR15706 piR-74994 (27 bp) tgaactcaggacctctggaagagcaga PIR67993 piR-87579 (26 bp) ttgaactcaggacctctggaagagca PIR81578 endo-siRNA-T67 AAGGACACATGTTCCACTAT 20 BX539316.6 Exon1, Known protein coding ENSMUST00000101266 endo-siRNA-T68 GCGCTACAGATTCTAATGAAC 21 piR-120702 (29 bp) ttgttcattagaatctgtagcgccttttc PIR214028 endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC 22 1700052N19Rik 3'UTR ENSMUST00000118544 2310008H09Rik 3'UTR ENSMUST00000063607, NM_023197 3, NM_001168218 1, NM_001168219 1, NM_001168220 1 2310010M20Rik 3'UTR ENSMUST00000093183, ENSMUST00000054267, NM_183283 2 2310046O06Rik 3'UTR ENSMUST00000114200, NM_175273 4, NM_001166364 1 4632433K11Rik 5'UTR ENSMUST00000076791 4930519G04Rik 3'UTR ENSMUST00000031547, NM_026263 2 4933404O12Rik Non-coding RNA NR_015555 1 6030458C11Rik 3'UTR ENSMUST00000057256, ENSMUST00000022804, NM_029998 3 6430550D23Rik 3'UTR ENSMUST00000086145, NM_001145351 1, NM_001145352 1 672718-201 Exon1 ENSMUST00000093133 A4galt 3'UTR ENSMUST00000049530, NM_001004150 3, NM_001170954 1 A530082C11Rik 3'UTR ENSMUST00000105608, NM_177186 4 AA386476 3'UTR ENSMUST00000098781 AC129188.3-1 Novel Pseudogene ENSMUST00000048874 AC148328.3 3'UTR, Known protein coding ENSMUST00000098854 Adora3 3'UTR ENSMUST00000000574 AI597468 3'UTR ENSMUST00000095383, NM_001013028 2 AL670169.9-2 Exon1, Known protein coding ENSMUST00000085330 AL732538.6 3'UTR, Known protein coding ENSMUST00000095145 Aldh16a1 3'UTR ENSMUST00000107815 B4galnt2 3'UTR ENSMUST00000103158, ENSMUST00000038343, NM_008081 3 BC023744 3'UTR ENSMUST00000111965, ENSMUST00000111967, NM_001033311 3 Bloc1s3 3'UTR ENSMUST00000077408, NM_177692 3 Btbd19 3' UTR NR_024078 1 Car5b 3'UTR ENSMUST00000033739, NM_181315 4 Car8 3'UTR ENSMUST00000098290, NM_007592 3 Ccdc114 3'UTR ENSMUST00000120643 Ccl9 3' UTR NM_011338 2 Cdk7 3' UTR NM_009874 3 Ctcfl 3'UTR ENSMUST00000094287, NM_001081387 2 Cyb5d2 3'UTR ENSMUST00000087640, ENSMUST00000079681, NM_001024926 3 D14Abb1e 3' UTR NM_028945 1, NM_001114879 1 D330012F22Rik 3'UTR ENSMUST00000062915, NM_178752 3 Dhx33 3'UTR ENSMUST00000108527, ENSMUST00000049048, NM_178367 4 Dhx37 3'UTR ENSMUST00000031443, NM_203319 1 Dnase2a 3'UTR ENSMUST00000003910, ENSMUST00000109744, NM_010062 3 Dqx1 3'UTR ENSMUST00000077502, NM_033606 3 Dusp3 3'UTR ENSMUST00000107172 Ecm2 3'UTR ENSMUST00000051504, NM_001012324 2 Efcab4a 3'UTR ENSMUST00000053670, NM_001025103 2 Efr3b 3'UTR ENSMUST00000111178, ENSMUST00000077156, NM_001082483 1 Elmo2 3'UTR ENSMUST00000071699, NM_207705 1 Exosc4 3' UTR NM_175399 4 Fam116a 3'UTR ENSMUST00000037585, NM_001134465 1 Fam65b 3'UTR ENSMUST00000110384, ENSMUST00000058009, ENSMUST00000110383, NM_029679 1 Fbxl18 3'UTR ENSMUST00000110766 Fnip2 3'UTR ENSMUST00000076136, NM_001162999 2 Ftsjd2 3'UTR ENSMUST00000087910 Gal3st3 3'UTR ENSMUST00000061169, NM_001024717 2 Gjc3 3'UTR ENSMUST00000077119, NM_080450 4 Gls 3' UTR NM_001081081 2 Glt8d1 3' UTR NM_029626 2, NM_001165930 1 Gm14461 5'UTR ENSMUST00000067618, NM_177843 3 Gm4925 3' UTR NM_001037166 2 Gmeb1 3' UTR NM_001122992 1, NM_020273 2 Gnb4 5'UTR ENSMUST00000108234 Gpr77 3'UTR ENSMUST00000098792, NM_176912 4, NM_001146005 1 Hhat 3'UTR ENSMUST00000110841 Hist1h2bk Exon2 ENSMUST00000110456 Il1rl1 3'UTR ENSMUST00000053043, ENSMUST00000097772, NM_001025602 2 Itpripl1 3'UTR ENSMUST00000099409, NM_001163527 1, NM_001163528 1 Lats1 3' UTR NM_010690 1 Lix1 3'UTR ENSMUST00000097389, ENSMUST00000115576, NM_025681 2 LOC100272221 Non-coding RNA NR_027452 1 Lpp 3' UTR NM_001145952 1, NM_178665 5, NM_001145954 1 Ltb4r2 3'UTR ENSMUST00000044554 March2 3' UTR NM_145486 4 Mbd4 3' UTR NM_010774 2 Mcm5 3' UTR NM_008566 2 Mfap1a 3'UTR ENSMUST00000089926, NM_026220 4 Mfn1 3' UTR NM_024200 4 Mfsd11 3'UTR ENSMUST00000021173, ENSMUST00000106365, NM_178620 3 Mrpl35 3'UTR ENSMUST00000065103, NM_025430 3 Nosip 3' UTR NM_025533 3, NM_001163684 1 Nrcam 3' UTR NM_176930 4, NM_001146031 1 Osbpl8 3'UTR ENSMUST00000105275, ENSMUST00000040683, ENSMUST00000095310, NM_175489 3, NM_001003717 1 P2rx4 3'UTR ENSMUST00000031429, ENSMUST00000077457, ENSMUST00000081554 Paxip1 3'UTR ENSMUST00000002291, NM_018878 2 Polr3c 3'UTR ENSMUST00000029741 Ptchd2 3' UTR NM_001083342 1 Rab11b 3'UTR ENSMUST00000057373, NM_008997 3 Rac2 3' UTR NM_009008 3 Ranbp3l 3'UTR ENSMUST00000053308, NM_198024 1 Rbm8a 3' UTR NM_025875 2, NM_001102407 1 S1pr4 5' UTR NM_010102 1 Sart1 3'UTR ENSMUST00000044207, NM_016882 3 Scn2b 3'UTR ENSMUST00000093855, NM_001014761 2 Sip1 3'UTR ENSMUST00000021379, ENSMUST00000072021 Slc15a1 3'UTR ENSMUST00000088386, NM_053079 2 Slc24a6 3'UTR ENSMUST00000111890, ENSMUST00000068326, ENSMUST00000076051, NM_133221 2 Slc28a3 3'UTR ENSMUST00000022036, NM_022317 3 Slc35e1 3‘UTR ENSMUST00000043238, NM_177766 3 Spib 3'UTR ENSMUST00000098483, ENSMUST00000035323, ENSMUST00000107921, NM_019866 1 Stam 3'UTR ENSMUST00000114738, ENSMUST00000102960, NM_011484 2 Stard7 3'UTR ENSMUST00000110374 Stat1 3'UTR ENSMUST00000087717, ENSMUST00000070968, NM_009283 3 Strbp 3' UTR NM_009261 3 Syt12 3‘UTR ENSMUST00000059295, NM_134164 5 Tcf25 3' UTR NM_001037877 2 Tigd3 3'UTR ENSMUST00000055911, NM_198634 1 Tnfrsf10b 3'UTR ENSMUST00000022663, NM_020275 4 Trpm1 3'UTR ENSMUST00000032737, ENSMUST00000107515 Ttc26 3'UTR ENSMUST00000039394, NM_153600 2 Ttyh2 3'UTR ENSMUST00000100242, ENSMUST00000045779, NM_053273 2 Ube2v2 3' UTR NM_023585 4, NM_001159351 1 Upf3a 3'UTR ENSMUST00000043767 Usp45 3'UTR ENSMUST00000040429, NM_152825 2 Xkrx 3'UTR ENSMUST00000033611, NM_183319 2 Zcchc4 3'UTR ENSMUST00000031077 Zdhhc2 3'UTR ENSMUST00000049389 Zfp113 3'UTR ENSMUST00000049393, NM_019747 4 Zfp317 3'UTR ENSMUST00000079042, NM_172918 4 Zfp345 3'UTR ENSMUST00000109914, NM_001034900 3 Zfp799 3'UTR ENSMUST00000079404, NM_177359 4 endo-siRNA-T70 TTAGTCAGGGTTCTCTAGAGTC 22 1110015M06Rik 3'UTR ENSMUST00000020963 Cmah 3' UTR NM_007717 4, NM_001111110 1 EG434019 3'UTR ENSMUST00000101355 LTR Retrotransposon MERVL_LTR endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT 22 1810012P15Rik 3'UTR ENSMUST00000100748 2210404J11Rik 3'UTR ENSMUST00000081476 2310003C23Rik 5'UTR ENSMUST00000078687, NM_029607 1 2310010M20Rik 3'UTR ENSMUST00000093183, ENSMUST00000054267, NM_183283 2 2410002O22Rik 3' UTR NM_001093759 1, NM_025879 2, NM_001093760 1 2600006K01Rik 3'UTR ENSMUST00000047607 2810006K23Rik 3'UTR ENSMUST00000077376, NM_001134717 1 4930594C11Rik Non-coding RNA NR_024017 1 4933432B09Rik 3' UTR NM_029407 1 6030458C11Rik 3'UTR ENSMUST00000057256, ENSMUST00000022804, NM_029998 3 A330035P11Rik Non-coding RNA NR_015586 1 A4galt 3'UTR ENSMUST00000049530, NM_001004150 3, NM_001170954 1 A530082C11Rik 3'UTR (2) ENSMUST00000105608, NM_177186 4 AC016522.1 Known processed pseudogene ENSMUST00000120986 AC016522.2 Known processed pseudogene ENSMUST00000121335 AC091523.23 3'UTR, Known protein coding ENSMUST00000097466 AC129188.3-1 Novel pseudogene ENSMUST00000048874 AC134329.2 3'UTR, Known protein coding ENSMUST00000116231 AC140047.8-2 3'UTR, Known protein coding ENSMUST00000115023 AL606521.24 Exon2, Known protein coding ENSMUST00000109941 AL670169.9-2 Exon2, Known protein coding ENSMUST00000085330 AL772249.6 Exon1, Known protein coding ENSMUST00000074761 AL831793.4 Novel pseudogene ENSMUST00000116247 AL928924.12-1 Novel pseudogene ENSMUST00000091477 AL928924.12-2 Exon1, Known protein coding ENSMUST00000100443 Arhgap19 3'UTR ENSMUST00000026150, NM_027667 3, NM_001163495 1 Atad2 3'UTR ENSMUST00000038194, ENSMUST00000022988, NM_027435 2 B4galnt2 3'UTR ENSMUST00000103158, ENSMUST00000038343, NM_008081 3 Bbs1 3‘UTR ENSMUST00000053506, NM_001033128 3 BC019943 5'UTR ENSMUST00000098842, NM_001112729 1, ENSMUST00000033982, NM_144927 3 BC024139 3'UTR ENSMUST00000054022, NM_001142968 1, ENSMUST00000068344, ENSMUST00000089654 C230096C10Rik 3' UTR NM_146157 3, NM_001039200 1 Car5b 3'UTR ENSMUST00000033739, NM_181315 4 Car8 3'UTR ENSMUST00000098290, NM_007592 3 Ccdc127 3'UTR ENSMUST00000022063, NM_024201 3, NM_001168659 1 Cd93 3'UTR ENSMUST00000099269, NM_010740 3 Cep97 3' UTR NM_028815 4 Ctcfl 3'UTR ENSMUST00000109117, NM_001081387 2, ENSMUST00000094287 Cybrd1 3'UTR ENSMUST00000028403, NM_028593 2, ENSMUST00000112154 D330050I16Rik 3'UTR ENSMUST00000093445, NR_033224 1 Dhx37 3'UTR ENSMUST00000031443, NM_203319 1 Dnase2a 3'UTR ENSMUST00000109744, NM_010062 3, ENSMUST00000003910 Fam65b 3'UTR ENSMUST00000110383, NM_029679 1, ENSMUST00000058009, ENSMUST00000110384 Ftsjd2 3'UTR ENSMUST00000087910 Gaa 3' UTR NM_008064 3, NM_001159324 1 Gdf3 3' UTR NM_008108 4 Gjc3 3'UTR ENSMUST00000077119, NM_080450 4 Gm4925 3' UTR NM_001037166 2 Gng2 3' UTR NM_010315 4, NM_001038637 1 Gngt1 3'UTR ENSMUST00000031673, NM_010314 2 Gnl3l 3'UTR ENSMUST00000112691, NM_198110 2, NM_001168600 1 Gpr157 3'UTR ENSMUST00000094451, NM_177366 3 Gpr77 3‘UTR ENSMUST00000098792, NM_176912 4, NM_001146005 1 Ifnar1 3' UTR NM_010508 2 Il1rl1 3'UTR ENSMUST00000097772, NM_001025602 2, ENSMUST00000053043 Irak2 3'UTR ENSMUST00000089023, NM_001113553 1, NM_172161 4, ENSMUST00000089022, ENSMUST00000059286 Iws1 3' UTR NM_173441 3 Kbtbd10 3'UTR ENSMUST00000100050, NM_001081087 1 Kbtbd2 3'UTR ENSMUST00000114323, ENSMUST00000081115, NM_145958 2, ENSMUST00000114321 Lilrb3 3'UTR ENSMUST00000049747, ENSMUST00000078451 Lpp 3' UTR NM_001145952 1, NM_178665 5, NM_001145954 1 Lrrc58 3'UTR ENSMUST00000078717, NM_177093 3 Lrrn4cl 3'UTR ENSMUST00000096257, NM_001013019 2 Mcm5 3' UTR NM_008566 2 Mfap1a 3'UTR ENSMUST00000089926, NM_026220 4 Mga 3'UTR ENSMUST00000110774, NM_001164274 1, NM_013720 2, ENSMUST00000110773, ENSMUST00000079934 Mmp25 3'UTR ENSMUST00000024696, NM_001033339 3 Mrgprb1 3' UTR NM_205810 4 Mrpl24 5'UTR ENSMUST00000121048 Mrpl35 3'UTR ENSMUST00000065103, NM_025430 3 N4bp2 3'UTR ENSMUST00000113738 Nip7 3' UTR NM_001164472 1, NM_025391 2, NR_028367 1 Nosip 3' UTR NM_025533 3, NM_001163684 1 Nsl1 3'UTR ENSMUST00000078259, NM_198654 3 Nucks1 3'UTR ENSMUST00000062264, NM_175294 3, NM_001145804 1, ENSMUST00000112381 Ostf1 3' UTR NM_017375 3 Paxip1 3'UTR ENSMUST00000002291, NM_018878 2 Pde4c 3'UTR ENSMUST00000034307, NM_201607 2, ENSMUST00000110095 Peo1 3'UTR ENSMUST00000026227, NM_153796 3 Pfas 3'UTR ENSMUST00000021282, NM_001159519 1, ENSMUST00000108668 Pin1 3' UTR NM_023371 3 Polh 3'UTR ENSMUST00000024749 Ppp1r7 3' UTR NM_023200 2 Ptrh2 5'UTR ENSMUST00000108021, NM_175004 2 Rab1 3‘UTR ENSMUST00000109602, NM_008996 3 Rab11b 3'UTR ENSMUST00000057373, NM_008997 3 Rad1 3'UTR ENSMUST00000022856, NM_011232 2 Rad51c 3'UTR ENSMUST00000007790, ENSMUST00000067692 Rbak 3'UTR ENSMUST00000049861, NM_021326 2, NM_001045482 1 Rbm11 3'UTR ENSMUST00000114249, NM_198302 2, ENSMUST00000114253 Rchy1 3' UTR NM_026557 3 Rfxank 3' UTR NM_011266 2, NM_001025589 1 Rg9mtd2 3'UTR ENSMUST00000040321, NM_175389 4 Riok3 3'UTR ENSMUST00000025270, NM_024182 4 RP23-40P1.1 Known processed pseudogene ENSMUST00000118379 RP24-392J24.7 Known processed pseudogene ENSMUST00000121066 Rufy3 3'UTR ENSMUST00000101048 S1pr4 5' UTR NM_010102 1 Sco1 3'UTR ENSMUST00000092996, ENSMUST00000108690, NM_001040026 1 Sema3e 3'UTR ENSMUST00000073957, NM_011348 2 Sgsm1 Exon22 ENSMUST00000100876, NR_027936 1, NM_001162965 1 Slc35e1 3'UTR ENSMUST00000043238, NM_177766 3 Slc38a10 Exon11 ENSMUST00000076697, NM_001164802 1 Slc3a2 3' UTR NM_008577 4, NM_001161413 1 Slfn5 3'UTR ENSMUST00000108158, NM_183201 4, ENSMUST00000067443 Soat1 3'UTR ENSMUST00000051396, NM_009230 3 Sod2 3' UTR NM_013671 3 Stard7 3'UTR ENSMUST00000110374 Tapbp 3'UTR ENSMUST00000114350, NM_001025313 1, NM_009318 2, ENSMUST00000025161 Tbx20 3'UTR ENSMUST00000052946, NM_194263 1 Tln2 3'UTR ENSMUST00000034771, NM_001081242 2, ENSMUST00000039662, ENSMUST00000085405, ENSMUST00000039509, ENSMUST00000040025 Tmem82 5' UTR NM_145987 2 Tnfaip6 3'UTR ENSMUST00000065927, NM_009398 2 Tnfrsf10b 3'UTR ENSMUST00000022663, NM_020275 4 Tor1aip2 3'UTR ENSMUST00000060404, NM_172843 4, ENSMUST00000111757 Tox4 3'UTR ENSMUST00000022766, NM_023434 3, ENSMUST00000071842 Tstd2 3'UTR ENSMUST00000107772, NM_173033 3 Ttc26 3'UTR ENSMUST00000039394, NM_153600 2 Txndc11 3'UTR ENSMUST00000118679 Ube2v2 3' UTR NM_023585 4, NM_001159351 1 Usp45 3'UTR ENSMUST00000040429, NM_152825 2 Wipf2 3' UTR NM_197940 2 Xpo1 3'UTR ENSMUST00000020538, NM_134014 3, NM_001035226 1, ENSMUST00000109548, ENSMUST00000109551, ENSMUST00000020538, ENSMUST00000102869 Xrcc2 3'UTR ENSMUST00000030773, NM_020570 2 Zbtb44 3' UTR NM_172765 3, NM_001115130 1 Zbtb6 3'UTR ENSMUST00000112932, NM_146253 5 Zc3hav1 3'UTR ENSMUST00000114900 Zfp113 3'UTR ENSMUST00000049393, NM_019747 4 Zfp187 3'UTR ENSMUST00000032820, NM_001013786 2 Zfp345 3'UTR ENSMUST00000109914, NM_001034900 3 Zfp385c 3'UTR ENSMUST00000103119, NM_177790 4, ENSMUST00000014342, ENSMUST00000107370 Zfp780b 3'UTR ENSMUST00000081618, NM_001081021 1 Zfp799 3'UTR ENSMUST00000079404, NM_177359 4 endo-siRNA-T72 TCTTGATGTCCTCTACCATCATC 23 A630089N07Rik 3' UTR NR_015491 1 endo-siRNA-T73 TCTGGAGCTCTGCAATCTTTCTT 23 Endogenous Retrovirus 2 IAPLTR1a_I_MM Table S2. Chromosome hits for all 73 endo-siRNAs identified in this study

ID Sequence Chr1 Chr2 Chr3 Ch4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 ChrX ChrY endo-siRNA-T1 ACAGTGTACTCACATATAT 21 23 13 16 18 17 10 11 9 9 21 5 14 5 5 10 11 6 8 9 1 endo-siRNA-T2 GCAGGCTGGCCTCGAACTC 9 13 6 15 5 9 8 3 6 7 10 8 5 4 4 6 11 5 7 11 0 endo-siRNA-T3 TCAGGTCCCTGTTCGGGCGCC 0 1 4 2 2 2 3 2 0 1 2 1 3 1 0 3 5 0 0 2 0 endo-siRNA-T4 GCTCTTCCGAAGGTCCAGAGT 69 94 64 85 88 62 75 60 64 59 96 36 57 60 46 42 64 41 38 48 2 endo-siRNA-T5 CTCGAACTCAGAAATCTACCTG 15 20 21 12 22 13 10 16 8 17 16 13 17 10 15 11 7 5 14 14 0 endo-siRNA-T6 CTGTGTAGCCTTGGCTGTCCTG 76 74 53 53 64 44 42 49 53 45 90 56 44 33 39 42 46 33 26 54 2 endo-siRNA-T7 CTCTGTAGAGCAGGCTGGCCTTG 3 2 5 0 2 3 4 1 1 2 1 4 2 2 1 2 1 2 1 2 0 endo-siRNA-T8 AAGTCATGTTCATTGTTTGAGTT 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 endo-siRNA-T9 GTTCCCGGGTTTCGGCACC 2 3 0 4 2 3 2 2 3 2 0 2 4 1 2 1 0 1 0 2 0 endo-siRNA-T10 TCTCCTGCTTTTTTACCAC 38 42 27 17 26 24 30 24 23 27 18 23 25 14 15 22 18 15 8 28 0 endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT 277 218 209 203 207 198 155 138 155 151 135 173 162 151 131 111 129 122 81 219 4 endo-siRNA-T12 CCCGGGTTTCGGCACCAAC 16 11 10 10 11 16 8 7 3 10 8 11 15 3 7 4 6 5 1 6 0 endo-siRNA-T13 TAGCCTGGTCTACAGAGTG 48 60 38 50 56 36 42 24 47 41 75 35 35 32 25 27 37 26 22 49 6 endo-siRNA-T14 TATTCCTGGTTGTCAACTT 112 69 83 76 92 57 91 50 44 73 62 63 84 67 43 55 49 30 23 74 2 endo-siRNA-T15 CCAGGACAGCCAGGGCAAT 9 11 3 6 3 6 4 2 4 9 7 5 2 4 5 1 7 3 1 5 0 endo-siRNA-T16 GCCCTGGCTGTCCTGGAACG 3 5 1 2 6 2 1 2 1 3 7 9 3 2 1 1 0 1 1 3 0 endo-siRNA-T17 TAACAAGATACCAGAACTAC 71 61 53 51 56 50 40 37 33 35 22 41 34 39 39 33 26 28 20 65 1 endo-siRNA-T18 CACAGAGAAACCCTGTCTTG 243 294 200 226 229 169 264 203 233 198 322 179 132 144 144 143 183 109 128 193 3 endo-siRNA-T19 TCACTTTGTAGACCAGGCTG 1131 1269 860 945 969 926 971 769 820 816 1204 833 736 714 646 682 814 606 508 875 16 endo-siRNA-T20 TCGGCACCAATTGTTATTAG 40 33 22 32 32 20 39 23 22 14 17 11 26 23 15 23 12 12 7 38 1 endo-siRNA-T21 GTTCAGCATCCTTAATCATC 157 128 134 94 102 95 155 79 84 81 57 78 63 121 90 66 49 55 33 247 7 endo-siRNA-T22 TCTGAGTTCAAGGCCAGCCT 508 564 352 457 464 353 459 349 401 398 545 360 290 296 265 298 362 277 227 420 4 endo-siRNA-T23 TGGTATCGGCTTCTGGAACAC 13 4 8 6 8 7 10 5 6 10 5 11 13 9 7 6 4 10 0 12 0 endo-siRNA-T24 TATCACAGAGAAAGGAGCTTC 350 283 268 224 227 233 192 172 178 202 164 214 192 178 164 154 148 159 103 232 4 endo-siRNA-T25 TCTGTGTTCATCTGACGAATT 6 2 5 5 5 3 8 2 4 2 5 2 10 2 3 4 3 2 0 9 1 endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG 1109 1398 888 1081 1207 907 1135 856 978 917 1421 863 786 799 675 669 938 647 627 1001 17 endo-siRNA-T27 AGAGAAAGTACCCAAGGAGCT 1228 1001 1062 938 835 891 825 664 578 685 434 723 594 682 587 567 420 452 282 1662 26 endo-siRNA-T28 TCACTCTGTAGACCAGGCTAG 44 49 28 30 46 19 33 40 37 28 51 29 21 22 23 22 37 23 22 32 2 endo-siRNA-T29 TCTGAGTTCGAGGCCAGCCTT 12 6 6 10 8 5 5 4 3 3 7 2 6 4 7 4 5 3 6 11 1 endo-siRNA-T30 TACACAGAGAAACCCTGTTTC 17 35 14 34 37 13 31 25 19 21 31 26 14 22 19 15 16 7 14 24 2 endo-siRNA-T31 TTACATATAATAAATAAATCTT 36 46 25 40 47 27 27 27 32 33 58 32 30 25 16 27 22 15 22 35 1 endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC 1016 1258 801 1012 1083 752 932 802 805 727 1262 760 606 646 542 630 766 508 518 920 22 endo-siRNA-T33 TCAGTTCGAGGCCAGCCTGGTC 5 6 4 8 3 1 1 4 1 2 3 1 3 2 3 2 3 2 1 3 1 endo-siRNA-T34 TCCCAGCAACCACATGGTGGTT 37 35 21 36 40 28 41 47 36 23 50 30 36 23 28 20 35 21 17 30 1 endo-siRNA-T35 TTTTAATGGAAACAACTTGACC 3 1 1 0 1 0 0 0 2 1 0 1 1 0 1 1 2 1 4 0 0 endo-siRNA-T36 TAGAGCAGGCTGGCCTCGAACT 5 10 4 12 4 8 7 3 7 7 11 7 5 4 2 6 6 5 5 9 0 endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC 862 1033 706 807 873 599 839 651 760 664 1184 654 573 546 486 501 708 452 482 667 7 endo-siRNA-T38 AACTCAGAAATCCACCTGCCTG 4 0 4 2 3 3 2 1 3 2 4 1 3 0 3 3 0 1 1 2 0 endo-siRNA-T39 TCTTTACCCCGGCAGGCCGACAT 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 endo-siRNA-T40 TTTCTCTGTGTAGCCCTGGCTAT 51 57 30 58 50 36 42 35 49 40 81 43 22 25 25 34 39 24 24 31 0 endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG 845 1023 667 807 871 640 787 679 713 645 1094 645 530 555 489 508 677 459 440 686 9 endo-siRNA-T42 TAAAAGCAGCACCAGCTCTGGGC 16 6 3 10 6 10 3 9 2 9 2 7 5 5 10 4 5 2 3 0 0 endo-siRNA-T43 TGGTTATGCACTAAGCCTCATTT 20 25 21 27 25 22 16 15 11 18 5 21 25 13 17 7 17 12 11 10 2 endo-siRNA-T44 CACTTCTGTGTTTGCTAGGCCCT 171 131 167 128 101 148 113 93 63 117 64 78 78 84 98 92 58 46 40 227 5 endo-siRNA-T45 CACTTCTGTGTTTGCTAGGCCCC 1114 862 881 812 704 852 712 644 498 624 399 560 472 587 534 486 367 392 198 1352 29 endo-siRNA-T46 CTGTGTAGCTCTGGCTGTCCTAG 8 5 4 7 4 1 6 6 1 5 9 2 3 1 3 2 4 0 1 2 0 endo-siRNA-T47 GGCTCCTCACAACAGGGTC 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 endo-siRNA-T48 ATGAGCCACCATGTGGTTG 33 50 49 43 57 29 47 31 38 46 54 37 38 30 23 27 31 22 26 40 0 endo-siRNA-T49 CCAGCCTGGTCTACAGAGC 63 70 50 58 72 57 69 51 58 61 120 62 44 50 56 38 52 27 38 48 0 endo-siRNA-T50 TCTGTAGGCTTCTTGTATG 570 443 517 473 374 443 464 315 280 351 198 296 275 288 286 222 202 225 108 857 14 endo-siRNA-T51 CTGTATTTCAGGGGAATGTT 42 31 30 43 39 28 37 25 29 19 20 23 30 31 19 29 25 19 7 47 1 endo-siRNA-T52 TACACTTCCATACTGCTGTTCAT 182 119 117 108 109 92 78 78 85 89 81 93 102 112 65 60 76 75 51 121 3 endo-siRNA-T53 TCCTAGGCGAAGGAGAATT 14 10 4 3 14 6 12 5 6 1 3 4 10 8 4 8 1 9 2 11 0 endo-siRNA-T54 ACAGCAACCAATCAGTGTG 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 endo-siRNA-T55 AAATGAGGAAAATACCTAAT 334 304 310 280 236 262 234 200 180 223 134 202 150 188 168 196 147 138 77 505 4 endo-siRNA-T56 TACAGTGTAAGACCACATATC 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT 334 387 231 297 354 237 261 250 279 284 426 211 219 172 178 157 275 178 147 218 7 endo-siRNA-T58 GCCCTGGCTGTCTTGGAAC 39 56 39 45 53 32 52 35 42 35 56 26 24 37 15 32 35 23 16 33 1 endo-siRNA-T59 GGCAGAGGCAGGTGGATTT 562 690 419 525 580 436 506 435 443 386 683 429 389 448 337 336 406 310 268 466 9 endo-siRNA-T60 TTTCTTTCGAGACAGGGTT 6 3 2 1 5 4 6 3 2 4 5 4 3 2 2 1 1 3 2 4 0 endo-siRNA-T61 TAAAATTTGAGCCTTGATC 24 12 21 7 3 7 20 11 10 17 4 8 12 11 3 9 15 6 1 11 0 endo-siRNA-T62 AAATAAATAAAATCTTTTT 3 5 3 4 2 1 6 8 7 4 6 2 5 1 1 5 4 1 2 5 0 endo-siRNA-T63 TCTCTCCTAGTTTGGGCCTT 64 49 43 61 61 45 51 42 42 43 29 28 48 46 33 44 28 35 8 68 3 endo-siRNA-T64 TCCCGGGTTTCGGCACCAAT 12 9 6 13 9 7 9 5 10 4 8 2 9 12 7 6 7 2 1 12 0 endo-siRNA-T65 AAATAAATAAATAAATCTTT 134 138 88 102 114 92 120 95 100 97 134 83 78 58 55 70 91 69 61 87 1 endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT 356 448 265 363 397 282 330 283 304 333 526 243 251 196 201 191 340 214 176 279 7 endo-siRNA-T67 AAGGACACATGTTCCACTAT 43 37 45 34 41 39 30 31 29 29 17 29 27 28 17 25 20 10 11 71 5 endo-siRNA-T68 GCGCTACAGATTCTAATGAAC 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC 828 1004 671 835 890 639 870 645 722 694 1120 617 598 580 511 496 765 461 484 689 10 endo-siRNA-T70 TTAGTCAGGGTTCTCTAGAGTC 83 96 70 81 57 60 82 65 58 63 63 77 67 58 46 45 49 33 34 86 8 endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT 1044 1297 835 1028 1133 855 1077 793 922 852 1331 801 750 754 640 630 882 609 597 942 17 endo-siRNA-T72 TCTTGATGTCCTCTACCATCATC 281 225 247 235 214 240 261 171 127 177 88 155 123 143 159 111 88 106 55 440 11 endo-siRNA-T73 TCTGGAGCTCTGCAATCTTTCTT 42 26 28 42 37 29 37 26 28 17 21 21 29 29 19 30 25 18 7 41 1 Table S3. All the primers used in this study including endo-siRNA primers, miRNA primers, other transcript primers, and primers for luciferase assay

ID Sequences ID Sequences ID Sequences Size ID Sequences Size endo-siRNA-T3 TCA GGT CCC TGT TCG G miR-188-5p CATCCCTTGCATGGTGGAG 1700052K11Rik-F AGGCTGCTTGGAAAGATGAA 166 Frmpd1-F GAGAAGCTGTCCATCCGAAG 160 endo-siRNA-T4 CTC TTC CGA AGG TCC AGA GT miR-20b-3p TGCAGTGTGAGCACTTCTAG 1700052K11Rik-R CCACTGTGCAGACTTGAGGA Frmpd1-R CAAAGCTCACCCTGAAGAGG endo-siRNA-T6 TGT GTA GCC TTG GCT GTC CT miR-201-3P GAACAGTGCCTTTCTGTGTAG 8030423F21Rik-F TTCTTGCCAGACAGCATCAC 213 Lrrc2-F CTGATGGATCTCCCCTTTGA 157 endo-siRNA-T7 TGT AGA GCA GGC TGG CCT TG miR-221-3P CTACATTGTCTGCTGGGTTTC 8030423F21Rik-R GAAGATCGCTAGGCAGGATG Lrrc2-R CTTGTGGCAGGTCACTCAGA endo-siRNA-T9 TTC CCG GGT TTC GGC A miR-222-3P GCTACATCTGGCTACTGGGT A630089N07Rik-F ATGCTGTGGATTGTGCTCAG 225 Kif17-F ACGTGAAGCTGTCCACACTG 170 endo-siRNA-T10 TCT CCT GCT TTT TTA CCA C miR-452-5P TGTTTGCAGAGGAAACTGAGA A630089N07Rik-R ATGCCTTCCATGTCTTCTGG Kif17-R CTGCCTGGCTGGATTGTTAT endo-siRNA-T11 TCT CTG GGC TGG TAG TCT T miR-501-5P AATCCTTTGTCCCTGGGTGA Abhd15-F AGAGGTTTCCCCTTCTTCCA 206 Spata1-F GCTCAATCCAAGTCGACCAT 197 endo-siRNA-T12 CGG GTT TCG GCA CCA AC miR-505-3P CGTCAACACTTGCTGGTTTTC Abhd15-R CAGGGCAACTCTTCTCAAGG Spata1-R CACCAAGAAACTCCCCAAGA endo-siRNA-T13 TAG CCT GGT CTA CAG AGT G miR-509-5P TACTCCAGAATGTGGCAATCA Acnat1-F TGTGATCTCCACGAGCAAAG 193 Syt11-F GACACTTGCCGAAGATGGAT 198 endo-siRNA-T14 ATT CCT GGT TGT CAA CT miR-542-5P TCGGGGATCATCATGTCACG Acnat1-R GCATACAGCCCCTGAAACAT Syt11-R TGACAAGGAACTCGATGCTG endo-siRNA-T15 AGG ACA GCC AGG GCA AT miR-717-5P CTCAGACAGAGATACCTTCTC BC039771-F GTCTCGGAAAACCAAAACCA 164 Gapdh-F AACTTTGGCATTGTGGAAGG 222 endo-siRNA-T16 CTG GCT GTC CTG GAA C miR-883a-5P TGCTGAGAGAAGTAGCAGTTAC BC039771-R ACAAAAATCACAGGGGCTTG Gapdh-R CACATTGGGGGTAGGAACAC endo-siRNA-T18 CAC AGA GAA ACC CTG TCT TG Bri3bp-F AGCCAGGGCTACACAGAGAA 249 Firefly-F GCCCCAGCTAACGACATCTA 208 endo-siRNA-T19 TCA CTT TGT AGA CCA GGC TG Bri3bp-R GCAGGTGGATCTCTGCAAGT Firefly-R AATGGGAAGTCACGAAGGTG endo-siRNA-T20 CGG CAC CAA TTG TTA TTA G C130036L24Rik-F CAAAGCAAATCCCACCAGAT 176 Renilla-F GATAACTGGTCCGCAGTGGT 223 endo-siRNA-T21 GTT CAG CAT CCT TAA TCA TC C130036L24Rik-R TGGTCAGCTGTGAGTGGAAG Renilla-R ACCAGATTTGCCTGATTTGC endo-siRNA-T23 TGG TAT CGG CTT CTG GAA CAC Ccdc36-F TTGGCTGACTCCGAGAAGTT 234 endo-siRNA-T24 TCA CAG AGA AAG GAG CTT C Ccdc36-R GGGTCACAGAGCAAATTCGT endo-siRNA-T25 TCT GTG TTC ATC TGA CGA Cd209c-F AGCTTCCTGCAGCAGACTTC 209 endo-siRNA-T27 AGA GAA AGT ACC CAA GGA GC Cd209c-R ATTGTACATGGGGCATCGTT endo-siRNA-T28 TCA CTC TGT AGA CCA GGC TA Ctcfl-F ACGACGAAATTGTCCTGACC 179 endo-siRNA-T30 ACA CAG AGA AAC CCT GTT TC Ctcfl-R GAGCTTGGAGGAAGTGAACG endo-siRNA-T32 TCA CTC TGT AGA CCA GGC TG Dcdc2c-F CACAGCTGCGACTGAACAAT 186 endo-siRNA-T33 TCA GTT CGA GGC CAG CCT Dcdc2c-R AGCCCATGTAACGCATTAGG endo-siRNA-T34 CCA GCA ACC ACA TGG TGG T ERVB7.1.I.MM-F GACACTTGGCTGAAACAGCA 206 endo-siRNA-T35 ATG GAA ACA ACT TGA CC ERVB7.1.I.MM-R TATCCAGCTCGCCCTTTAGA endo-siRNA-T37 TCC AGG ACA GCC AGG GCT ACA Esr2-F GAAGCTGGCTGACAAGGAAC 187 endo-siRNA-T39 TTT ACC CCG GCA GGC CGA CAT Esr2-R AACGAGGTCTGGAGCAAAGA endo-siRNA-T40 TTC TCT GTG TAG CCC TGG CT ETNERV-F GCTGACCTCTGGCTTTTCAC 243 endo-siRNA-T41 TGT GTA GCC CTG GCT GTC CT ETNERV-R GCGATGCCCATACTGAATTT endo-siRNA-T42 AAA GCA GCA CCA GCT CTG G Gadl1-F AGACAGTGGCCAGAAGGAGA 232 endo-siRNA-T43 TGG TTA TGC ACT AAG CCT CA Gadl1-R GTCCCTCATCTCCAGGTCAA endo-siRNA-T44 CAC TTC TGT GTT TGC TAG GC Gm10389-F CTGTTGTGTTCGCTGTCGTT 179 endo-siRNA-T45 CAC TTC TGT GTT TGC TAG GC Gm10389-R CAGGATGGTGTCCGAAAGTT endo-siRNA-T46 TGT GTA GCT CTG GCT GTC CTA G Gm14443-F GGTGATCAACAGCAATGTGG 150 endo-siRNA-T47 CTC CTC ACA ACA GGG TC Gm14443-R CATGGTCAGGTTGTCACAGG endo-siRNA-T48 ATG AGC CAC CAT GTG GTT G Hmmr-F CTTTGAAGCCGAGAAACAGG 167 endo-siRNA-T49 CAG CCT GGT CTA CAG AG Hmmr-R CCTCCGATTTGAGTTGGCTA endo-siRNA-T50 CTG TAG GCT TCT TGT ATG Hsd3b2-F TCCAGCTCAGTTGATGTTGC 172 endo-siRNA-T51 CTG TAT TTC AGG GGA ATG Hsd3b2-R AAGTGCCACCATTTTTCAGC endo-siRNA-T52 ACA CTT CCA TAC TGC TGT TC IAPEZI-F GGGATGGAGTGAGTGTGCTT 193 endo-siRNA-T53 TCC TAG GCG AAG GAG AA IAPEZI-R ACAGGCTTTTACCCAGAGCA endo-siRNA-T54 ACA GCA ACC AAT CAG TGT G IAPLTR1a.I.MM-F CATGGAGCTTCCCCTGATAA 239 endo-siRNA-T56 CAG TGT AAG ACC ACA TAT C IAPLTR1a.I.MM-R TGCCTGGAGAGAAGGACACT endo-siRNA-T57 TTC CAG AGG TCC TGA GTT CA L1B.MM.L1-F CACCACGGACTAAGGCTGAT 169 endo-siRNA-T58 CCC TGG CTG TCT TGG AAC L1B.MM.L1-R TTGGGTATGTTGTGGCTTCA endo-siRNA-T59 GGC AGA GGC AGG TGG ATT T Lrrc2-F CTGATGGATCTCCCCTTTGA 157 endo-siRNA-T60 TTT CTT TCG AGA CAG GGT Lrrc2-R CTTGTGGCAGGTCACTCAGA endo-siRNA-T63 TCT CTC CTA GTT TGG GCC TT MERVL.LTR-F AGGCTCAGCAGTGACCCTTA 201 endo-siRNA-T64 CGG GTT TCG GCA CCA AT MERVL.LTR-R AGCAGAAGGTGTAGCCCAGA endo-siRNA-T66 CTC TTC CAG AGG TCC TGA GT Mxra7-F CAGTCACGCCTTGAGTGTGT 239 endo-siRNA-T67 AAG GAC ACA TGT TCC ACT Mxra7-R TTCTAGAGGACACCGGGATG endo-siRNA-T68 GCG CTA CAG ATT CTA ATG AAC Ncan-F AGCATCCCTGTGCTGAGACT 162 endo-siRNA-T69 CTA CAC AGA GAA ACC CTG TCT C Ncan-R GTGCTTGTGCAGTGTGTGTG endo-siRNA-T70 AGT CAG GGT TCT CTA GAG TC Noc2l-F TCAGTGTGGACGAGTTCCTG 203 endo-siRNA-T71 TGA GTT CGA GGC CAG CCT GGT Noc2l-R CCGAGAGAGCTGGTCTTTGT endo-siRNA-T72 CTT GAT GTC CTC TAC CAT CAT C Padi2-F TTCTTGGGCTCATTGCTCTT 250 endo-siRNA-T73 CTG GAG CTC TGC AAT CTT TC Padi2-R TATCTGGATGGGAGCCTTTG U6 GCA AAT TCG TGA AGC GTT CC Ptpn7-F GAAAACCCAGCACTCTCTGC 238 ReversePrimer-47 AAT TCT AGA GCT CGA GG Ptpn7-R ATGATGATGAGGGCTGAAGG ReversePrimer-49 GAA TTC TAG AGC TCG AGG RP23-174L3.1-F TGTGCCAATCTACCAAGTGC 184 ReversePrimer-51 ATT CTA GAG CTC GAG GC RP23-174L3.1-R GGCCTATGATGACGTTCTCC ReversePrimer-53.5 ATT CTA GAG CTC GAG GCA G RP23-276E19.2-F AATGGTGGAGTCGGTAGGTG 184 ReversePrimer-55 GAA TTC TAG AGC TCG AGG CAG RP23-276E19.2-R GGTGCCTTGTTCACTTGGAT ReversePrimer-57 CGA ATT CTA GAG CTC GAG GCA G RP23-413M3.2-F TGAGGTGGAGGAGATGATCC 230 ReversePrimer-59 CGA ATT CTA GAG CTC GAG GCA GG RP23-413M3.2-R TCTGGGCTGACCTCAGTTCT ReversePrimer-61 CGA ATT CTA GAG CTC GAG GCA GGC Rtkn2-F CTGAAGACGTCCATCAGCAA 227 ReversePrimer-63 CGA ATT CTA GAG CTC GAG GCA GGC G Rtkn2-R ACGTTGCCATACAAGGGAAG M13 Forward GTA AAA CGA CGG CCA G Samd11-F TAGACGCTCTGCCAGAATCC 163 M13 Reverse CAG GAA ACA GCT ATG AC Samd11-R GTGCACCTGACGGTCTGTAA Slc17a5-F GATTTTGGCGTTCTGTGGTT 172 Slc17a5-R ACCGGGAATTGTGTGATTGT Slc28a3-F ATGGTCGCCAAACTCATAGG 171 Slc28a3-R ACCACAGAGGGCATAGGTTG Slc38a6-F TGTGATGGCTAACACGGGTA 247 Slc38a6-R CAAAAGCGAAGAGTCCCAGA Tmed5-F AGTTCCCTCAGATCGGGATT 236 Tmed5-R TGGGCTGGTAGAAACACTCC Tmod1-F TATTCCCATACCCACCCTCA 224 Tmod1-R GAGAAGTGTTGTGGGGGAGA Tstd2-F CCATGCTTTTGTTGATGTGG 175 Tstd2-R AGGCAGCTACCATGCTGAGT Unc13d-F GGGACCTGCTGTATGAGGAA 203 Unc13d-R CTGTTTCACTGTGGCCTTCA Xcr1-F TCATCTTCACCGTCGTGGTA 156 Xcr1-R AGCAATGAGAGAAGGCCAAA Xpnpep2-F ACGGTGGATGAGTTTTCTGG 247 Xpnpep2-R CAGTAGGAGTGCCCCAATGT Zfp345-F ACTTCACGTGGGAAGAGTGG 172 Zfp345-R TGACTTCTTTCATGCCTTCC Zfp353-F GTGGGTCTTGGATTTCCTGA 210 Zfp353-R AGAAAACGCAAAGGGAGACA Zfp488-F ACCCCAAAGCCCTGTAGACT 201 Zfp488-R TCCTGCAGCAGTGTCAGAGT Zfp937-F TGAGAGGAGATGGTGTGCTG 191 Zfp937-R AGCCTTTCCGTTCCAGATTT Zfp933-F AATCCATCCCTCTGTTGGTG 221 Zfp933-R AGGAAAGGGGTTTGAGTCGT Psmb11-F CAGTGGACCTCTTCCACGTT 198 Psmb11-R CCTCCTCTTGCTCCACAAAG Zfp459-F AGGAACCCCAATTGACTGAC 211 Zfp459-R CCCAGCTTCTGGTGACTTTC Car5b-F AATGGCTTGGCTGTGATAGG 250 Car5b-R GGTCACGGTCAACCTCAACT Casc5-F GACGAGCACGGTCAACATAG 152 Casc5-R AGACTTGCAAGATGGCAACC AC158558.2-F AGCACTGGGATCAAAGGTGT 190 AC158558.2-R ACAGGTTCAATTCCCTGCAC A830018L16Rik-F GGGCAGAAAATGATGCTGAT 202 A830018L16Rik-R AAGGAGTCCTGGGAAAGCAT Zfp874b-F CGGCTCTTTCCTGTTTTGAT 151 Zfp874b-R GCCTGACTCCATGCTTTCTC A630055G03Rik-F GCCTCCTCCCAGGAAAGTAT 150 A630055G03Rik-R TCCTGTGTAAATCTTCCACCTC 9030025P20Rik-F AGGCCACAGTTCATCTGTCC 231 9030025P20Rik-R TGCGACTTGAACTTGCTCAC Slfn5-F TGGATCGGAACCTACCATGT 186 Slfn5-R TCCCTTGTGACTCCACTTCC Gen1-F TTTATCCCCAAGATGGCAAC 155 Gen1-R CATCCGCTTCCATTTTCACT Bri3bp-F AGCCAGGGCTACACAGAGAA 249 Bri3bp-R GCAGGTGGATCTCTGCAAGT Zfp353-F GTGGGTCTTGGATTTCCTGA 210 Zfp353-R AGAAAACGCAAAGGGAGACA SI Dataset 1A-Predicted intermolecular dsRNAs

Trans-Natural Antisense Transcript- dsRNA (Trans-nat-dsRNA) or Cis-Natural Antisense Transcript-dsRNA (Cis-nat-dsRNA)

Format: endo-siRNA ID, Sequence

1st Transcript ID (Accession Number), Type/dsRNA Source Region, Chromosome Number/+ or – strand, Expression Profile During Developing Testis (GEO/GDS or Our Data) Sequence of forward strand of dsRNA from 1st transcript

2nd Transcript ID (Accession Number), Type/dsRNA Source Region, Chromosome Number/+ or – strand, Expression Profile During Developing Testis (GEO/GDS or Our Data) Sequence of reverse strand of dsRNA from 2nd transcript

Type of dsRNA (Trans-nat- dsRNA or Cis-nat-dsRNA), dsRNA length, Percentage of Complementary Match of Two Strands

Other endo-siRNAs in this dsRNA (ID, sequence)

1/2 endo-siRNA-T1 ACAGTGTACTCACATATAT Xpnpep2 (ENSMUST00000114998) mRNA/3’UTR ChrX/+ strand Our Data AGGGCTGGAGAGATGGCTCAGTGATTGAGAGCACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGTAA CCACATGGTGGCTCACAACCATCTGTAATGGGATCTTATGCCCTCTTCTGATGTGTCTGAAGACAAGAAC AGTGTACTCACATATATAAAATAAACAAATCTTTAGAAACAAAA Gm10389 (ENSMUST00000100773) mRNA/3’UTR Chr15/+ strand Our Data TTTTATTTATTTACTTATTTTATATATGTGAGTACACTGTAGCTATCTTCAGATACACCA GAAGAGGGCATCGGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATT GAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACTCTTGAGCCATCTCTCCAGCC CT Trans-nat-dsRNA 184bp 86.2% Endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT Endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT

2/2 endo-siRNA-T1 ACAGTGTACTCACATATAT Nol11 (ENSMUST00000018577, ENSMUST00000106757, NM_133702, NM_001161329) mRNA/3’UTR Chr11/- strand GEO/GDS606, 409 GGGCTGGAGAGATGGCTCAGCAATTAAGAGCACTGACTGCTCTTTCAGAGTTCCTGAGTTCAAT TCCTGCCAACCACATGGTGGCTTACAACCATCTGTAATGTTATCTGATGCCCTCTTCTGGTGTG TCTGGAGATAGTGACAGTGTACTCACATATATGAAAT Gm10389 (ENSMUST00000100773) mRNA/3’UTR Chr15/+ strand Our Data ATTTTATATATGTGAGTACACTGTAGCTATCTTCAGATACACCAGAAGAGGGCATCGGATCCCA TTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCA GTCAGTGCTCTTAACTCTTGAGCCATCTCTCCAGCCC Trans-nat-dsRNA 165bp 89.7%

1/2 endo-siRNA-T4 GCTCTTCCGAAGGTCCAGAGT Ppm1k (ENSMUST00000042766, NM_175523) mRNA/3ʼUTR Chr6/- strand GEO/GDS606,409 GGGGGCTGGTGAGATGGCTCAGTGGTTAGGAGCACCCGACTGCTCTTCCGAAGGTCCAGAGTTC AAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAACAAGATCTGACTCCCTCTTCTGGT GTGTCTGAAGACAGCTACAGTGTACTTACATATAATAATAAATAAATCTTTAAAAACTAAAA Zmynd8 (ENSMUST00000109262) mRNA/3ʼUTR Chr2/- strand GEO/GDS606,401,409 TTTTTTTTTTTAAAGATTTATTTATTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACAC CAGAAGAGGGAGTCAGATCTTGTTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGA ACTCTGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCC Trans-nat-dsRNA 190bp 97.9%

2/2 endo-siRNA-T4 GCTCTTCCGAAGGTCCAGAGT Mfsd11 (NM_178620, ENSMUST00000021173) mRNA/3’UTR Chr11/+ strand GEO/GDS606,409 CAGTCAAGGGCTGGCGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCCAG AGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCCCAACAAGATCTGACTCCCTCTT CTAGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATCAATAAATAAATCTTT Zmynd8 (ENSMUST00000109262) mRNA/3’UTR Chr2/- strand GEO/GDS606,401,409 AAAGATTTATTTATTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACACCAGAAGAGGGA GTCAGATCTTGTTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCT TCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCCGAAAG Trans-nat-dsRNA 185bp 94.6%

1/2 Endo-siRNA-T6 CTGTGTAGCCTTGGCTGTCCTG Lpp (NM_001145952, NM_178665, NM_001145954) mRNA/3’UTR Chr16/+ strand GEO/GDS607,605 CTTAATTTTTTTTTTTCGAGACAGGGTTTCTCTGTGTAGCCTTGGCTGTCCTGGAACTCACTCT ATAGACCAGGCTGGCCTCGAACTCAGAAATCCACCTGCCTCTTCCTCCCAAATACTGGGATTAA AGGCGTGTGCCATAACTACCCAGCTTAATATTTTTTAA A130010J15Rik (NM_001160359, NM_181048, NM_001160360) mRNA/3’UTR Chr1/+ strand GEO/GDS606,409 TTAAAAAAGAACTATTCAGCTGGGCAGTGGTGGCACACACCTTTAATCACAGCACTTGGGAGGC AGATGCAGGTGGATTTCTGAGTTCGAGGTCAGCTTGGTCTACAGAGTGAGTTCCAGGACAGCCA AGGCTACACAGAGAAACCCTGTCTCAAAGAAAAAAAAAAAAG Trans-nat-dsRNA 170bp 87.6% Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC

2/2 Endo-siRNA-T6 CTGTGTAGCCTTGGCTGTCCTG Lpp (NM_001145952, NM_178665, NM_001145954) mRNA/3’UTR Chr16/+ strand GEO/GDS607,605 AAAATACTTAATTTTTTTTTTTCGAGACAGGGTTTCTCTGTGTAGCCTTGGCTGTCCTGGAACT CACTCTATAGACCAGGCTGGCCTCGAACTCAGAAATCCACCTGCCTCTTCCTCCCAAATACTGG GATTAAAGGCGTGTGCCATAACTACCCAGCTTAATATTTTT Frmpd1 (ENSMUST00000044773) mRNA/3’UTR Chr4/+ strand GEO/GDS409 AAAAATAAAAAAGTCGCCGGGCAGTGGTGGCACATGCCTTTAATCCCAGCACTTGGGAGGCAGA GACAGGCAGATTTCTGAGTTCGAGCCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAAGG CTACACAGAGAAACCCTGTCTCGGAAAAAAAATAATAAAAAATTTT Trans-nat-dsRNA 174bp 86.2% Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC

1/2 Endo-siRNA-T10 TCTCCTGCTTTTTTACCAC IAPEZI Endogenous Retrovirus Our Data CACCCGAAAAATCCAGACTGACCAAGGGAATACTAATGTCCCTCGTCTTGGTGATGTCCA GGGCGTCAATAATAAAGAGAGAGCAGCGTTGGGGGATAATGTCGACATTTCCACTCCCAA TGACGGTGATGTATAATGCTCAAGTATTCTCCTGCTTTTTTACCACTAACTAGGAACTGG GTTTGGCCTTAATTCAGACAGCCTTGGCTCTGTCTGGACAGGTCCAGATGACTGACACCA TTAACACTTTGTCAGCCTCAGTGACTACAGTCATAGATAAACAGGCCTCAACTAATGTCT AGATACAGAGAGGTCTCATGCTGGTTAATCAACTCATAGATCTTGTCCAGATACAACTAG ATGTATTATGACAAATAACTCAGCAGGGTTGTGAACAAAAGTTTCCGGGATTGTGTGTTA TTTCCATTCAGTATGTTAAATTTACTAGGGCAGCTAATTTGTCAAAAAGTCTTTTTCAGT ATATGTTACAGAATTGGATGGCTGAATTTGAACAGATCCCTTCGGGAATTGAGACTTCAG GTCAACTCCACGCGCTTGGACCTGTCCCTGACCAAAGGATTACCCAATTGGATCTCCTCA GCATTTTCTTTCTTTAAAAAATGGGTGGGATTAATATTATTTGGAGATACACTTTGCTGT GGATTAGTGTTGCTTCTTTGATTGGTCTGTAAGCTTAAGGCCTAAACTAGGAGAGACAAG GTGGTTATTGCCCAGGCGCTTGCAGGACTAGAACATGGAGCTTCCCCTGATATATCTATG TTTAGGCAATAGGTCGCTGGCCACTCAGCTCTTACATCTCACGAGGCTAGACTCATTGCA CGGGATGGAGTGAGTGTGCTTCAGCAGCCCGAGAGAGTTGCAAGGCTAAGCACTGCAATG GAAAGGCTCTGCGGCATATATGAGCCTATTCTAGGGAGACATGTCATCTTTCATGAAGGT TCAGTGTCCTAGTTCCCTTCCCCCAGGCAAAACGACACGGGAGCAGGTCAGGGTTGCTCT GGGTAAAAGCCTGTAAGCCTAAGAGCTAATCCTGTACATGGCTCCTTTACCTACACACTG GGGATTTGACCTCTATCTCCACTCTCATTAATATGGGTGGCCTATTTGCTCTTATTAAAA GGATAGGGGGAGA Slc38a6 (ENSMUST00000058139) mRNA/3’UTR Chr12/+ strand Our Data TCTCCCCCTTTTTCTTTTAATAAGAGCAAATAGGCCACCCATATTAATGAGAGTGGAGAT AGAGGTCAAATCCCCAGTGTGTAGGTAAAGGAGCCATGTACAGGATTAGCTCTTAGGCTT ACAGGCTTTTACCCAGAGCAACCCTGACCTGCTCCCGTGTCGTTTTGCCTGGGGGAAGGG AACTAGGACACTGAACCTTCATGAAAGATGACATGTCTCCCTAGAATAGGCTCATATATG CCGCAGAGCCTTTCCATTGCAGTGCTTAGCCTTGCAACTCTCTCGGGCTGCTGAAGCACA CTCACTCTATCCCGTGCAATGAGTCTAGCCTCATGGGATATAAGAGCTGAGTGGCCAGCG ACCTATTGCCTAAGCATAGATATATCAGGGGAAGCTCCATGTTCTAGTCCTGCAAGCGCC TGGGCAATAACCACCTTGTCTCTCCTAGTTTGGGCCTTAAGCTTACAGACCAATCAAAGA AGCAACACTAATCCACAGCAAAGTGTATCTCCAAATAATATTAATCCCACCCATTTTTTA AAGAAAGAAAATGCTGAGGAGATCCAATTGGGTAATCCTTTGGTCAGCGACAGGTCCAAG CGCGTGGAGTTGACCTGAAGTCTCAATTCCCGAAGGATCTGTTCAAATTCAGCCATCCAA TTCTGTAACATATACTGAAAAAGACTTTTTGACAAATTAGCTGTCCTAGTAAATTTAACA TACTGAATGGAAATAACACACAATCCCGGAAACTTTTGTTCACATCCCTGCTGAGTTATT TGTCATAATACATCTAGTTGTATCTGGACAAGATCTATGAGTTGATTAACCAGCATGAGA CCTCCCTGTATCTTGACATTAGCTGAGGCCTGTTCATCTATGACTGTAGTCACTGAGGCT GACAAAGTGTTAATGGTGTCAGTCGTCTGGACCTGTCCAGACAGAGCCAAGGCTGTCTGA ATTAAGGCCAAACCCAGTTCCTAGTTAGTGGTAAAAAAGCAGGAGAATACTTGAGCATTA TACATCACCGTCATTGGGAGTGGAAATGTCGACATTATCCCCCAACGCTGCTCTCTCTTT ATTATTGACGCCCTGGACATCACCAAGACGAGGGACATTAGTATTCCCTTGGTCAGTCTG GATTTTTCGGGTG Trans-nat-dsRNA 1153bp 98.4% Endo-siRNA-T63 TCTCTCCTAGTTTGGGCCTT

2/2 Endo-siRNA-T10 TCTCCTGCTTTTTTACCAC IAPLTR1a_I_MM Endogenous Retrovirus Our Data CACCCGAAAAATCCAGACTGACCAAGGGAATACTGATGTCCCTCGTCTTGGTGATGTCCA GGGCGTCAATAATAAAGAGAGAGCAGCGTTGGGGGATAATGTCGACATTTCCACTCCCAA TGACGGTGATGTATAATGCTCAAGTATTCTCCTGCTTTTTTACCACTAACTAGGAACTGG GTTTGGCCTTGATTCAGACAGCCTTGGCTCTGTCTGGACAGGTCCAGACGACTGACACCA TTAACACTTTGTCAGCCTCAGGACTACAGTCATAGATAAACAGGCCTCAGCTAATGTCAA GATACAGGGAGGTCTCATGCTGGTTAATCAACTCATAGATCTTGTCCAGATACAACTAGA TGTATTATGGCAAATAGCTCAGCTGGGATGTGAACAAAAGTTTCCGGGATTGTGTGTTAC TTCCATTCAGTATGTTAAATTTACTAGGGCAGCTAATTTGTCAAAAAGTCTTTTTCAGTA TATGTTACAGAATTGGACGGCTGAATTTGAACAGATCCTTCGGGAATTGAGACTTCAGGT CAACTCCACGCGCTTGGACCTGTCCCTGACCAAAGGATTACCCAATTGGATCTCCTCAGC ATTTTCCTTCTTTAAAGAATGGGTGGGATTGATATTATTTGGAGATACACTTTGCTGTGG ATTAGTGTTGCTTCTTTGATTGGTCTGTAAGCTTAAGGCCCAAACTAGGAGAGACAAGGT GGTTATTGCCCAGGCGCTTGCAGGACTAGAACATGGAGCTTCCCCTGATAATATCTATGC TTAGGCAATAGGTCGCTGGCCACTCAGCTCTTATATCCCATGAGGCTAGTCTCATTGCAC GGGATAGAGTGAGTGTGCTTCAGCAGCCCGAGAGAGTTGCACGGCTAAGCACTGCAGTAG AAGGGCTCTGCGGCATAATATGAGCCTATTCTAGGGAGACATGTCATCTTTCAAGAAGGT TGAGTGTCCAAGTGTCCTTCTCTCCAGGCAAAACGACACGGGAGCAGGTCAGGGTTGCTC TGGGTAAAAGCCTGTGAGCCTAAGAGCTAATCCTGTACATGGCTCCTTTACCTACACACT GGGGATTTGACCTCTATCTCCACTCTCATTAATATGGGTGGCCTATTTGCTCTTATTAAA AGGAAAGGGGGAGA Slc38a6 (ENSMUST00000058139) mRNA/3’UTR Chr12/+ strand Our Data TCTCCCCCTTTTTCTTTTAATAAGAGCAAATAGGCCACCCATATTAATGAGAGTGGAGAT AGAGGTCAAATCCCCAGTGTGTAGGTAAAGGAGCCATGTACAGGATTAGCTCTTAGGCTT ACAGGCTTTTACCCAGAGCAACCCTGACCTGCTCCCGTGTCGTTTTGCCTGGGGGAAGGG AACTAGGACACTGAACCTTCATGAAAGATGACATGTCTCCCTAGAATAGGCTCATATATG CCGCAGAGCCTTTCCATTGCAGTGCTTAGCCTTGCAACTCTCTCGGGCTGCTGAAGCACA CTCACTCTATCCCGTGCAATGAGTCTAGCCTCATGGGATATAAGAGCTGAGTGGCCAGCG ACCTATTGCCTAAGCATAGATATATCAGGGGAAGCTCCATGTTCTAGTCCTGCAAGCGCC TGGGCAATAACCACCTTGTCTCTCCTAGTTTGGGCCTTAAGCTTACAGACCAATCAAAGA AGCAACACTAATCCACAGCAAAGTGTATCTCCAAATAATATTAATCCCACCCATTTTTTA AAGAAAGAAAATGCTGAGGAGATCCAATTGGGTAATCCTTTGGTCAGCGACAGGTCCAAG CGCGTGGAGTTGACCTGAAGTCTCAATTCCCGAAGGATCTGTTCAAATTCAGCCATCCAA TTCTGTAACATATACTGAAAAAGACTTTTTGACAAATTAGCTGTCCTAGTAAATTTAACA TACTGAATGGAAATAACACACAATCCCGGAAACTTTTGTTCACATCCCTGCTGAGTTATT TGTCATAATACATCTAGTTGTATCTGGACAAGATCTATGAGTTGATTAACCAGCATGAGA CCTCCCTGTATCTTGACATTAGCTGAGGCCTGTTCATCTATGACTGTAGTCACTGAGGCT GACAAAGTGTTAATGGTGTCAGTCGTCTGGACCTGTCCAGACAGAGCCAAGGCTGTCTGA ATTAAGGCCAAACCCAGTTCCTAGTTAGTGGTAAAAAAGCAGGAGAATACTTGAGCATTA TACATCACCGTCATTGGGAGTGGAAATGTCGACATTATCCCCCAACGCTGCTCTCTCTTT ATTATTGACGCCCTGGACATCACCAAGACGAGGGACATTAGTATTCCCTTGGTCAGTCTG GATTTTTCGGGTG Trans-nat-dsRNA 1154bp 97.3% Endo-siRNA-T63 TCTCTCCTAGTTTGGGCCTT

1/2 Endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT RP23-413M3.2 (ENSMUST00000117166) Pseudogene Chr2/- strand OUR DATA TACTGGCTAGTTTTGTGTCAACTTGACACAGCTGGAGTTATCACAGAGAAAGGAGCTTCA GTTGAGGAAATGCCTCCATGAGATCCAACTGTAAGGCATTTTCTCAATTAGTGATCAAGG GGGAAAGGCCCCTTGTGGGTGGGACCATCTCTGGGCTGGTAGTCTTGGGTTCTATAAGAG AGCAGGCTGAGCAAGGCAGGGGAAGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGC ATCAGCTCCTGCTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTGGTGATGAACAG CAGTATGGAAGTGTAAGCTGAATAAACCCTTTCCTCCCCAACTTGCTTCTTGGTCATGAT GTTTGTGCAGGAATAGAAACCCTGACTAAGACA 3110048L19Rik (NR_003549) Non-coding RNA Chr17/- strand GEO/GDS605,401 TGTCTTAGTCAGGGTTTCTATTCCTGCACAAACATCATGACCAAGAAGCAGGTTGGGGAGGAAA GGGTTTATTCACCTTACACTTCCATACTGCTGTTCATCACCAAGGAAGTCAGGACTAGAACTCA AGCAGGTCAGGAAGCAAGAGCTGATTCAGAAGCCATGGAGGGATGTTCTTTACTGGCTTGCTTC CCCTGGCTTGCTCAGCCTGCTCTCTTATAGAACCCAAGACTGCCAGCCCAGAGATGTTCCCACC CACAAGGGGCCTTTCCCCCTTGATCACTAATTGAGAAAATAACCCACAACTAGATCTCATGGAG GCACTTCGCCAACCAAATCTCCTTTCTCTCTGATAACTCCAGCCTGTGTCAAGTTGATACATAA AATCAGCCAGTA Trans-nat-dsRNA 396bp 92.7% Endo-siRNA-T24 TATCACAGAGAAAGGAGCTTC Endo-siRNA-T52 TACACTTCCATACTGCTGTTCAT

2/2 Endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT RP23-413M3.2 (ENSMUST00000117166) Pseudogene Chr2/- strand Our Data AGTTTTGTGTCAACTTGACACAGCTGGAGTTATCACAGAGAAAGGAGCTTCAGTTGAGGA AATGCCTCCATGAGATCCAACTGTAAGGCATTTTCTCAATTAGTGATCAAGGGGGAAAGG CCCCTTGTGGGTGGGACCATCTCTGGGCTGGTAGTCTTGGGTTCTATAAGAGAGCAGGCT GAGCAAGGCAGGGGAAGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGCATCAGCTC CTGCTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTGGTGATGAACAGCAGTATGG AAGTGTAAGCTGAATAAACCCTTTCCTCCCCAACTTGCTTCTTGGTCATGATGTTTGTGC AGGAATAGAAACCCTGACTAAGACACCTCTC 1810030O07Rik (NM_175141, ENSMUST00000060108) mRNA/3’UTR ChrX/- strand GEO/GDS605,401 GCCACCTGTCTTAGTAAGGGTTCTATTCCTGCACAAACATCGTGACCAAGAAGCAAGTTG GGGAGGAAAGGGTTTATTCAGCTTACACTTCCATACTGCTGTTCATCACCAAAGGAAGTC AGGACTGAACTCACACAGGTCAGGAAGCAGGAGCTGATGCAGAGGCCATTGAGAGATCTT CCTTACTGGCTTGCTTTCCACTGGCTTGCTCAGCCTGCTCTCTTATAGAACCCAAGACTA CCAGCCCAGAGATGGCACCACCCACAATGGACCCTCCACCCTTGACCACTAATTGAGAAA ATGCCTTACAGCTGGATCTCGTGGAGGCATTTCCCCAACTGAAGCTCCCTTCTCAGTGAT AACTGCAGCTGTGTCAACTGACACACAAAT Trans-nat-dsRNA 391bp 90.8% Endo-siRNA-T24 TATCACAGAGAAAGGAGCTTC

1/2 Endo-siRNA-T13 TAGCCTGGTCTACAGAGTG Tgfbr2 (ENSMUST00000061101, ENSMUST00000035014) mRNA/3’UTR Chr9/- strand GEO/GDS606,409 TCTAAAAATAGACACAGCCGCTGGGCGGTGGTGGCACACGCCTTTAATCCCAGCACTTGGGAGG CAGAGGCAGGCAGATTTCTGAGTTCCAGGCTAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCC AGGGCTACACAGAGAAATCCTGTCTCGAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAA Tmbim1 (ENSMUST00000113796) mRNA/5’UTR Chr1/- strand GEO/GDS401 TCTTTTCTTCTTCTTCTTTTGTTTAATGGCTTTTTCAAGATAGGGTTTCTCTGTGTAGCCCTGG CTGTCCTGGAACTCACTCTGTAGACCAGGCTAGCCTCGAACTCAGAAATCCGCCTGCCTCTGCC TCCCCAGTGCTGGGATTAAAGGCATGCGCCACCACTGCCCAGCCCCTCTTTCTTTATA Trans-nat-dsRNA 188bp 85.3% Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T28 TCACTCTGTAGACCAGGCTAG Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

2/2 Endo-siRNA-T13 TAGCCTGGTCTACAGAGTG BC039771 (NR_033220) Non-coding RNA Chr2/+ strand Our Data GCCTGGTAGTGGTGGTGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCT GAGTTTGAGGCTAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGTTACACAGAGAAACC CTGTCTCGGAAAACCAAAACCAAAAAACAACAACAA Dynll1 (NM_019682, ENSMUST00000009157) mRNA/3’UTR Chr5/- strand GEO/GDS605,401 TTAGTGTTCCTTTTTGTTTTTGTTTTGAGGCAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGA ACTCACTCTGTAGACCAGGCTAGCCTCGAACTCAGAAATCCACCTGCCTCTGCCTCCCGAGTGC TGGGATTAAAGGTATGCGCCACCACTGCCTGGC Trans-nat-dsRNA 164bp 89.0% Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT Endo-siRNA-T28 TCACTCTGTAGACCAGGCTAG Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

1/2 Endo-siRNA-T14 TATTCCTGGTTGTCAACTT Kif2a (ENSMUST00000122233, NM_008442) mRNA/5’UTR Chr13/- strand GEO/GDS605,401 TGTAGTGGCTATTCCTGGTTGTCAACTTGACTATATTTGGAATGAACTACAATCCAGAAT TGGAAGGCTCACCAGTGACCCTATTCTGGAGGCTGGGAGATAGAAGTTTCTGATCTGGAT CTTGGTATGGAGATCTTGAGGCATAGAGGCTTTGGATTCCAGAAGATTAAGACAGGGAGA TCTTCGAGTTCAAGGTCA Rhbdd2 (ENSMUST00000043707, NM_146002) mRNA/3’UTR Chr5/+ strand GEO/GDS606,409 TGACCTTGAACTCGAGATCTCCCTGTCTTAATCTGGAATCCATAGCCACTATGCTTCAAG ATCTCCATACCAAGATCCAGATCAGAAACTTCTATCTCCCAGCCTCCAGGATAGGGTCAC TGGTAAGCCTTCCAATTCTGGATTGTAGTTCATTCCAAATATAGTCAAGTTGACAACCAG GAATAGCCACTACA Trans-nat-dsRNA 198bp 95.5%

2/2 Endo-siRNA-T14 TATTCCTGGTTGTCAACTT C130036L24Rik (ENSMUST00000097665, NR_015507) Non-coding RNA Chr1/+ strand Our Data CTGTAATGGCTATTCCTGGTTGTCAACTTGACTATATCTGGAATAAAATACAATCCAGAA TTGAAAGACTCACCTGTGATCCTGATCTTGAGGCTGGGAGATAGAAGTTTCTGACCTGGA TCTTGGCATGAAGATCTTGAGGCATAATGGCTATGAATCCCAGGAGACTAAGGCAAGGAG ATCTCGGAGTTCAAGGTCATCTGGGACAAA Rhbdd2 (ENSMUST00000043707, NM_146002) mRNA/3’UTR Chr5/+ strand GEO/GDS606,409 TTAATTCCAGATGACCTTGAACTCGAGATCTCCCTGTCTTAATCTGGAATCCATAGCCAC TATGCTTCAAGATCTCCATACCAAGATCCAGATCAGAAACTTCTATCTCCCAGCCTCCAG GATAGGGTCACTGGTAAGCCTTCCAATTCTGGATTGTAGTTCATTCCAAATATAGTCAAG TTGACAACCAGGAATAGCCACTACAG Trans-nat-dsRNA 210bp 86.3%

1/2 Endo-siRNA-T17 TAACAAGATACCAGAACTAC Ccdc82 (ENSMUST00000110583, NM_025534) mRNA/3’UTR Chr9/+ strand GEO/GDS606,409 TGGAACTTTGGGCTTGAAGATCCATCCGTTGTTAAGAGCTCTGTCGGATGTTGTGTAAGAACTTGGAAGA TAATGTTGAGAACACTGCAAAAGATGGAGGTCTGGTTTGTGAAATTTCAGAGGGGAAAAATTAAAGACTC TTTTCAGGGCCATTGCTGTTTTGATTGTGAAGGTTCTGTAGTTCTGGTTAGCTGGGGCTGAAGAATCAGC TGTGATTAACAAGATACCAGAACTACCAAAGCAAAAACTTTGCATTACTGGGACTATTGATGCTGGTTAG CTGGAGCTAAGAAATTAGCGGTGATTAAGAAGAGACCAGCATCATTGAGGTGACATCTTCTGGGAAGTGT TTTCTGAAAGCA Acnat1 (NM_001164565) mRNA/3’UTR Chr4/- strand Our Data TACTCTCTGAAAACACTTCCCAGAATATTTCACCTCAATGATGCTGGTCTCTTCTTAATC ACAGCTAATTTCTTAGCTCCAGCTAACCAGCATCAATAGTCCCAGTAATGCAAGGTTTTC ACTTTAGTAGTTCTGGTATCTTGTTAATCACAGCCAACTCTTCAGCCCCAGCTAACCAGA ACCATAGAATCTTCACAATCAAATACCAATGGCTCTGTGAAGAGTCTTTAATCTTCCCTC TGAAATTTCACAAGCCAGGCCTCCATCTTCTGCACTGTTCTCAACATTATCTTCCAAACT CCTACATAACATTTGACAGAGCCCTTAACACGAAATGGATCTTCTAGCCCAAAGTTCCA Trans-nat-dsRNA 362bp 89.0%

2/2 Endo-siRNA-T17 TAACAAGATACCAGAACTAC Gm14443 (ENSMUST00000109054) mRNA/3’UTR Chr2/- strand Our Data GACTGTGTGGGATGTTGTGTAGGAGCTTGGAAGATAATGTTGAGAACAGTGCAGAAGATGGAGG CTTGGCTTTTGAAATTTCAGAGGGAAAATTAAAGACTCTTTTCAGGGTCATTACTATTTTGGAT TGTGAAGATTCTGTGGTTCTGGTTAGCTGGGGCTGAAGAATCAGGTGTGATTAACAAGATACCA GAACTACTAGAGTGAAAACTTTGCATTGCTGGGAATATTGATGATAGTTAGCTGGAGCTAAGAA TTTAGCAGTGATTAAGAAGAGACCAGCATCATTGAGGTGGCATCTTCTGGGAAGTGTTTTCTGA GAGCACAGAGGCAGTG Acnat1 (NM_001164565) mRNA/3’UTR Chr4/- strand Our Data CACTTTCCACATTACTCTCTGAAAACACTTCCCAGAATATTTCACCTCAATGATGCTGGT CTCTTCTTAATCACAGCTAATTTCTTAGCTCCAGCTAACCAGCATCAATAGTCCCAGTAA TGCAAGGTTTTCACTTTAGTAGTTCTGGTATCTTGTTAATCACAGCCAACTCTTCAGCCC CAGCTAACCAGAACCATAGAATCTTCACAATCAAATACCAATGGCTCTGTGAAGAGTCTT TAATCTTCCCTCTGAAATTTCACAAGCCAGGCCTCCATCTTCTGCACTGTTCTCAACATT ATCTTCCAAACTCCTACATAACATTTGACAGAGCC Trans-nat-dsRNA 336bp 87.8%

1/2 Endo-siRNA-T18 CACAGAGAAACCCTGTCTTG Tlk2 (ENSMUST00000106939, ENSMUST00000106936) mRNA/5’UTR Chr11/+ strand 105040334-105040655 GEO/GDS605,606,401,409 TTTATAGAAAATTAAAATTGCTGGGCAGTGGTGGCATTCGCCTTTAATCCCAGCTCTCGGGAGG CAGAGGCAGGCGGATCTCTATGAGTTTCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTG ACCCCCCATCTTCCCCCCCAAAAAGGTGAAACTAAAAATTTCATCTGTCTTCAAATGGTTCCTT TAAAACTGCACTCAGGAAACAGGCATCAGGGCATATGCCTATACTGCCAGCTCCTAGGGCCTGG GACAAAAGGACTGAGAATTTAGAACAATCTTGGCTACATAGTGAGACTCTCTGAAAACAGATAA AG 1700052K11Rik (NR_027956) Pseudogene Chr11/- strand 105040334-105040655 Our Data CTTTATCTGTTTTCAGAGAGTCTCACTATGTAGCCAAGATTGTTCTAAATTCTCAGTCCTTTTG TCCCAGGCCCTAGGAGCTGGCAGTATAGGCATATGCCCTGATGCCTGTTTCCTGAGTGCAGTTT TAAAGGAACCATTTGAAGACAGATGAAATTTTTAGTTTCACCTTTTTGGGGGGGAAGATGGGGG GTCAAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGAAACTCATAGAGATCCGCCTGCCTC TGCCTCCCGAGAGCTGGGATTAAAGGCGAATGCCACCACTGCCCAGCAATTTTAATTTTCTATA AA Cis-nat-dsRNA 322bp 100.0%

2/2 Endo-siRNA-T18 CACAGAGAAACCCTGTCTTG Xcr1 (ENSMUST00000078755, NM_011798) mRNA/3’UTR Chr9/123761436-123771246 bp, - strand Our Data TAAAATGAAGATGGTTCTGAGCCGGGTGTGGTGGCGCATGCCTTTAATCCCAGCACTCAGGAGGCAGAGA CAGGCAGATTTCTGAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAG AGAAACCCTGTCTTGAAAAACAAAACAAAACAAAACAAAACAAAACAAAAAAACAACAACAACAAAGA Zbtb44 (NM_172765, NM_001115130) mRNA/3’UTR Chr9/30838229-30877844 bp, + strand GEO/GDS606,607,410,409 TTTTTGGTTTTGTTTTGTTTTTGGGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCA AGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGG CCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAATTCTGGGATTAAAGGCGTGCGC CACCACGCCCGGCTGAAATTTAATTTCTA Trans-nat-dsRNA 209bp 85.1% Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

1/2 Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Noc2l (NM_021303) mRNA/Last Exons + 3’UTR Our Data GATGGAGACACAGACACGGGAGTGGATCTGAGCGAACTGTGGCAGCTGGCTCAGGGACCACAAGATGAGC TGGAGGATCTTCAGCTCTCAGAAGAGGACTGAGGCCTCCTGCTGCCTCCTGGAGGCCTCGACAGCAACTG TGCGGCGAGAGGACAGCAGAGCGTAAACAGGCTTTTATTGTTACAGCACAGCAGAACAAGTGTACTAGGA GCCATTTTGACCCTGAAAGGGAGGGAACTGTTTCTGCAGAGCCTTCTGCTGCCGGAAGCCGAAGGCTGAC CCTGACGTTGTCCCAGTTCAGAGTGGGGAGGGCGGCTCCATGGCCTCTCCTCTCCACTTTGTCTTTGGTT TGTCTGCAGAGCACTGCAGTTACCTCTAGAAGATAAACCCATTACTTTTGTTTGTTTGTTTGTTTGTTTG TTTTTTCGAGACAGGGTGTCTCTGTGTAGCCCTGGCTATCCTGGAACTCACTTTGTAGACCAGGCTGGCC GCGAACTCTGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCTCTGCCCA GCTCATTGCTTTTCTTCTTAAGCCTTATGTTTTCCTTTT Samd11 (NM_001110516) mRNA/3’UTR Our Data AAAAGGAAAACATAAGGCTTAAGAAGAAAAGCAATGAGCTGGGCAGAGGTGGCGCACGCCTTTAATCCCA GCACTTGGGAGGCAGAGGCAGGCGGATTTCAGAGTTCGCGGCCAGCCTGGTCTACAAAGTGAGTTCCAGG ATAGCCAGGGCTACACAGAGACACCCTGTCTCGAAAAAACAAACAAACAAACAAACAAACAAAAGTAATG GGTTTATCTTCTAGAGGTAACTGCAGTGCTCTGCAGACAAACCAAAGACAAAGTGGAGAGGAGAGGCCAT GGAGCCGCCCTCCCCACTCTGAACTGGGACAACGTCAGGGTCAGCCTTCGGCTTCCGGCAGCAGAAGGCT CTGCAGAAACAGTTCCCTCCCTTTCAGGGTCAAAATGGCTCCTAGTACACTTGTTCTGCTGTGCTGTAAC AATAAAAGCCTGTTTACGCTCTGCTGTCCTCTCGCCGCACAGTTGCTGTCGAGGCCTCCAGGAGGCAGCA GGAGGCCTCAGTCCTCTTCTGAGAGCTGAAGATCCTCCAGCTCATCTTGTGGTCCCTGAGCCAGCTGCCA CAGTTCGCTCAGATCCACTCCCGTGTCTGTGTCTCCATC Trans-nat-dsRNA 599bp 100.0%

2/2 Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Zbtb8a (ENSMUST00000030610, NM_028603) mRNA/3’UTR Chr4/- strand GEO/GDS606,409 TTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTGTTTTGTTTTGTTTTGTTTTGTTT TGTTTTTTCAAGACAGGGTTTCTCTGTATGGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCA GGCTGGCCTCAAATTCAGAAATCCACCTGCCTCTGCCTCCCAAGTCCTGGGATTAAAGGCGTGT GCCACCACCTCATGGC Tmed5 (ENSMUST00000002837, ENSMUST00000119437, NM_028876) mRNA/3’UTR Chr5/- strand OUR DATA GCCGGGCAGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCT GAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACC CTGTCTTGAAAAAACAAAAATAAAAATAAAAATAAACAAAAAAAAAAAAAAAAAGAAGAAAGAA AAGAAAAAAAGAAGAA Trans-nat-dsRNA 208bp 89.6% Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT

1/2 Endo-siRNA-T22 TCTGAGTTCAAGGCCAGCCT Ptpn7 (ENSMUST00000049449, NM_177081) mRNA/3’UTR Chr1/+ strand Our Data AAGCAGCGGGGCATGGTGGTGCATACCTTTAATTCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTGA GTTCAAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGCCTCG AAAGAAAAAAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA A Ppm1k (ENSMUST00000042766, NM_175523) mRNA/3’UTR Chr6/- strand GEO/GDS606,409 TTTTGTTTGTTTTTTGGTTTTGGTGTTTTTTTTTTTTGGTGTTTTTTTTTTTTTTTTTTT TGGTTTTTCAAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAG ACCAGGCTGGCCTTGAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTACTGGAATTAA AGGCATGTGCCACCACATCCTGGCTT Trans-nat-dsRNA 211bp 81.2% Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

2/2 Endo-siRNA-T22 TCTGAGTTCAAGGCCAGCCT Samd8 (ENSMUST00000119430) mRNA/3’UTR Chr14/+ strand GEO/GDS607,410 AAATTGTCCTTGAAGCTGGGCATGGTGGAGCACGCCTTTAATCCCAGCACTTGGTAGGCAGAGG CAGGCGGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAAGGCT ACACAGAGAAACCCTGTCTCAAAAAACCAAAAAAAAAAAAAAATTGTCCTTGGTTTT Slc28a3 (ENSMUST00000022036, NM_022317) mRNA/3’UTR Chr13/- strand Our Data AAAACAGTGGACACTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTG GCTGTCCTGGCACTCACTTTGTAGACCAGGCTGGCCTTGAACTCAGAAATCCACCTGCCTCTGC CTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCACGCCCGGCTACAACAGTGAACACTTT Trans-nat-dsRNA 189bp 88.9% Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

1/2 Endo-siRNA-T24 TATCACAGAGAAAGGAGCTTC RP23-413M3.2 (ENSMUST00000117166) Pseudogene Chr2/- strand OUR DATA TACTGGCTAGTTTTGTGTCAACTTGACACAGCTGGAGTTATCACAGAGAAAGGAGCTTCA GTTGAGGAAATGCCTCCATGAGATCCAACTGTAAGGCATTTTCTCAATTAGTGATCAAGG GGGAAAGGCCCCTTGTGGGTGGGACCATCTCTGGGCTGGTAGTCTTGGGTTCTATAAGAG AGCAGGCTGAGCAAGGCAGGGGAAGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGC ATCAGCTCCTGCTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTGGTGATGAACAG CAGTATGGAAGTGTAAGCTGAATAAACCCTTTCCTCCCCAACTTGCTTCTTGGTCATGAT GTTTGTGCAGGAATAGAAACCCTGACTAAGACA 3110048L19Rik (NR_003549) Non-coding RNA Chr17/- strand GEO/GDS605,401 TGTCTTAGTCAGGGTTTCTATTCCTGCACAAACATCATGACCAAGAAGCAGGTTGGGGAGGAAA GGGTTTATTCACCTTACACTTCCATACTGCTGTTCATCACCAAGGAAGTCAGGACTAGAACTCA AGCAGGTCAGGAAGCAAGAGCTGATTCAGAAGCCATGGAGGGATGTTCTTTACTGGCTTGCTTC CCCTGGCTTGCTCAGCCTGCTCTCTTATAGAACCCAAGACTGCCAGCCCAGAGATGTTCCCACC CACAAGGGGCCTTTCCCCCTTGATCACTAATTGAGAAAATAACCCACAACTAGATCTCATGGAG GCACTTCGCCAACCAAATCTCCTTTCTCTCTGATAACTCCAGCCTGTGTCAAGTTGATACATAA AATCAGCCAGTA Trans-nat-dsRNA 396bp 92.7% Endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT Endo-siRNA-T52 TACACTTCCATACTGCTGTTCAT

2/2 Endo-siRNA-T24 TATCACAGAGAAAGGAGCTTC RP23-413M3.2 (ENSMUST00000117166) Pseudogene Chr2/- strand Our Data AGTTTTGTGTCAACTTGACACAGCTGGAGTTATCACAGAGAAAGGAGCTTCAGTTGAGGA AATGCCTCCATGAGATCCAACTGTAAGGCATTTTCTCAATTAGTGATCAAGGGGGAAAGG CCCCTTGTGGGTGGGACCATCTCTGGGCTGGTAGTCTTGGGTTCTATAAGAGAGCAGGCT GAGCAAGGCAGGGGAAGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGCATCAGCTC CTGCTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTGGTGATGAACAGCAGTATGG AAGTGTAAGCTGAATAAACCCTTTCCTCCCCAACTTGCTTCTTGGTCATGATGTTTGTGC AGGAATAGAAACCCTGACTAAGACACCTCTC 1810030O07Rik (NM_175141, ENSMUST00000060108) mRNA/3’UTR ChrX/- strand GEO/GDS605,401 GCCACCTGTCTTAGTAAGGGTTCTATTCCTGCACAAACATCGTGACCAAGAAGCAAGTTG GGGAGGAAAGGGTTTATTCAGCTTACACTTCCATACTGCTGTTCATCACCAAAGGAAGTC AGGACTGAACTCACACAGGTCAGGAAGCAGGAGCTGATGCAGAGGCCATTGAGAGATCTT CCTTACTGGCTTGCTTTCCACTGGCTTGCTCAGCCTGCTCTCTTATAGAACCCAAGACTA CCAGCCCAGAGATGGCACCACCCACAATGGACCCTCCACCCTTGACCACTAATTGAGAAA ATGCCTTACAGCTGGATCTCGTGGAGGCATTTCCCCAACTGAAGCTCCCTTCTCAGTGAT AACTGCAGCTGTGTCAACTGACACACAAAT Trans-nat-dsRNA 391bp 90.8% Endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT

1/2 Endo-siRNA-T25 TCTGTGTTCATCTGACGAATT Cmah (NM_007717, NM_001111110) mRNA/3’UTR Chr13/+ strand GEO/GDS606,409 CCTCAGCATTTTTGGATGACAGGTGGGAAACAGGGAGGAAGGG TATGACCGGCTCGGTAGTACAAGGCCAATTGTCTTTTTTAGGGTGGGAGACTGTGAAGGG CTTGCCCTTCTAACAGTACGGTCTCCAACCTCTCTCCCCCCTATTAATTAAGTTTAAAAA GGCCACACTTAACTGAGGTGATCAAATGATTTTCTCATCCGTAGATGAGTGAGCTTTTAA CCTTGGCTTGGGTGGACATTGACCCGATTCCTCTCGTGGGTGCTGTTACGACCCACACCT GTGGCTCTTGGTATCTTTTGGGGAGGGGAGGCAGAGCCGTAGATATTTTTGTTTTTTAGC TGTAAATAGATACCAACCTCCGTCAAACCGGGTTTATCCCACAGGAAACTCAGAAATGGT CAAGCTGGACCTTCCCCTGCAGTAATTCTCTGCACCAAGCCATACCCATACTGTATTTGT AAGATCACGAACCAGTGTGCACAGTTCTGAGGACTGTGCAGCTCCTAAGGGAGAATTGTC AACCTCAGATTTAGCAAGGCCTAGGCAAGAATTATGTCATTAGTAACACCACGATTTGTG GCTAAAATAGGAGCTGGAAGTCGTTCCTCTTCATCCCTGTTATTCCCATAGCCTGAGGAA CTAAGGACACCTTGCAGTAACAGCAAGGGTGAAAAGCCAGAGGCTAGCTAAGGGACTAAG CCCGTCTATCAGAATAAAAACCAATCTCTATTAATATTAGAAATATCTACTTTCCTAGCC CTCTTGGTAAACCTAAATTTTAACTCAGACTGAAAGCCACATGCTGGAATGTCCTTGGAA TGAAGATAGCATTTGCCACCTGTGTGCTCTTGGGGGCGGGGGATGCATGCCCACTGTAGT TCTGCTGAAGGTGTAGATTGACCTGCTTGAAAGACAAAAATCTTAGAGAGTGAAGAGTAA CATCACAAAGCTTCTTTTGGGGAAGTTCAGGTACTTTATTCATTTGCAAATTGTAAGGCT AAGGCTAGTCTCAGGCCTCCTGTGGGGGAGCTGGCTCAGAGAGTAGCAGGAAAACAGCTT TCCTGGGAGCTTTAGTTTCCAGCTGAATTTTAAGCAAAAGAGGAATTTTAGTCCTCAAGG TGATACTTATAAGAAGATTCAGAATCTGTGTTCATCTGACGAATTAATCTCTCTGGCAGC CACCATGCTCTATCTTCATCTCGTGAAAAAACACAAACTGAGCCCCTTCCCCAGATTAGA ACCGGATCCGGACCCTACTATTTGCTAGTCAGTGGGTCCTTCCATTTTACCAATGCATAA GAATTAGAAGTAACTAGATGCCAGTGGCAATCCACTGCTGACTGACCTTTAATATTGGTT GCAAAATATTTAGAACAAATAAGGTAAAGGCAAGATG ETNERV Endogenous Retrovirus OUR DATA CACCTTGCCTTCACCTTATTTGTCCTAAATTTCTTGCACACCGATATCAAGGGCCAGTCT GCAGCGGATCGCCACTGGCATCCAGTTACTTCTAATTCTTATGCATTGGTAAAATGGAAG GACCCCCTGACTAATGAATGGAAGGGTCCAAATCCAGTTCTAATTTGGGGTAGGGGCTCA GTTTGTGTTTTTTCACGAGATGAAGATGGAGCGCGGTGGCTGCCAGAGAGATTAATTCGT CAGATGAACACAGATTCTGACTCTTCTGGTAAGTATCATTCTAAAGACTAAAATTCCTTT TGTGCTTAGAATTCAGCTGAGAGCGAAAGCTCCCAAAGCTGTTCTCCAGCTACTCTCTGA GCCAGCTCCCAACAGGAGGCCCGGAGACTAGCCTCAGCTTTACAATTTGCATTTGAATAA AGTACCTAGACTTCCCCGAAAGAAGTTCTGCTTTCCTACTTTCTCACTGTCGAGAATTTG TCTTACAAGCAGGTAAATCAACATTCTCGAAGCGGACCAGCGGATGTGCATCCCCGCCCC CCTAGAGCACACAGGTGGCTGCTGTTATCTCCTTTCCAAGGACATTTCCAGCACGTGGCT TTCAGTCTGAGTTAAAAATTAGGTTTACCAAGAGGGCTAGAAGAGTAGATATTTCTATAT TAATAAAGATTGGTTTTTATTTTGATAGACAGGCTTAGCCCCTTAGCTGACCTCTGGCTT TTCACCCTTGCTGTTACTGCAAGGTGTCCTTAGCTCAATAAGGCTGTGGAAAAAACAGGG ATGAGGAGGAACGACTTCCAGCTCCTATTTTAGCCACAAATCGTGGTGTTACTAAGGACA TAATTCTTGCTTAGGCTTTGCTAAATCTGAGGTTGATAATTCTCCTTTAGGAGCACTCAG AACTGTGCATACTGGTTTGTGATCGTACAAATTCAGTATGGGCATCGCTTGGTGCAGAGG CACTGCAGGGGAAGGTCCAGCTTGACCATTTCTGAGTTTCCTGTGAGATAAACCCGGTTT GAAAGAGGTTGGTACCAAATTTTGGCTAAAAATGAAAAATAGTTTTCGGCTCTGCCTCAC CTCCCCAAAAGGTACCCAGAGCCACAGGTGTGGGTCTTAACAGTACCCACGGGAAGAATC GGGTCAATGTCCACCCAAGCCAAGGTTAAAAGCCCACTCATCAACGGATGAGAAAATCAT TTGATCACCTCAGTTAAGCGCTGCCTTATTTAACTTAATTAATAGGGGGGAGAGAGATTG GAGACGTACTATTGAAAGGGCAAGCCCTTCACTGCCTCCCACCCAAATAAAAAAGCCAAT TGGCTTTGTACTACAGAGCCGGCCGAACCCCTTCTCCCTGTTTCCCACCTATCATCCAAA AATGCGGAGG Trans-nat-dsRNA 1400bp 86.4%

2/2 Endo-siRNA-T25 TCTGTGTTCATCTGACGAATT Cmah (NM_007717, NM_001111110) mRNA/3’UTR Chr13/+ strand GEO/GDS606,409 TCTTTTTTAGGGTGGGAGACTGTGAAGGGCTTGCCCTTCTAACAGTACGGTCTCCAACCTCTCTCCCCCC TATTAATTAAGTTTAAAAAGGCCACACTTAACTGAGGTGATCAAATGATTTTCTCATCCGTAGATGAGTG AGCTTTTAACCTTGGCTTGGGTGGACATTGACCCGATTCCTCTCGTGGGTGCTGTTACGACCCACACCTG TGGCTCTTGGTATCTTTTGGGGAGGGGAGGCAGAGCCGTAGATATTTTTGTTTTTTAGCTGTAAATAGAT ACCAACCTCCGTCAAACCGGGTTTATCCCACAGGAAACTCAGAAATGGTCAAGCTGGACCTTCCCCTGCA GTAATTCTCTGCACCAAGCCATACCCATACTGTATTTGTAAGATCACGAACCAGTGTGCACAGTTCTGAG GACTGTGCAGCTCCTAAGGGAGAATTGTCAACCTCAGATTTAGCAAGGCCTAGGCAAGAATTATGTCATT AGTAACACCACGATTTGTGGCTAAAATAGGAGCTGGAAGTCGTTCCTCTTCATCCCTGTTATTCCCATAG CCTGAGGAACTAAGGACACCTTGCAGTAACAGCAAGGGTGAAAAGCCAGAGGCTAGCTAAGGGACTAAGC CCGTCTATCAGAATAAAAACCAATCTCTATTAATATTAGAAATATCTACTTTCCTAGCCCTCTTGGTAAA CCTAAATTTTAACTCAGACTGAAAGCCACATGCTGGAATGTCCTTGGAATGAAGATAGCATTTGCCACCT GTGTGCTCTTGGGGGCGGGGGATGCATGCCCACTGTAGTTCTGCTGAAGGTGTAGATTGACCTGCTTGAA AGACAAAAATCTTAGAGAGTGAAGAGTAACATCACAAAGCTTCTTTTGGGGAAGTTCAGGTACTTTATTC ATTTGCAAATTGTAAGGCTAAGGCTAGTCTCAGGCCTCCTGTGGGGGAGCTGGCTCAGAGAGTAGCAGGA AAACAGCTTTCCTGGGAGCTTTAGTTTCCAGCTGAATTTTAAGCAAAAGAGGAATTTTAGTCCTCAAGGT GATACTTATAAGAAGATTCAGAATCTGTGTTCATCTGACGAATTAATCTCTCTGGCAGCCACCATGCTCT ATCTTCATCTCGTGAAAAAACACAAACTGAGCCCCTTCCCCAGATTAGAACCGGATCCGGACCCTACTAT TTGCTAGTCAGTGGGTCCTTCCATTTTACCAATGCATAAGAATTAGAAGTAACTAGATGCCAGTGGCAAT CCACTGCTGACTGACCTTTAATATTGGTTGCAAAATATTTAGAACAAATAAGGTAAAGGCAAGATGAGCC TTTGGTGACCTTGGGGGATGTGC ERVB7_1-I_MM Endogenous Retrovirus OUR DATA GCTATATCCCCCAAGGTCACCAAAGGCCCACCTTGCCTTCACTTTATTTGTCCTAAATTT CTTGCACACCGATATCAAGGGCCAGTCTGCAGCGGATCGCCACTGGCATCCAGTTACTTC TAATTCTTATGCATTGGTAAAATGGAAGGACCCCCTGACTAATGAATGGAAGGGTCCAGA TCCAGTTCTAATTTGGGGTAGGGGCTCAGTTTGTGTTTTTTCACGAGATGAAGATGGAGC GCGGTGGCTGCCAGAGAGATTAATTCGTCAGATGAACACAGATTCTGACTCTTCTGGTAA GTATCATTCTAAAGACTAAAATTCCTTTTGTGCTTAAAATTCAGCTGAGAGCAACAGCTC TCAAAGCTGTTCTCCAGCTACTCTCTGAGCCAGCTCCCGACAGGAGGCCGGAGACTAGCC TCAGCTTTACAATTTGCATTTGAATAAAGTACCTAGACTTCCCCGAAAGAAGTTCTGCTT TCCTACTTTCTCACTGTCTTTCAAGATTTTGTCTTTCAAGCAGGTAAATCAACATTCTCG AGGCGGACCAGCGGATGTGCATCCCCGCCCCCCTAGAGCACACAGGTGGCAGCTGTTATC CCCAGTCTCAGGACATTTCCAGCACGTGGTTTTCAGTCTGAGTTAAAAATTTAGGTTTAC CTAGAGGGCTAGAAGAGTAGATATTTCTATATTAATAAAGATTGGTTTTTATTTTGATAG ACAGGCTTAGCCCCTTAGCTGACCTCTGGCTTTTCACCCTTGCTGTTACTGCAAGGTGTC CTTAGCTCAATAGGCTGTGGAAAAAACAGGGATGAGGAGGAACGACTTCCAGCTCCTATT TTAGCCACAAATCGTGGTGTTACTAACGACATAATTCTTGCTTAGGCTTTGCTAATTCTG AGGTTGATAATTCTCCTTTAGGAGCTGCACAGCACTCAGAACTGTGCATACTGGTTTGTG ATTGTACAAATTCAGTATGGGCACCGCTTGGTGCAGAGGTACTGCAAGGGAAGGTCCGGC TTGACCATTTCTGAGTTTCCTGTGAGATAAACCCGGTTTGAAAGAGGTTGGTACCAAATT TTGGTTAAAAATAAAAAATATTTTCCGGCTCTACCTCGCCTCCCCAAAAGGTACCGAGAG CCACATGTGTGGGTTTTACCCACGGGAGGAATCGGGTCCATGTCCACCCAAGCCAAGGTT AAAAGCCCACTCATCTACGGATGAGAAAATCATTTGATCACCTCAGTTAAGCGTTGCCTT ATTTAACTTAATTAATAGGGGGGAGAGAGATTGGAGACGTACTATTGAAAGGGCAAGCCC TTCACTGCCTCCCACCCAAATAAAAGA Trans-nat-dsRNA 1353bp 86.1%

1/2 Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Tmod1 (ENSMUST00000107773, NM_021883) mRNA/3’UTR Chr4/+ strand 46127618-46128904 Our Data TTTGGAAGCGTGGTGAAACAATCTTTTATTTCCAATTTGATCGTAGCAACTCAGTAAAAAGAACACATAA TCATGATCTGTCAACCCCCACTTGAAACTTTGACATCAAGATTAAAGCTGCCAAATTGATTCCAGGATCA AACCCCCACCCCTAAGAATGAAAGACAAGCCACAGAATTTTCTAAGAGTCAGAAAGACACAGGATTCCTT TTGCCAGGTAAGATAAAGAGGGAGAAAAAGGCAATGGTGAATTTTCAAGTTTCAAAACCCACCACACCAG GCAACAGACATCCTTCTGAGTGCTGTGGGAACACCTGCGGGGTACTCATCTGCAGTCAGAAATCATTTCT TCTTTATTGAATTCCAACTTCATGATGGATGAAAACTTACAGCCGCTGGGCAGTGGTGGCACACGCCTTT AATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAG TTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAAAGGAAAAA AAAAGAAAACTTACAGCCACATAAAAACATCTTCCTATACCACAGTGGGCAATGGCTTATGTGAGATCAA CACCATTGGGTGAATTTCCAGTCCACCATGCCTGTGGTATTTAGCATGGCCCTGCTTACAGACACCAAGT GCCTGCCTGGTCATTTATGAGACAAATCAAATCACACAGAGCTCTTGCCTACAAACAAAGCCTCTAGAGG ACAGCAGAGTACAGCATCTTAATGGTAAGGAATTAGGAGATCCTGGCCAAACAACACACGGGATTACTCT GAAACCTAATCTTGGTGTTCCTACTGGATTTCCTTTTTTAACACCATGGGAGCCAGTAAAAATGTTCAAA TACACTGTTCTTGTGCCTTTTAATAGACCACAGTGCCAGTTAAACTAGTATTTTTGTTGTTTTGGGGAGT TATTTTCCTTAGGGATTCAGCCAATATTATAGTAATGATAAGGCTCAAAAGCTGTTGAGCATAGCCAGGG GGCTTCTGACTTAAGAGAAAGCCTGCACACCGAACTGTAACAGTATGGACAGTACAGGGTAACTAGAGGT GGCATCGGGGCCTCAGCACTGAGTGTCCACTGAGGCTGCACACGGGCCCAGGAGTGGCACCAAGCTGCAG GGACAGCCAGCCCCACTCAGCTTCTCCTTGAAACACAACTGCAGCTGCATTCTGCATCACTGGAAACTGC AAAATAATATTAAAGCCATTTGGTCTA Tstd2 (ENSMUST00000107772, NM_173033) mRNA/3’UTR Chr4/- strand 46127618-46128904 Our Data TAGACCAAATGGCTTTAATATTATTTTGCAGTTTCCAGTGATGCAGAATGCAGCTGCAGTTGTGTTTCAA GGAGAAGCTGAGTGGGGCTGGCTGTCCCTGCAGCTTGGTGCCACTCCTGGGCCCGTGTGCAGCCTCAGTG GACACTCAGTGCTGAGGCCCCGATGCCACCTCTAGTTACCCTGTACTGTCCATACTGTTACAGTTCGGTG TGCAGGCTTTCTCTTAAGTCAGAAGCCCCCTGGCTATGCTCAACAGCTTTTGAGCCTTATCATTACTATA ATATTGGCTGAATCCCTAAGGAAAATAACTCCCCAAAACAACAAAAATACTAGTTTAACTGGCACTGTGG TCTATTAAAAGGCACAAGAACAGTGTATTTGAACATTTTTACTGGCTCCCATGGTGTTAAAAAAGGAAAT CCAGTAGGAACACCAAGATTAGGTTTCAGAGTAATCCCGTGTGTTGTTTGGCCAGGATCTCCTAATTCCT TACCATTAAGATGCTGTACTCTGCTGTCCTCTAGAGGCTTTGTTTGTAGGCAAGAGCTCTGTGTGATTTG ATTTGTCTCATAAATGACCAGGCAGGCACTTGGTGTCTGTAAGCAGGGCCATGCTAAATACCACAGGCAT GGTGGACTGGAAATTCACCCAATGGTGTTGATCTCACATAAGCCATTGCCCACTGTGGTATAGGAAGATG TTTTTATGTGGCTGTAAGTTTTCTTTTTTTTTCCTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTT CTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCC TGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCAGCGGCTGTAAGTTTTCATC CATCATGAAGTTGGAATTCAATAAAGAAGAAATGATTTCTGACTGCAGATGAGTACCCCGCAGGTGTTCC CACAGCACTCAGAAGGATGTCTGTTGCCTGGTGTGGTGGGTTTTGAAACTTGAAAATTCACCATTGCCTT TTTCTCCCTCTTTATCTTACCTGGCAAAAGGAATCCTGTGTCTTTCTGACTCTTAGAAAATTCTGTGGCT TGTCTTTCATTCTTAGGGGTGGGGGTTTGATCCTGGAATCAATTTGGCAGCTTTAATCTTGATGTCAAAG TTTCAAGTGGGGGTTGACAGATCATGATTATGTGTTCTTTTTACTGAGTTGCTACGATCAAATTGGAAAT AAAAGATTGTTTCACCACGCTTCCAAA Cis-nat-dsRNA 1287bp 100.0% Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC

2/2 Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Tmed5 (ENSMUST00000002837, ENSMUST00000119437, NM_028876) mRNA/3’UTR Chr5/- strand OUR DATA GCCGGGCAGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCT GAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACC CTGTCTTGAAAAAACAAAAATAAAAATAAAAATAAACAAAAAAAAAAAAAAAAAGAAGAAAGAA AAGAAAAAAAGAAGAA Zbtb8a (ENSMUST00000030610, NM_028603) mRNA/3’UTR Chr4/- strand GEO/GDS606,409 TTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTGTTTTGTTTTGTTTTGTTTTGTTT TGTTTTTTCAAGACAGGGTTTCTCTGTATGGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCA GGCTGGCCTCAAATTCAGAAATCCACCTGCCTCTGCCTCCCAAGTCCTGGGATTAAAGGCGTGT GCCACCACCTCATGGC Trans-nat-dsRNA 208bp 89.6% Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT

1/2 Endo-siRNA-T27 AGAGAAAGTACCCAAGGAGCT Hsd3b2 (ENSMUST00000107022) mRNA/3’UTR Chr3/- strand OUR DATA GACACATGCTCCACTATGTTCATAGCAGCCTTATTTATAATAGCCAGAAGCTGGAAAGAA CCCAGATGTCCCTCAACAGAGGAATGGATAAAAAAATGTGGTACATTTACATAATGGAGT ACTACTCAGCTATTAAAAAGAATGAATTTATGAAATTCCTAGCCAAATGAATGGACCTGG AGGGCATCATCCTGAGTGAGGTAACACATTCACAAAGGAACTCACACAATATGTACTCAC TGATAAGTGGATATTAGCCCAAAACCTAGGATACCCAAGATATAAGATACAATTTGCTAA ACACATGAAACTCAAGAAGAATGAAAACTGAAGTGTGGACACTATGCCCCTCCTTAGAAT TGGGAACAAAACACCCATGGAAGGAGTTACAGAGACAAAGTTTGGAGCTGAGACAAAAGG ATGGACCATCTAGAGACTGCCATATCCAGGGATCCACCCCATAATCAGCTTCCAAACGCT GACACCATTGCATACACTAGCAAGATTTTATCGAAAGAACCCAGATGTAGCTGTCTCTTG TGAGACTATGCCGGGGCCTAGCAAACACAGAAGTGGATGCTCACAGTCAGCTATTGGATG GATCACAGGGCCCCCAATGGAGGAGCTAGAGAAAGTACCCAAGGAGCTAAAGGGATCTGC AACCATATAGGTGGAACAACATTATGAACTAACCAGTACCCCGGAGCTCTTGACTCTAGC TGCATATGTATCAAAAGATGGCCTAGCCGGCCATCACTGGAAAGAGATGCCCATTGGACA TGCAAACTGTATATGCCCCAGTACAGGGGAATGCCAGGGCCAAAAAAAATGGGAATGGGT GGGTAGGGAAGTGAGGGGAGGGTATGGGGGACTTTTGGGATAGCATTGGAAATGTAATTG AGGAAAATATGTAATAAAAAATATTTTTAAAAAAA Zfp488 (ENSMUST00000052871, NM_001013777) mRNA/3’UTR Chr14/- strand OUR DATA TATTTTTATATTTTTCCATTTTTTATTAGGTATTTAGCTCATTTACATTTCCAATGTTAT ACCAAAAGTCCCCCACAGCCACCCACCCCCACTCCCCTACCCACCCACTCCCCCTTTTTG GCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTT CCAGTGATGGCCGACTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGG GGTACTGGTTAGTTCATTATGTTGTTCCACCTATAGGGTTGCAGATCCCTTTAGCTCCTT GGCTACTTTCTCTAGCTCCTCCATTGGGAGCCCTGTGATTCATCCATTAGCTGACTGTGA GCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGTCTCACAAGAGACAGCTACATCTGG GTCCTTTCAATAAAATCTTGCTAGTGTATGCAATGGTCTCAGCGTTTGGAAGCTGATTAT GGGGTGGATCCCTGGATATGGCAGTCTCTACATGGTCCATCCTTTCATCTCAGCTCCAAA CTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTCCCAATTCTAAGGAGGGGCATAGT GTCCACACTTCAGTCTTCATTCTTCTTGAGTTTCATGTGTTTAGCAAATTGTATCTTATA TCTTGGGTATCCTAGGTTTGGGGCTAATATCCACTTATCAGTGAGTACATATTGTGTGAG TTCCTTTGTGATTGTGTTACCTCACTCAGGATGATGCCCTCCAGGTCCATCCATTTGGCT AGGAATTTCATAAATTCATTCTTTTTAATAGCTGAGTAGTACTCCATTGTGTAGATGTAC CACATTTTCTGTATCCATTCCTCTGTTGAGGGGCATCTGGGTTCTTTCCAGCTTCTGGCT ATTATAAATAAGGCTGCTATGAACATAGTGGAGCATGTGTC Trans-nat-dsRNA 941bp 94.3% Endo-siRNA-T45 CACTTCTGTGTTTGCTAGGCCCC

2/2 Endo-siRNA-T27 AGAGAAAGTACCCAAGGAGCT Hsd3b2 (ENSMUST00000107022) mRNA/3’UTR Chr3/- strand OUR DATA ATTCACAAAGGAACTCACACAATATGTACTCACTGATAAGTGGATATTAGCCCAAAACCTAGGATACCCA AGATATAAGATACAATTTGCTAAACACATGAAACTCAAGAAGAATGAAAACTGAAGTGTGGACACTATGC CCCTCCTTAGAATTGGGAACAAAACACCCATGGAAGGAGTTACAGAGACAAAGTTTGGAGCTGAGACAAA AGGATGGACCATCTAGAGACTGCCATATCCAGGGATCCACCCCATAATCAGCTTCCAAACGCTGACACCA TTGCATACACTAGCAAGATTTTATCGAAAGAACCCAGATGTAGCTGTCTCTTGTGAGACTATGCCGGGGC CTAGCAAACACAGAAGTGGATGCTCACAGTCAGCTATTGGATGGATCACAGGGCCCCCAATGGAGGAGCT AGAGAAAGTACCCAAGGAGCTAAAGGGATCTGCAACCATATAGGTGGAACAACATTATGAACTAACCAGT ACCCCGGAGCTCTTGACTCTAGCTGCATATGTATCAAAAGATGGCCTAGCCGGCCATCACTGGAAAGAGA TGCCCATTGGACATGCAAACTGTATATGCCCCAGTACAGGGGAATGCCAGGGCCAAAAAAAATGGGAATG GGTGGGTAGGG RP23-174L3.1 (ENSMUST00000121552) Pseudogene ChrX/+ strand OUR DATA CCCCACCCACCCACTCCCACTTCTTGGCCCTGGCGTTCACCTGTACTGAGGC AAATAAAGTCTGCACGACCAATGGGCCTCTCTTTCCACTGATGGCCACCTAGGCCATCTT CTGATACATATGCAGCTAGAGACACGAGATCCGGAGGGTACTGGTTAGTTCACATTTTTT TTCCACCTATAGGGTTGCAGATCTCTTTAGCTCCTTGGATACTTTCTCTAGCTCCTCCAT TGGGGGCCCTGTGATCCATCCAATAGCTGACTGTGAGCATTCACTTCTGTGTTTGCTAGG CCCCAGCCTAGTCTCACAAGAGACAGCTATATCTGGGTCCTTTCAGCAAAATCTTGCTAG TGTATGCAATGGTGTCAGCGTTTGGAGGCTGATTATGGGATGGATCCCCGGATATGACAG TCTCTAGATGGTCCATCCTTTCGTCTCAGCTCCAAACTGTGTCTCTGTAACTCCTTCCAT GGGTGTTTTGTTCCCAATTCTAAGAAGGGGCAAAGTGTTCACACTTTGGTCTTCGTTCTT TTTGAGTTTCATGAGTTTCACAAATTGTATCTTATATCTTGGGTATTCTAAGTTTCTGGG CTAATATCCACTTATCAGTGAGTACATATCATTTGAGTGCTTGAGGAT Trans-nat-dsRNA 641bp 89.6% Endo-siRNA-T45 CACTTCTGTGTTTGCTAGGCCCC

1/2 Endo-siRNA-T28 TCACTCTGTAGACCAGGCTAG Tmbim1 (ENSMUST00000113796) mRNA/5’UTR Chr1/- strand GEO/GDS401 TCTTTTCTTCTTCTTCTTTTGTTTAATGGCTTTTTCAAGATAGGGTTTCTCTGTGTAGCCCTGG CTGTCCTGGAACTCACTCTGTAGACCAGGCTAGCCTCGAACTCAGAAATCCGCCTGCCTCTGCC TCCCCAGTGCTGGGATTAAAGGCATGCGCCACCACTGCCCAGCCCCTCTTTCTTTATA Tgfbr2 (ENSMUST00000061101, ENSMUST00000035014) mRNA/3’UTR Chr9/- strand GEO/GDS606,409 TCTAAAAATAGACACAGCCGCTGGGCGGTGGTGGCACACGCCTTTAATCCCAGCACTTGGGAGG CAGAGGCAGGCAGATTTCTGAGTTCCAGGCTAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCC AGGGCTACACAGAGAAATCCTGTCTCGAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAA Trans-nat-dsRNA 188bp 85.3% Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG Endo-siRNA-T13 TAGCCTGGTCTACAGAGTG Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC

2/2 Endo-siRNA-T28 TCACTCTGTAGACCAGGCTAG Dynll1 (NM_019682, ENSMUST00000009157) mRNA/3’UTR Chr5/- strand GEO/GDS605,401 TTAGTGTTCCTTTTTGTTTTTGTTTTGAGGCAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGA ACTCACTCTGTAGACCAGGCTAGCCTCGAACTCAGAAATCCACCTGCCTCTGCCTCCCGAGTGC TGGGATTAAAGGTATGCGCCACCACTGCCTGGC BC039771 (NR_033220) Non-coding RNA Chr2/+ strand OUR DATA GCCTGGTAGTGGTGGTGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCT GAGTTTGAGGCTAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGTTACACAGAGAAACC CTGTCTCGGAAAACCAAAACCAAAAAACAACAACAA Trans-nat-dsRNA 164bp 89.0% Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG Endo-siRNA-T13 TAGCCTGGTCTACAGAGTG Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT

1/2 Endo-siRNA-T29 TCTGAGTTCGAGGCCAGCCTT Abhd15 (NM_026185) mRNA/3’UTR Chr11/+ strand OUR DATA TAGATTAAGTAAGAATCAATGAACCTAGCCGGGCAGTGATGGCTCATGCCTTTAATCCCAGCAC TAGGGAGGCAGAAGCAGGTGGAATTCTGAGTTCGAGGCCAGCCTTGTCTACAAAGTGAGTTCCA GGACAGCCAGGGGAACACAGAGAAACCCTGTCTCGAAAAAACAAAAA Ttyh1 (NM_021324, NM_001001454, NM_001109765, ENSMUST00000129423) mRNA/3’UTR Chr7/+ strand GEO/GDS606,409 TTTTTGGTTTTTCAAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAG ACAAGGCTGGCCTCGAACTCAGAAACCCACCTGCCTCTTCCTCCCAAGTGCTGGGATTAAAGGC GTGGGCCACCACTGCCCAGTTTTTTTTTTTTTTTTTTTGTTGTTGTT Trans-nat-dsRNA 175bp 80.7% Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

2/2 Endo-siRNA-T29 TCTGAGTTCGAGGCCAGCCTT BC026590 (ENSMUST00000045368, NM_001081420) mRNA/3’UTR Chr4/+ strand GEO/GDS607,410 CAGCCAGGCGTGATGGCGCACACCTTTAATCCCAGCACTCAGGAGGCAGAGGCAGGTGGGTTTC TGAGTTCGAGGCCAGCCTTGTCTACGAAGTGAGTTCCAGGTCAGCCAGGGCTATACAGAGAAAC CCCGTCTTGAAAAACCAAAAAGATATATTGCAT Ttyh1 (NM_021324, NM_001001454, NM_001109765, ENSMUST00000129423) mRNA/3’UTR Chr7/+ strand GEO/GDS606,409 ACTGAACCTCTTTTTTTGGTTTTTCAAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAA CTCACTCTGTAGACAAGGCTGGCCTCGAACTCAGAAACCCACCTGCCTCTTCCTCCCAAGTGCT GGGATTAAAGGCGTGGGCCACCACTGCCCAGTT Trans-nat-dsRNA 161bp 85.9% Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

1/2 Endo-siRNA-T30 TACACAGAGAAACCCTGTTTC Lrrc2 (ENSMUST00000035076, NM_028838) mRNA/3’UTR Chr9/+ strand OUR DATA TTCTTCCTCACACTTAAAACTGTTTCATCCGGGCGTGGTGGCGCACACCTTTAATCCCAGCACT CGGGAGGCAGAGGCGGGCGGATTTCTGAGTTCGAGGCCAACCTGGTCTACAAAGTGAATTCCAG GACAGCCAAGGCTACACAGAGAAACCCTGTTTCAAAATAAACAAACAAACAAAAAAAACCAAAA CA Ncan (ENSMUST00000002412, NM_007789) mRNA/3’UTR Chr8/- strand OUR DATA TTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTGAAACAGGGTTTCTCTGTGTAGCCCTGGCTG TCCTGGAACTCACTTTGTAGACCAGGCTAGCCTCGCACTCAGAAATCTGCCTGCCGCTGCCTCC CAAGAGCTGGGATTAAAGGTGTGCGCCACCACGCCCGGTTCTACATTTTTCAAAATGTGAAATA A Trans-nat-dsRNA 194bp 85.7% Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

2/2 Endo-siRNA-T30 TACACAGAGAAACCCTGTTTC Lrrc2 (ENSMUST00000035076, NM_028838) mRNA/3’UTR Chr9/+ strand OUR DATA CTGTTTCATCCGGGCGTGGTGGCGCACACCTTTAATCCCAGCACTCGGGAGGCAGAGGCGGGCG GATTTCTGAGTTCGAGGCCAACCTGGTCTACAAAGTGAATTCCAGGACAGCCAAGGCTACACAG AGAAACCCTGTTTCAAAATAAACAAACAAACAAAAAAAACC Trim14 (ENSMUST00000046897) mRNA/3’UTR Chr4/- strand GEO/GDS607,410 GTTTTCTTTTTCTTACTTTGGTTTTTCGAAACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGG AACTCACTTTGTAGACCATGCTGGCCTCGAACTCAGCAATCTGCCTGCCTCTGCCTCCCGAGTG CTGGGATTAAAGGTGTGCACCACCACACCCAGCTCAGACAA Trans-nat-dsRNA 169bp 86.5% Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

1/2 Endo-siRNA-T31 TTACATATAATAAATAAATCTT Klhl7 (NM_001161800, NM_026448) mRNA/3’UTR Chr5/+ strand GEO/GDS605,401 GGGCTGGTGAGATGGCTCAGTAGTTATGAGCACTGACTGCTCTTCCAAAGGTCCTGAGTTCAAT TCCCAGCAACCACATGGTGGCTCATAACCATCCGTAACAAGACCTGACGCCCTCTTCTGGAGTG TCTGAAGACAACTACAGTGTACTTACATATAATAAATAAATCTTTTTTAAAAAG Papola (ENSMUST00000109901, ENSMUST00000093264, ENSMUST00000101063) mRNA/3’UTR Chr12/+ strand GEO/GDS605,606,401,409 CTTTTTAAAAGATTTATTTATTATATGTAAGTACACTGTAGCTGCCTTCAGACACGCCAGAAGA GGGCGCCAGATCTCGATACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGG ACCTTTGGAAGAGCAGTCAGTGCTCTTAACTGCTGAGCCACCCCTCCAGCCC Trans-nat-dsRNA 182bp 91.2%

2/2 Endo-siRNA-T31 TTACATATAATAAATAAATCTT Wdr34 (NM_001008498, ENSMUST00000113711) mRNA/3’UTR Chr2/- strand GEO/GDS607,410 GGGCTGGTGAGATGGCTCAGCGGGTAAGAGCACTGACTACTCTTCTGAAGGTCCTGAGTTCAAA TCCCAGCAACCACATGGTGGCTCACAACCAACCGTAATGAGATCTGATGCCCTCTTCTGGTGTG TTTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATCTTTTAAAAA Papola (ENSMUST00000109901, ENSMUST00000093264, ENSMUST00000101063) mRNA/3’UTR Chr12/+ strand GEO/GDS605,606,401,409 TTTTTAAAAGATTTATTTATTATATGTAAGTACACTGTAGCTGCCTTCAGACACGCCAGAAGAG GGCGCCAGATCTCGATACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGA CCTTTGGAAGAGCAGTCAGTGCTCTTAACTGCTGAGCCACCCCTCCAGCCC Trans-nat-dsRNA 179bp 89.9%

1/2 Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC Tstd2 (ENSMUST00000107772, NM_173033) mRNA/3’UTR Chr4/- strand 46127618-46128904 Our Data TAGACCAAATGGCTTTAATATTATTTTGCAGTTTCCAGTGATGCAGAATGCAGCTGCAGTTGTGTTTCAA GGAGAAGCTGAGTGGGGCTGGCTGTCCCTGCAGCTTGGTGCCACTCCTGGGCCCGTGTGCAGCCTCAGTG GACACTCAGTGCTGAGGCCCCGATGCCACCTCTAGTTACCCTGTACTGTCCATACTGTTACAGTTCGGTG TGCAGGCTTTCTCTTAAGTCAGAAGCCCCCTGGCTATGCTCAACAGCTTTTGAGCCTTATCATTACTATA ATATTGGCTGAATCCCTAAGGAAAATAACTCCCCAAAACAACAAAAATACTAGTTTAACTGGCACTGTGG TCTATTAAAAGGCACAAGAACAGTGTATTTGAACATTTTTACTGGCTCCCATGGTGTTAAAAAAGGAAAT CCAGTAGGAACACCAAGATTAGGTTTCAGAGTAATCCCGTGTGTTGTTTGGCCAGGATCTCCTAATTCCT TACCATTAAGATGCTGTACTCTGCTGTCCTCTAGAGGCTTTGTTTGTAGGCAAGAGCTCTGTGTGATTTG ATTTGTCTCATAAATGACCAGGCAGGCACTTGGTGTCTGTAAGCAGGGCCATGCTAAATACCACAGGCAT GGTGGACTGGAAATTCACCCAATGGTGTTGATCTCACATAAGCCATTGCCCACTGTGGTATAGGAAGATG TTTTTATGTGGCTGTAAGTTTTCTTTTTTTTTCCTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTT CTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCC TGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCAGCGGCTGTAAGTTTTCATC CATCATGAAGTTGGAATTCAATAAAGAAGAAATGATTTCTGACTGCAGATGAGTACCCCGCAGGTGTTCC CACAGCACTCAGAAGGATGTCTGTTGCCTGGTGTGGTGGGTTTTGAAACTTGAAAATTCACCATTGCCTT TTTCTCCCTCTTTATCTTACCTGGCAAAAGGAATCCTGTGTCTTTCTGACTCTTAGAAAATTCTGTGGCT TGTCTTTCATTCTTAGGGGTGGGGGTTTGATCCTGGAATCAATTTGGCAGCTTTAATCTTGATGTCAAAG TTTCAAGTGGGGGTTGACAGATCATGATTATGTGTTCTTTTTACTGAGTTGCTACGATCAAATTGGAAAT AAAAGATTGTTTCACCACGCTTCCAAA Tmod1 (ENSMUST00000107773, NM_021883) mRNA/3’UTR Chr4/+ strand 46127618-46128904 Our Data TTTGGAAGCGTGGTGAAACAATCTTTTATTTCCAATTTGATCGTAGCAACTCAGTAAAAAGAACACATAA TCATGATCTGTCAACCCCCACTTGAAACTTTGACATCAAGATTAAAGCTGCCAAATTGATTCCAGGATCA AACCCCCACCCCTAAGAATGAAAGACAAGCCACAGAATTTTCTAAGAGTCAGAAAGACACAGGATTCCTT TTGCCAGGTAAGATAAAGAGGGAGAAAAAGGCAATGGTGAATTTTCAAGTTTCAAAACCCACCACACCAG GCAACAGACATCCTTCTGAGTGCTGTGGGAACACCTGCGGGGTACTCATCTGCAGTCAGAAATCATTTCT TCTTTATTGAATTCCAACTTCATGATGGATGAAAACTTACAGCCGCTGGGCAGTGGTGGCACACGCCTTT AATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAG TTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAAAGGAAAAA AAAAGAAAACTTACAGCCACATAAAAACATCTTCCTATACCACAGTGGGCAATGGCTTATGTGAGATCAA CACCATTGGGTGAATTTCCAGTCCACCATGCCTGTGGTATTTAGCATGGCCCTGCTTACAGACACCAAGT GCCTGCCTGGTCATTTATGAGACAAATCAAATCACACAGAGCTCTTGCCTACAAACAAAGCCTCTAGAGG ACAGCAGAGTACAGCATCTTAATGGTAAGGAATTAGGAGATCCTGGCCAAACAACACACGGGATTACTCT GAAACCTAATCTTGGTGTTCCTACTGGATTTCCTTTTTTAACACCATGGGAGCCAGTAAAAATGTTCAAA TACACTGTTCTTGTGCCTTTTAATAGACCACAGTGCCAGTTAAACTAGTATTTTTGTTGTTTTGGGGAGT TATTTTCCTTAGGGATTCAGCCAATATTATAGTAATGATAAGGCTCAAAAGCTGTTGAGCATAGCCAGGG GGCTTCTGACTTAAGAGAAAGCCTGCACACCGAACTGTAACAGTATGGACAGTACAGGGTAACTAGAGGT GGCATCGGGGCCTCAGCACTGAGTGTCCACTGAGGCTGCACACGGGCCCAGGAGTGGCACCAAGCTGCAG GGACAGCCAGCCCCACTCAGCTTCTCCTTGAAACACAACTGCAGCTGCATTCTGCATCACTGGAAACTGC AAAATAATATTAAAGCCATTTGGTCTA Cis-nat-dsRNA 1287bp 100.0% Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

2/2 Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC Ctcfl (ENSMUST00000094287, NM_001081387) mRNA/3’UTR Chr2/- strand OUR DATA TTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTTCT CTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATC CGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGTGCCACCACACCCGGCTGATATTT CTGA Bri3bp (NM_029752) mRNA/3’UTR Chr5/+ strand Our Data TTAAAAACTTCAACCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCTGGAGGCAGAGGCA GGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTAC ACAGAGAAACCCTGTCTCGAAAATCAAAAAAACAAAAAACAAAAAAAAATAAAACAAAACAAAA CAAA Trans-nat-dsRNA 196bp 91.8% Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

1/2 Endo-siRNA-T34 TCCCAGCAACCACATGGTGGTT Prr5l (NM_175181, NM_001110849, NM_001083810) mRNA/3’UTR Chr2/- strand GEO/GDS607,410 GGGCTGGAGAGATGGCTCAGGAGTTAAGAGCCCTGACTGCTCTTCCACAGGTCCTGAGTTCAAT TCCCAGCAACCACATGGTGGTTCCCAACCATCTGTAATGGGATCTGATGCCCTCTTCTGGTGTG TCTGAAGACAACAGTAGTGTACTCACGTATATGAAATAAATAAATCTT 8030423F21Rik (ENSMUST00000064097) mRNA/3’UTR Chr5/- strand OUR DATA AAGATTTGTTTTATTTATATGAGTACACTGTTGCTCTCTTCAGACACACCAAAAGAGTGCATCA GATCCCATTACAGATGGTTGTAAACCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGG AAGAACAGTCAGTGCTCTTAATTGCTGAGCCATCTCTCCAGCCC Trans-nat-dsRNA 176bp 88.7%

2/2 Endo-siRNA-T34 TCCCAGCAACCACATGGTGGTT Prr5l (NM_175181, NM_001110849, NM_001083810) mRNA/3’UTR Chr2/- strand GEO/GDS607,410 GGGCTGGAGAGATGGCTCAGGAGTTAAGAGCCCTGACTGCTCTTCCACAGGTCCTGAGTTCAAT TCCCAGCAACCACATGGTGGTTCCCAACCATCTGTAATGGGATCTGATGCCCTCTTCTGGTGTG TCTGAAGACAACAGTAGTGTACTCACGTATATGAAATAAATAAATCTT Flt3 (ENSMUST00000110549) mRNA/3’UTR Chr5/- strand GEO/GDS605,606,401,409 AAGATTTACTTATTACTATATGTAAGTACACTATACCTGTCTTCAGACACACCAGAAGAGGGCA TCAGATCTCATTAGGGATGGTTTTGAACCACCATGTGGTTGCTGGGATTTGAACTCAGGACTTT CGGAAGAGCCATCAGTGCTCTTAACCGCGGAGCCACCTCTCCAGCCC Trans-nat-dsRNA 176bp 85.8%

1/2 Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Mobkl3 (NM_025283, ENSMUST00000162364) mRNA/3’UTR Chr1/+ strand GEO/GDS606,409 AAGAATTTAAGTGCAGCCGGGCGGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGA GGCAGGTGGATTTCTGAGTTGGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGG CTACACAGAGAAACCCTGTCTCAGAAAACCAAAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAA AAAAAAAAAA Git2 (ENSMUST00000102579, ENSMUST00000112185, ENSMUST00000043283, ENSMUST00000112183) mRNA/3’UTR Chr5/- strand GEO/GDS606,409 TTATTTCTTGACATTTTTCTTTTCTTTTCTTTTCTTTTTTTTTTTTTTGGTTTTTCGAGACAAG GTTTCTCTGTGTAGCCCTGGCTGTCGTGGAACTCACTTTGTAGACCAGGCTGTCCTGGAACTCA GAAATCCACCTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGCGTACGCCACCACCGCCAGGCT TCATGACATTTTT Trans-nat-dsRNA 205bp 88.8% Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT

2/2 Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Bri3bp (NM_029752) mRNA/3’UTR Chr5/+ strand Our Data TTAAAAACTTCAACCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCTGGAGGCAGAGGCA GGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTAC ACAGAGAAACCCTGTCTCGAAAATCAAAAAAACAAAAAACAAAAAAAAATAAAACAAAACAAAA CAAA Ctcfl (ENSMUST00000094287, NM_001081387) mRNA/3’UTR Chr2/- strand OUR DATA TTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTTCT CTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATC CGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGTGCCACCACACCCGGCTGATATTT CTGA Trans-nat-dsRNA 196bp 91.8% Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

1/1 Endo-siRNA-T39 TCTTTACCCCGGCAGGCCGACAT Rpl24 (ENSMUST00000122365, ENSMUST00000023269, NM_024218) mRNA/5’UTR+First Exons Chr16/+ strand GEO/GDS605,401 AAGGTTCTCCCATGATTCTTTCTTTCTCTTCGCCATCTTTACCCCGGCAGGCCGACATCTATCA CCATGAAGGTCGAGCTGTGCAGTTTCAGCGGGTACAAGATCTACCCGGGACACGGGCGGCGCTA CGCCAGGACCGACGGGAAGGTTTTCCAGTTTCTTAATGCAAAATGTGAGTCAGCATTCCTTTCC AAAAGGAATCCTCGGCAGATAAACTGGACTGTCC Gadl1 (ENSMUST00000084841, ENSMUST00000119291) mRNA/Last Exons + 3’UTR Chr9/+ strand OUR DATA GGACAGTCCAGTTTATCTGCCGAGGATTCCTTTTGGAAAGGAATGCTGACTCACATTTTGCATT AAGAAACTGGAAAACCTTCCCGTCGGTCCTGGCGTAGCGCCGCCCGTGTCCCGGGTAGATCTTG TACCCGCTGAAACTGCACAGCTCGACCTTCATGGTGATAGATGTCGGCCTGCCGGGGTAAAGAT GGCGAAGAGAAAGAAAGAATCATGGGAGAACCTT Trans-nat-dsRNA 226bp 100.0%

1/2 Endo-siRNA-T40 TTTCTCTGTGTAGCCCTGGCTAT Stat1 (ENSMUST00000070968, ENSMUST00000087717, NM_009283) mRNA/3’UTR Chr1/+ strand GEO/GDS605,606,401,409 GTATCAGATAATTTTATTATTTTTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTATTCT GGAACTCACTCTGTAGATCAGGCTGGCCTGGAACTCAGAAATCCGCCTGTCTCTGCCTCCCGAG TGCTGGGATTAAAGGTGTGCACCACCA Crtc3 (ENSMUST00000122255, NM_173863) mRNA/3’UTR Chr7/- strand GEO/GDS409,410 TGGTGGCACCCGCCTTTAATCCCAGCACTTGGGAGACAGAGGCAGTATGATTTCTGAGTTTGAG GCCAGCCTGGTCTGCAGAGTGAGTTCCAGGATAGCCAGGGCTACACAGAGAAACCCTGTCTCGA AAAAACAAAACAAAACAAAACAAACAA Trans-nat-dsRNA 155bp 82.4% Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC

2/2 Endo-siRNA-T40 TTTCTCTGTGTAGCCCTGGCTAT Stat1 (ENSMUST00000070968, ENSMUST00000087717, NM_009283) mRNA/3’UTR Chr1/+ strand GEO/GDS605,606,401,409 TATTTTTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTATTCTGGAACTCACTCTGTAGA TCAGGCTGGCCTGGAACTCAGAAATCCGCCTGTCTCTGCCTCCCGAGTGCTGGGATTAAAGGTG TGCACCACCAATGCC Rab3d (ENSMUST00000122211, NM_031874) mRNA/3’UTR Chr9/- strand GEO/GDS401,409 GGCGTTGTGGTGGTGAAAATTTTTGATCCCAGCATTCTGGAGGCAGAGGCAGGTGGATCTCTGA GTTCGAGACCAGCCTGATCTACAGAGCAAGTTCCAGGATAGCCAGGGCTACACAGAGAAACCCT GTTTTGAAAAACAGAGA Trans-nat-dsRNA 145bp 84.1%

1/2 Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG Ctcfl (ENSMUST00000094287, NM_001081387) mRNA/3’UTR Chr2/- strand OUR DATA TTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTTCT CTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATC CGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGTGCCACCACACCCGGCTGATATTT CTGA Bri3bp (NM_029752) mRNA/3’UTR Chr5/+ strand Our Data TTAAAAACTTCAACCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCTGGAGGCAGAGGCA GGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTAC ACAGAGAAACCCTGTCTCGAAAATCAAAAAAACAAAAAACAAAAAAAAATAAAACAAAACAAAA CAAA Trans-nat-dsRNA 196bp 91.8% Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

2/2 Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG Mrpl35 (ENSMUST00000065103, NM_025430) mRNA/3’UTR Chr6/- strand GEO/GDS605,401 TTTTTGTTTTGTTTTGTTTTGTTTTGCTTTGTTTTGTTTTGTTTTGTTTTTCGAGACAGGGTTT CTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCTTCGAACTCAGAAA TCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCAGCTTAGG TTTGTTTTTTTTTTA Syt11 (ENSMUST00000107503, ENSMUST00000107505, ENSMUST00000090945, NM_018804) mRNA/3’UTR Chr3/- strand GEO/GDS606,607,409,410 TAAGAAAGCCACGTGGGCCGGGCGGTGGTGGCACACGCCTTTAATCCCAGCACTCGGGAGGCAG AGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGG GCTACACAGAGAAACCCTGTCTCAAAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAGAAGAA Trans-nat-dsRNA 201bp 87.0% Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

1/2 Endo-siRNA-T42 TAAAAGCAGCACCAGCTCTGGGC Cd209c (ENSMUST00000044060, NM_130903) mRNA/5’UTR Chr8/- strand OUR DATA AGAGAGTAGCCAATCGGATGTGAGACATGCAAATGAGGCTTAGTGCATAACCAATCAGGGTATG AGACACGCCTCTCCTAGGCCTATAAAAGCAGCACCAGCTCTGGGCAAAAAGTCTTTTCGCCTCT GCAATCAAGCTCTCCCAATAAACGTGTGCAGAAGGATCCTGTTGCAGCGTCGTTCTTCCTGGCC AGTCGAGCGCGCGCAAGAG Atp13a2 (NM_029097, NM_001164366) mRNA/3’UTR Chr4/+ strand GEO/GDS605,401 GTCTTGCGCGCGCTCGACTGGCCAGGAAGAACGATGCTGCAACAGGATCCTTCTGCACATGTTT ATTGGGAGAGCTTGATTGTAGAGGCGAAAAGACTTCGAGCCCAGAACTGGTACTGCTTTTATAG GCCTAGGAGGGGCGTGTCTCACACCCGGATTGGTTATGCACTAAGCCTCATTTGCATGTTCCTC ATCTGATTGGTTACTCTCT Trans-nat-dsRNA 211bp 91.9% Endo-siRNA-T43 TGGTTATGCACTAAGCCTCATTT

2/2 Endo-siRNA-T42 TAAAAGCAGCACCAGCTCTGGGC Cd209c (ENSMUST00000044060, NM_130903) mRNA/5’UTR Chr8/- strand OUR DATA ACATGCAAATGAGGCTTAGTGCATAACCAATCAGGGTATGAGACACGCCTCTCCTAGGCCTATA AAAGCAGCACCAGCTCTGGGCAAAAAGTCTTTTCGCCTCTGCAATCAAGCTCTCCCAATAAACG TGTGCAGAAGGATCCTGTTGCAGCGTCGTTCTTCCTGGCCAGTCGAGCGCGCGCAAGAGTCAAT CCC RP23-276E19.2 (ENSMUST00000118067) Pseudogene Chr13/+ strand OUR DATA GCCATTCTCTTGCGCGCACCGGACTCGACCAGCAAGAACGACGCTGCAACAGGATCCTTC TGCACACGTTTATTGGGAGAGCTTGATTGCAGAGGCGAAAAGACTTTTTGCCCAGAGCTG GTGCTGCTTTTATAGGCCTAGGAGAGGCGTGTCTCATACCCTGATTGGTTATGCACTAAG CCTCATTTGCATGT Trans-nat-dsRNA 195bp 94.9% Endo-siRNA-T43 TGGTTATGCACTAAGCCTCATTT

1/2 Endo-siRNA-T43 TGGTTATGCACTAAGCCTCATTT Atp13a2 (NM_029097, NM_001164366) mRNA/3’UTR Chr4/+ strand GEO/GDS605,401 GTCTTGCGCGCGCTCGACTGGCCAGGAAGAACGATGCTGCAACAGGATCCTTCTGCACATGTTT ATTGGGAGAGCTTGATTGTAGAGGCGAAAAGACTTCGAGCCCAGAACTGGTACTGCTTTTATAG GCCTAGGAGGGGCGTGTCTCACACCCGGATTGGTTATGCACTAAGCCTCATTTGCATGTTCCTC ATCTGATTGGTTACTCTCT Cd209c (ENSMUST00000044060, NM_130903) mRNA/5’UTR Chr8/- strand OUR DATA AGAGAGTAGCCAATCGGATGTGAGACATGCAAATGAGGCTTAGTGCATAACCAATCAGGGTATG AGACACGCCTCTCCTAGGCCTATAAAAGCAGCACCAGCTCTGGGCAAAAAGTCTTTTCGCCTCT GCAATCAAGCTCTCCCAATAAACGTGTGCAGAAGGATCCTGTTGCAGCGTCGTTCTTCCTGGCC AGTCGAGCGCGCGCAAGAG Trans-nat-dsRNA 211bp 91.9% Endo-siRNA-T42 TAAAAGCAGCACCAGCTCTGGGC

2/2 Endo-siRNA-T43 TGGTTATGCACTAAGCCTCATTT RP23-276E19.2 (ENSMUST00000118067) Pseudogene Chr13/+ strand OUR DATA GCCATTCTCTTGCGCGCACCGGACTCGACCAGCAAGAACGACGCTGCAACAGGATCCTTC TGCACACGTTTATTGGGAGAGCTTGATTGCAGAGGCGAAAAGACTTTTTGCCCAGAGCTG GTGCTGCTTTTATAGGCCTAGGAGAGGCGTGTCTCATACCCTGATTGGTTATGCACTAAG CCTCATTTGCATGT Cd209c (ENSMUST00000044060, NM_130903) mRNA/5’UTR Chr8/- strand OUR DATA ACATGCAAATGAGGCTTAGTGCATAACCAATCAGGGTATGAGACACGCCTCTCCTAGGCCTATA AAAGCAGCACCAGCTCTGGGCAAAAAGTCTTTTCGCCTCTGCAATCAAGCTCTCCCAATAAACG TGTGCAGAAGGATCCTGTTGCAGCGTCGTTCTTCCTGGCCAGTCGAGCGCGCGCAAGAGTCAAT CCC Trans-nat-dsRNA 195bp 94.9% Endo-siRNA-T42 TAAAAGCAGCACCAGCTCTGGGC

1/2 Endo-siRNA-T45 CACTTCTGTGTTTGCTAGGCCCC Zfp488 (ENSMUST00000052871, NM_001013777) mRNA/3’UTR Chr14/- strand OUR DATA TATTTTTATATTTTTCCATTTTTTATTAGGTATTTAGCTCATTTACATTTCCAATGTTAT ACCAAAAGTCCCCCACAGCCACCCACCCCCACTCCCCTACCCACCCACTCCCCCTTTTTG GCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTT CCAGTGATGGCCGACTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGG GGTACTGGTTAGTTCATTATGTTGTTCCACCTATAGGGTTGCAGATCCCTTTAGCTCCTT GGCTACTTTCTCTAGCTCCTCCATTGGGAGCCCTGTGATTCATCCATTAGCTGACTGTGA GCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGTCTCACAAGAGACAGCTACATCTGG GTCCTTTCAATAAAATCTTGCTAGTGTATGCAATGGTCTCAGCGTTTGGAAGCTGATTAT GGGGTGGATCCCTGGATATGGCAGTCTCTACATGGTCCATCCTTTCATCTCAGCTCCAAA CTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTCCCAATTCTAAGGAGGGGCATAGT GTCCACACTTCAGTCTTCATTCTTCTTGAGTTTCATGTGTTTAGCAAATTGTATCTTATA TCTTGGGTATCCTAGGTTTGGGGCTAATATCCACTTATCAGTGAGTACATATTGTGTGAG TTCCTTTGTGATTGTGTTACCTCACTCAGGATGATGCCCTCCAGGTCCATCCATTTGGCT AGGAATTTCATAAATTCATTCTTTTTAATAGCTGAGTAGTACTCCATTGTGTAGATGTAC CACATTTTCTGTATCCATTCCTCTGTTGAGGGGCATCTGGGTTCTTTCCAGCTTCTGGCT ATTATAAATAAGGCTGCTATGAACATAGTGGAGCATGTGTC Hsd3b2 (ENSMUST00000107022) mRNA/3’UTR Chr3/- strand OUR DATA GACACATGCTCCACTATGTTCATAGCAGCCTTATTTATAATAGCCAGAAGCTGGAAAGAA CCCAGATGTCCCTCAACAGAGGAATGGATAAAAAAATGTGGTACATTTACATAATGGAGT ACTACTCAGCTATTAAAAAGAATGAATTTATGAAATTCCTAGCCAAATGAATGGACCTGG AGGGCATCATCCTGAGTGAGGTAACACATTCACAAAGGAACTCACACAATATGTACTCAC TGATAAGTGGATATTAGCCCAAAACCTAGGATACCCAAGATATAAGATACAATTTGCTAA ACACATGAAACTCAAGAAGAATGAAAACTGAAGTGTGGACACTATGCCCCTCCTTAGAAT TGGGAACAAAACACCCATGGAAGGAGTTACAGAGACAAAGTTTGGAGCTGAGACAAAAGG ATGGACCATCTAGAGACTGCCATATCCAGGGATCCACCCCATAATCAGCTTCCAAACGCT GACACCATTGCATACACTAGCAAGATTTTATCGAAAGAACCCAGATGTAGCTGTCTCTTG TGAGACTATGCCGGGGCCTAGCAAACACAGAAGTGGATGCTCACAGTCAGCTATTGGATG GATCACAGGGCCCCCAATGGAGGAGCTAGAGAAAGTACCCAAGGAGCTAAAGGGATCTGC AACCATATAGGTGGAACAACATTATGAACTAACCAGTACCCCGGAGCTCTTGACTCTAGC TGCATATGTATCAAAAGATGGCCTAGCCGGCCATCACTGGAAAGAGATGCCCATTGGACA TGCAAACTGTATATGCCCCAGTACAGGGGAATGCCAGGGCCAAAAAAAATGGGAATGGGT GGGTAGGGAAGTGAGGGGAGGGTATGGGGGACTTTTGGGATAGCATTGGAAATGTAATTG AGGAAAATATGTAATAAAAAATATTTTTAAAAAAA Trans-nat-dsRNA 941bp 94.3% Endo-siRNA-T27 AGAGAAAGTACCCAAGGAGCT

2/2 Endo-siRNA-T45 CACTTCTGTGTTTGCTAGGCCCC RP23-174L3.1 (ENSMUST00000121552) Pseudogene ChrX/+ strand OUR DATA CCCCACCCACCCACTCCCACTTCTTGGCCCTGGCGTTCACCTGTACTGAGGC AAATAAAGTCTGCACGACCAATGGGCCTCTCTTTCCACTGATGGCCACCTAGGCCATCTT CTGATACATATGCAGCTAGAGACACGAGATCCGGAGGGTACTGGTTAGTTCACATTTTTT TTCCACCTATAGGGTTGCAGATCTCTTTAGCTCCTTGGATACTTTCTCTAGCTCCTCCAT TGGGGGCCCTGTGATCCATCCAATAGCTGACTGTGAGCATTCACTTCTGTGTTTGCTAGG CCCCAGCCTAGTCTCACAAGAGACAGCTATATCTGGGTCCTTTCAGCAAAATCTTGCTAG TGTATGCAATGGTGTCAGCGTTTGGAGGCTGATTATGGGATGGATCCCCGGATATGACAG TCTCTAGATGGTCCATCCTTTCGTCTCAGCTCCAAACTGTGTCTCTGTAACTCCTTCCAT GGGTGTTTTGTTCCCAATTCTAAGAAGGGGCAAAGTGTTCACACTTTGGTCTTCGTTCTT TTTGAGTTTCATGAGTTTCACAAATTGTATCTTATATCTTGGGTATTCTAAGTTTCTGGG CTAATATCCACTTATCAGTGAGTACATATCATTTGAGTGCTTGAGGAT Hsd3b2 (ENSMUST00000107022) mRNA/3’UTR Chr3/- strand OUR DATA ATTCACAAAGGAACTCACACAATATGTACTCACTGATAAGTGGATATTAGCCCAAAACCTAGGATACCCA AGATATAAGATACAATTTGCTAAACACATGAAACTCAAGAAGAATGAAAACTGAAGTGTGGACACTATGC CCCTCCTTAGAATTGGGAACAAAACACCCATGGAAGGAGTTACAGAGACAAAGTTTGGAGCTGAGACAAA AGGATGGACCATCTAGAGACTGCCATATCCAGGGATCCACCCCATAATCAGCTTCCAAACGCTGACACCA TTGCATACACTAGCAAGATTTTATCGAAAGAACCCAGATGTAGCTGTCTCTTGTGAGACTATGCCGGGGC CTAGCAAACACAGAAGTGGATGCTCACAGTCAGCTATTGGATGGATCACAGGGCCCCCAATGGAGGAGCT AGAGAAAGTACCCAAGGAGCTAAAGGGATCTGCAACCATATAGGTGGAACAACATTATGAACTAACCAGT ACCCCGGAGCTCTTGACTCTAGCTGCATATGTATCAAAAGATGGCCTAGCCGGCCATCACTGGAAAGAGA TGCCCATTGGACATGCAAACTGTATATGCCCCAGTACAGGGGAATGCCAGGGCCAAAAAAAATGGGAATG GGTGGGTAGGG Trans-nat-dsRNA 641bp 89.6% Endo-siRNA-T27 AGAGAAAGTACCCAAGGAGCT

1/2 Endo-siRNA-T48 ATGAGCCACCATGTGGTTG Esr2 (ENSMUST00000110421, ENSMUST00000110418, ENSMUST00000110419, ENSMUST00000110420, ENSMUST00000076634, ENSMUST00000101291, NM_010157, NM_207707) mRNA/3’UTR Chr12/-strand OUR DATA TTTTTTCCCAAGACTTATTTATTTCATGTATATGAGTGCATTGTCGCTGTCTTCAGACACACCAGAAGAG GGCATCAGATCCCATTATAGATGGTTATGAGCCACCATGTGGTTGCTGGGAGTTGATCTCAAGATCTCCG GAAGAGCAGAGGTCTTAACTGCTGAGACATCTCTCCAGC 1600002H07Rik (NM_028056, ENSMUST00000024930) mRNA/3’UTR Chr17/- strand GEO/GDS606,409 GCTGGAGAGATGGCTTGACGGTTAAGAGTACTGACTGCTCTTCCAGGGGTCCTGAGTACA ATTCTCAGCAACCACATGGTGGCTCATAACCATCTTTAATGGGATCTGATGCCCTCTTCT GGTGTGTCTGAAGACAGCTACAGTATATTTATATACATAAAATAAATAAACCTTTTTTAA AAA Trans-nat-dsRNA 183bp 82.5%

2/2 Endo-siRNA-T48 ATGAGCCACCATGTGGTTG Rtkn2 (ENSMUST00000118160) mRNA/3’UTR Chr10/+ strand OUR DATA AGTACACCATAGCTGTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATTACAGATGGTCAT GAGCCACCATGTGGTTGTTGGGAACTGAACTCAGCACCTCTGGAAGAGCAAGTC Slc17a5 (ENSMUST00000117645, ENSMUST00000052441) mRNA/3’UTR Chr9/- strand OUR DATA GATTGCTCTTGGAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCATAACCATCTG TAATGGGATCAGATGCCCTCTTCTGGTGTGTCTGAAGACAGAGACAGTGTACT Trans-nat-dsRNA 118bp 89.8%

1/2 Endo-siRNA-T49 CCAGCCTGGTCTACAGAGC Ccdc36 (ENSMUST00000076592, NM_001135198) mRNA/3’UTR Chr9/- strand OUR DATA CCTGGTGCTGGTGATGCACACCTTTAATCCCAGCACTGGGGAGGCAGAGGCAGGCAGATCTCTGAGTTTG AGGCCAGCCTGGTCTACAGAGCGAATTCCAGGACAGCCAGAGCTACACAGAGAAATCTTGTCCTGAAAAG CCAAAAACAACAACAATAACAACAACAACTCAAAACAAACAAAGAACA Zfp345 (ENSMUST00000109914, NM_001034900) mRNA/3’UTR Chr2/- strand OUR DATA TTTTTTTTGTTTGTTTGTTTGTTTTTTTTTGTTTTTTTTTTTGAGACAGGGTTTCTCTGT GTAGTCCTGGCTGTCCTGGAACTCGCTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATC CGCCTGCCTCTGCCTGCCAAGTGCTAGAATTAAAGGCGTGTGCCACCACGCCCGG Trans-nat-dsRNA 188bp 80.5%

2/2 Endo-siRNA-T49 CCAGCCTGGTCTACAGAGC Ccdc36 (ENSMUST00000076592, NM_001135198) mRNA/3’UTR Chr9/- strand OUR DATA TGGTGATGCACACCTTTAATCCCAGCACTGGGGAGGCAGAGGCAGGCAGATCTCTGAGTTTGAGGCCAGC CTGGTCTACAGAGCGAATTCCAGGACAGCCAGAGCTACACAGAGAAATCTTGTCCTGAAAAGCCAAAAAC AACAA Mxra7 (ENSMUST00000021170, NM_026280) mRNA/3’UTR Chr11/- strand OUR DATA TTTTTGTTTTTCTTTTTCCAGACAGGGTTTCTCTGTGTAGCCCCGGCTGTCCTGGAGCTC GCTCTGTAGACCAGGCTGGTCTGGAACTCAGAGATCCACCTGCCTCTGCCTCCGAGTGCT GGGATTAAAGCCTTGCGCCACCA Trans-nat-dsRNA 145bp 83.7%

1/2 Endo-siRNA-T50 TCTGTAGGCTTCTTGTATG Zfp353 (NM_153096) mRNA/5’UTR Chr8/- strand OUR DATA TAATCTAATAGGCCTGCCTTTATATGTTACTTGACCTTTTTACCTTACTGCTTTTAATATTCTG TCTTTATTTAGTGCATTTTTGGTTCTGATTATTATGTGTTGGGAGGAATTTCTTTTCTGGTCCA GTCTATTTGGAGTTCTGTAGGCTTCTTGTATGTTCATGGGCATATCTTTCTTTAGGTTAGGGAA GTTTTCTTCTATAATTTTGCTGAAGATATTTGCTGGCCCTTTAAGTTGAAAATCTTCATTCTCA TGTACTCCTATTATCTGTAGGTTTAGTCTTCTCAGTGGGTCTTGGATTTCCTGAATGTTTTGAG TTAGGATCTTTTTGCATTTTGCATTTTCTTCAATTGTTATGTCCATGCTCTCTATAGAATCTTC TGCATCTGATATTCTCTCTTCCATCTCTTGTATTCTGTTGCTGATGCTCAGATCTATGATTCCT GATTTCTTTCCTAGGATTTCTATATCCAGAGTTGTCTCCCTTTGCGTTTTCTTTATTGTTCCTA CTTCCATTTTTAGATCTTGGATGTTTTTGTGCAATTCTGTCACGTGTTTGGTAATGTTTTCCTG TAATTCTTTAAGGGATTTTTTTGTGTTTCTTCT L1B_MM L1 Non-LTR Retrotransposon OUR DATA AAAGAGGAAACACAAAAATCCCTTAAAGAATTACAGGAAAACACAACCAAACAGGTGAAGGAAT TGAACAAAACCATCCAAGATCTAAAAATGGAAGTAGAAACAATAAAGAAATCACAAAGGGAGAC AACTCTGGAGATAGAAAACCTAGGAAAGAAATCAGGAGCCATAGATGCGAGCATCACCAACAGA ATACAAGAGATGGAAGAGAGAATCTCAGGTGCAGAAGATWCCATAGAAAACATTGACACAACAA TCAAAGAAAATGCAAAATGCAAAAAGATCCTAACCCAAAACATCCAGGAAATCCAGGACACAAT GAGAAGACCAAACCTAAGGATAATAGGTATAGAAGAGAATGAAGATTTTCAACTTAAAGGGCCA GTAAATATCTTCAACAAAATTATAGAAGAAAACTTCCCTAACCTAAAGAAAGAGATGCCCATGA ACATACAAGAAGCCTACAGAACTCCAAATAGACTGGACCAGAAAAGAAATTCCTCCCGACACAT AATAATCAAAACACCAAATGCACTAAACAAAGAAAGAATATTAAAAGCAGTAAGGGAAAAAGGT CAAGTAACATATAAAGGCAGACCTATCAGAATT Trans-nat-dsRNA 609bp 90.5%

2/2 Endo-siRNA-T50 TCTGTAGGCTTCTTGTATG Zfp353 (NM_153096) mRNA/5’UTR Chr8/- strand OUR DATA GTGTGATGTAATCTAATAGGCCTGCCTTTATATGTTACTTGACCTTTTTACCTTACTGCT TTTAATATTCTGTCTTTATTTAGTGCATTTTTGGTTCTGATTATTATGTGTTGGGAGGAA TTTCTTTTCTGGTCCAGTCTATTTGGAGTTCTGTAGGCTTCTTGTATGTTCATGGGCATA TCTTTCTTTAGGTTAGGGAAGTTTTCTTCTATAATTTTGCTGAAGATATTTGCTGGCCCT TTAAGTTGAAAATCTTCATTCTCATGTACTCCTATTATCTGTAGGTTTAGTCTTCTCAGT GGGTCTTGGATTTCCTGAATGTTTTGAGTTAGGATCTTTTTGCATTTTGCATTTTCTTCA ATTGTTATGTCCATGCTCTCTATAGAATCTTCTGCATCTGATATTCTCTCTTCCATCTCT TGTATTCTGTTGCTGATGCTCAGATCTATGATTCCTGATTTCTTTCCTAGGATTTCTATA TCCAGAGTTGTCTCCCTTTGCGTTTTCTTTATTGTTCCTACTTCCATTTTTAGATCTTGG ATGTTTTTGTGCAATTCTGTCACGTGTTTGGTAATGTTTTCCTGTAATTCTTTAAGGGATT A630089N07Rik (NR_015491) Non-coding RNA OUR DATA AAGTCCTTAAAGAAAAACAGGAAAACACAACCAAACAGGTGATGGAAATGAACAAAATCA TACTAGACCTAAAAAGGGAAGTAGAAACAATAAAGAAAACCCAAAGTGAGGCAACGCTGG AGATAGAAACCCTAGGAAAGAAATCTGGAACCATAGATGCGAGCATCAGCAACAAATTAC AAGAAATGGAAGGGAGAATCTCGGGTGCAGAAGATTCCATAGAGAACATGGGCACAACAA TCAAAGAAAATGCAAAATGCAAAAAGATCCTAACTCAAAATATCCAGGACACAATGACAA GACCAAACCTATGGATAATAGGAGTAGAAGAGAATGAAGATTTTCACTTTAAAGGGCCAG CAAATATCTTCAACAAAATTATAGAAGAAAACTTCCCAAACCTAAAGAAAGAGAGAGATG CCCATGAACATACAAGAAGCCTACAGAACTCCAAATAGACTGAACCAGAAAAGAAATTCC TCCCGACACATAATAATCAGAACAACAAATGCACTAAATAAAGATAGAATATTAAAAGCA GTAAGGGAAAAAGGTCAAGTAACATGAAGGCAGGCCTATCAGAATTACACCAGAC Trans-nat-dsRNA 601bp 86.6%

1/2 Endo-siRNA-T52 TACACTTCCATACTGCTGTTCAT 3110048L19Rik (NR_003549) Non-coding RNA Chr17/- strand GEO/GDS605,401 TGTCTTAGTCAGGGTTTCTATTCCTGCACAAACATCATGACCAAGAAGCAGGTTGGGGAGGAAA GGGTTTATTCACCTTACACTTCCATACTGCTGTTCATCACCAAGGAAGTCAGGACTAGAACTCA AGCAGGTCAGGAAGCAAGAGCTGATTCAGAAGCCATGGAGGGATGTTCTTTACTGGCTTGCTTC CCCTGGCTTGCTCAGCCTGCTCTCTTATAGAACCCAAGACTGCCAGCCCAGAGATGTTCCCACC CACAAGGGGCCTTTCCCCCTTGATCACTAATTGAGAAAATAACCCACAACTAGATCTCATGGAG GCACTTCGCCAACCAAATCTCCTTTCTCTCTGATAACTCCAGCCTGTGTCAAGTTGATACATAA AATCAGCCAGTA RP23-413M3.2 (ENSMUST00000117166) Pseudogene Chr2/- strand OUR DATA TACTGGCTAGTTTTGTGTCAACTTGACACAGCTGGAGTTATCACAGAGAAAGGAGCTTCA GTTGAGGAAATGCCTCCATGAGATCCAACTGTAAGGCATTTTCTCAATTAGTGATCAAGG GGGAAAGGCCCCTTGTGGGTGGGACCATCTCTGGGCTGGTAGTCTTGGGTTCTATAAGAG AGCAGGCTGAGCAAGGCAGGGGAAGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGC ATCAGCTCCTGCTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTGGTGATGAACAG CAGTATGGAAGTGTAAGCTGAATAAACCCTTTCCTCCCCAACTTGCTTCTTGGTCATGAT GTTTGTGCAGGAATAGAAACCCTGACTAAGACA Trans-nat-dsRNA 396bp 92.7% Endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT Endo-siRNA-T24 TATCACAGAGAAAGGAGCTTC

2/2 Endo-siRNA-T52 TACACTTCCATACTGCTGTTCAT Hmmr (ENSMUST00000109302, ENSMUST00000020579, ENSMUST00000109303, NM_013552) mRNA/3’UTR Chr11/- strand OUR DATA CTCTGTCTTAGTCAGGGTTTCTGTTCCTGCATAAACATCAGACCAAGAAACAAGCTGGGGAGGA AAGGGTTTATTCAGCTTACACTTCCATACTGCTGTTCATCACCAAAGGAAGTCAGGACTGGAAC TCAAGCAGGTCAGGAAGTAGGAGCTGATGCAGAGGCCATGGAGGGACATTCCTTACTGGCTTGC TTCCCCTGGCTTGCTCAGCTTGCTTTCTTACAGAACCCAAGTCTACCAGCCTAGAGACAGCACC AACCACAAGGGGCCCTCCCAC Ccdc82 (NM_025534, ENSMUST00000110583) mRNA/3’UTR Chr9/+ strand GEO/GDS606,409 GTGGGAAAGCCCCTTGTGGGTGGGACCATCTCTGGGCTGGTAGTCTTGGGTTCTATAAGAGAGC AGGCTGAGCAAGCCAGGTGAGGCAAGCCAGTAAAGAACATCCCTCCATGGCCTTTGTATCAGCT CCTGTTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTTGGTGATGAACAGCAGTATGGAA GTGTAAGCCGAATAAACCCTTTCCTCCCCAACTGCTTCTTGGTCATGATGTTTGTGCAGGAATA GAAACCCTGACTAAGACAAAT Trans-nat-dsRNA 277bp 89.2% Endo-siRNA-T11 TCTCTGGGCTGGTAGTCTT

1/2 Endo-siRNA-T55 AAATGAGGAAAATACCTAAT Zfp937 (NM_001142411) mRNA/3’UTR Chr2/+ strand OUR DATA AGTGGATGCTCACAGTCAGCTATTGGATGGATCACAGGGCCCCCAATGGAGGAGCTAGAGAAAG TATCCAAGGAGCTAAAGAGATCGGCAACCCTGTAGGTGCAACAACATTATGAACTAACCAGTAC CCCGGAGCTCTTGACTCTAGCTGCATATGTATCAAAAGATGTCCTAGTAGGCCATCACTGGAAA GAGAGGCCCATTGGACTTGCAAACTTTATATGCCCCAGTACAGGGGAACGCCAGGGCCAAAAAG GCAGAGTGGGTGGGTAGGGGAGTGTGGGGGTGGGTATGGGGGACTTTTGGGATAGCATTGGAAA TGTAAATGAGGAAAATACCTAATAAAAAAAGTAAA Tyms (ENSMUST00000026846, NM_021288) mRNA/3’UTR Chr5/- strand GEO/GDS605,401 TTTTTTTTTAATTAGGTATTTTCCTCATTTACATTTCCAATGCTATACCAAAAGTCCCCCATAC CCTCCCCTCCACTCCCCTACCCACCCACTCCCACTTCTTGGCCCTGGCATTCCCTTGTACTGGG GCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTTCCAGTGATGGCCGACTAGGCCATCTTTT GATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATAATGTTGTTCCACCT ATAGGGTTGCAGATCCCTTTAGCTCCTTGGGTACTTTCTCTAGCTCCTCCATTGGGGGCCCTGT GATCCATCCAATAGCTGACAGTGAGCATCCACT Trans-nat-dsRNA 355bp 94.1%

2/2 Endo-siRNA-T55 AAATGAGGAAAATACCTAAT Zfp937 (NM_001142411) mRNA/3’UTR Chr2/+ strand OUR DATA GAGCTCTTGACTCTAGCTGCATATGTATCAAAAGATGTCCTAGTAGGCCATCACTGGAAAGAGA GGCCCATTGGACTTGCAAACTTTATATGCCCCAGTACAGGGGAACGCCAGGGCCAAAAAGGCAG AGTGGGTGGGTAGGGGAGTGTGGGGGTGGGTATGGGGGACTTTTGGGATAGCATTGGAAATGTA AATGAGGAAAATACCTAATAAAAAAAGTAAAATTATATTTAAAAAT Tyms-ps (NR_000040) Pseudogene Chr10/+ strand GEO/GDS605,401 ATGCTGTGAATATCGACGTTTTTTTTTAAATTAGGTATTTTCCTCATTTACATTTCCAATACTA TCCCAAAAGTCCGCTATACCCTCCCACCCACTCCCCTACCCACCCACTCCCACTTATTGGCCCT GGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTTCCAGTGATG GCCGACTAGGCTATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTC Trans-nat-dsRNA 240bp 89.3%

1/2 Endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT Ripply3 (ENSMUST00000023660, NM_133229) mRNA/3’UTR Chr16/+ strand GEO/GDS410 TCCCATTTTAAGAGTTCATTTGCAGGGCTGGAGAGATGGCTCAGCAGTTAAGAGCACTGACTGC TCTTCCAGAGGTCCTGAGTTCAATTCTCAGCAACCACATGGTGGCTCCCAACCATCCGTAATGA GATCTGATGCCCTCTTCTGGTGTATCTGAAGACAGCTACAGTGTGCTTATATAAATAACATAAA TAAAT Gm10389 (ENSMUST00000100773) mRNA/3’UTR Chr15/+ strand OUR DATA ATTTACTTATTTTATATATGTGAGTACACTGTAGCTATCTTCAGATACACCAGAAGAGGGCATC GGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTG GAAGAGCAGTCAGTGCTCTTAACTCTTGAGCCATCTCTCCAGCCCTATAAATGAAATTTTTAAA GGA Trans-nat-dsRNA 197bp 89.3% Endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT

2/2 Endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT Ifnar1 (NM_010508, ENSMUST00000023689, ENSMUST00000117748) mRNA/3’UTR Chr16/+ strand GEO/GDS607,401,410 AAAAAGAAACACCACGGGCTGGAGAGATGGCTCAGTGGTTAAGAACACTGACCACTCTTCCAGA GGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATAGGATCTGATG CCCCCTTCTGGTGTGTCTGAAGATAGCTACAGTGTATTCATATATAAAATAATAAATACATCCT TTTTTTTCT 0610040B10Rik (ENSMUST00000087782) mRNA/3’UTR Chr5/+ strand GEO/GDS606 AAAAAAAAAAAGATTTGTTTTATTTATTTTATGTGAGTCCAATGTCGCTGTCTCCAGACACACC AGAAGAGGGCATCAAATCCCATTACAGATGGTTGTGAGCCACCATATGGTTGGGGGGATTTGAA CTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCTAGCTA TTTTCTTTTT Trans-nat-dsRNA 202bp 84.9% Endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT

1/2 Endo-siRNA-T58 GCCCTGGCTGTCTTGGAAC Zfp799 (ENSMUST00000079404, NM_177359) mRNA/3’UTR Chr17/- strand GEO/GDS606,409 TTTTTGGTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCTTGGAACTCACTCTGTAG ACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAATGCTGGGAATAAAGGC GTGCGCCACCATGCCCGGCTTTTTGTTTGTTTTAAGAATGCCTTAGAAAATGC Kif5b (NM_008448) mRNA/3’UTR Chr18/- strand GEO/GDS605,606 GTATATTTTAAGGATCTATAAAAGTGACAGGAAGACCGGGTGTGGTGGCGCACACCTTTAATCC CAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGA GTTCCAAGACAGCCAGGGCTACACAGAGAAACCTTGTCTCGAAAAACCAAAAA Trans-nat-dsRNA 181bp 89.1% Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

2/2 Endo-siRNA-T58 GCCCTGGCTGTCTTGGAAC Ube2v2 (NM_023585, NM_001159351) mRNA/3’UTR Chr16/- strand GEO/GDS605,401 TCTCTTTTTTTCTTTTTTTCTTTTTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCTTGGAA CTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCT GCGATTAAAGGCGTGCGCCACCACGTCTGGCTTTTATCTCATATTTTTAATCCATT Kif5b (NM_008448) mRNA/3’UTR Chr18/- strand GEO/GDS605,606 AAGGATCTATAAAAGTGACAGGAAGACCGGGTGTGGTGGCGCACACCTTTAATCCCAGCACTTG GGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAAGA CAGCCAGGGCTACACAGAGAAACCTTGTCTCGAAAAACCAAAAAAAAAAAAAAAAA Trans-nat-dsRNA 184bp 86.6% Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

1/2 Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT Tmed5 (ENSMUST00000002837, ENSMUST00000119437, NM_028876) mRNA/3’UTR Chr5/- strand OUR DATA GCCGGGCAGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCT GAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACC CTGTCTTGAAAAAACAAAAATAAAAATAAAAATAAACAAAAAAAAAAAAAAAAAGAAGAAAGAA AAGAAAAAAAGAAGAA Zbtb8a (ENSMUST00000030610, NM_028603) mRNA/3’UTR Chr4/- strand GEO/GDS606,409 TTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTGTTTTGTTTTGTTTTGTTTTGTTT TGTTTTTTCAAGACAGGGTTTCTCTGTATGGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCA GGCTGGCCTCAAATTCAGAAATCCACCTGCCTCTGCCTCCCAAGTCCTGGGATTAAAGGCGTGT GCCACCACCTCATGGC Trans-nat-dsRNA 208bp 89.6% Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG

2/2 Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT Mobkl3 (NM_025283, ENSMUST00000162364) mRNA/3’UTR Chr1/+ strand GEO/GDS606,409 AAGAATTTAAGTGCAGCCGGGCGGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGA GGCAGGTGGATTTCTGAGTTGGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGG CTACACAGAGAAACCCTGTCTCAGAAAACCAAAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAA AAAAAAAAAA Git2 (ENSMUST00000102579, ENSMUST00000112185, ENSMUST00000043283, ENSMUST00000112183) mRNA/3’UTR Chr5/- strand GEO/GDS606,409 TTATTTCTTGACATTTTTCTTTTCTTTTCTTTTCTTTTTTTTTTTTTTGGTTTTTCGAGACAAG GTTTCTCTGTGTAGCCCTGGCTGTCGTGGAACTCACTTTGTAGACCAGGCTGTCCTGGAACTCA GAAATCCACCTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGCGTACGCCACCACCGCCAGGCT TCATGACATTTTT Trans-nat-dsRNA 205bp 88.8% Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG

1/2 Endo-siRNA-T63 TCTCTCCTAGTTTGGGCCTT Slc38a6 (ENSMUST00000058139) mRNA/3’UTR Chr12/+ strand Our Data TCTCCCCCTTTTTCTTTTAATAAGAGCAAATAGGCCACCCATATTAATGAGAGTGGAGAT AGAGGTCAAATCCCCAGTGTGTAGGTAAAGGAGCCATGTACAGGATTAGCTCTTAGGCTT ACAGGCTTTTACCCAGAGCAACCCTGACCTGCTCCCGTGTCGTTTTGCCTGGGGGAAGGG AACTAGGACACTGAACCTTCATGAAAGATGACATGTCTCCCTAGAATAGGCTCATATATG CCGCAGAGCCTTTCCATTGCAGTGCTTAGCCTTGCAACTCTCTCGGGCTGCTGAAGCACA CTCACTCTATCCCGTGCAATGAGTCTAGCCTCATGGGATATAAGAGCTGAGTGGCCAGCG ACCTATTGCCTAAGCATAGATATATCAGGGGAAGCTCCATGTTCTAGTCCTGCAAGCGCC TGGGCAATAACCACCTTGTCTCTCCTAGTTTGGGCCTTAAGCTTACAGACCAATCAAAGA AGCAACACTAATCCACAGCAAAGTGTATCTCCAAATAATATTAATCCCACCCATTTTTTA AAGAAAGAAAATGCTGAGGAGATCCAATTGGGTAATCCTTTGGTCAGCGACAGGTCCAAG CGCGTGGAGTTGACCTGAAGTCTCAATTCCCGAAGGATCTGTTCAAATTCAGCCATCCAA TTCTGTAACATATACTGAAAAAGACTTTTTGACAAATTAGCTGTCCTAGTAAATTTAACA TACTGAATGGAAATAACACACAATCCCGGAAACTTTTGTTCACATCCCTGCTGAGTTATT TGTCATAATACATCTAGTTGTATCTGGACAAGATCTATGAGTTGATTAACCAGCATGAGA CCTCCCTGTATCTTGACATTAGCTGAGGCCTGTTCATCTATGACTGTAGTCACTGAGGCT GACAAAGTGTTAATGGTGTCAGTCGTCTGGACCTGTCCAGACAGAGCCAAGGCTGTCTGA ATTAAGGCCAAACCCAGTTCCTAGTTAGTGGTAAAAAAGCAGGAGAATACTTGAGCATTA TACATCACCGTCATTGGGAGTGGAAATGTCGACATTATCCCCCAACGCTGCTCTCTCTTT ATTATTGACGCCCTGGACATCACCAAGACGAGGGACATTAGTATTCCCTTGGTCAGTCTG GATTTTTCGGGTG IAPEZI Endogenous Retrovirus Our Data CACCCGAAAAATCCAGACTGACCAAGGGAATACTAATGTCCCTCGTCTTGGTGATGTCCA GGGCGTCAATAATAAAGAGAGAGCAGCGTTGGGGGATAATGTCGACATTTCCACTCCCAA TGACGGTGATGTATAATGCTCAAGTATTCTCCTGCTTTTTTACCACTAACTAGGAACTGG GTTTGGCCTTAATTCAGACAGCCTTGGCTCTGTCTGGACAGGTCCAGATGACTGACACCA TTAACACTTTGTCAGCCTCAGTGACTACAGTCATAGATAAACAGGCCTCAACTAATGTCT AGATACAGAGAGGTCTCATGCTGGTTAATCAACTCATAGATCTTGTCCAGATACAACTAG ATGTATTATGACAAATAACTCAGCAGGGTTGTGAACAAAAGTTTCCGGGATTGTGTGTTA TTTCCATTCAGTATGTTAAATTTACTAGGGCAGCTAATTTGTCAAAAAGTCTTTTTCAGT ATATGTTACAGAATTGGATGGCTGAATTTGAACAGATCCCTTCGGGAATTGAGACTTCAG GTCAACTCCACGCGCTTGGACCTGTCCCTGACCAAAGGATTACCCAATTGGATCTCCTCA GCATTTTCTTTCTTTAAAAAATGGGTGGGATTAATATTATTTGGAGATACACTTTGCTGT GGATTAGTGTTGCTTCTTTGATTGGTCTGTAAGCTTAAGGCCTAAACTAGGAGAGACAAG GTGGTTATTGCCCAGGCGCTTGCAGGACTAGAACATGGAGCTTCCCCTGATATATCTATG TTTAGGCAATAGGTCGCTGGCCACTCAGCTCTTACATCTCACGAGGCTAGACTCATTGCA CGGGATGGAGTGAGTGTGCTTCAGCAGCCCGAGAGAGTTGCAAGGCTAAGCACTGCAATG GAAAGGCTCTGCGGCATATATGAGCCTATTCTAGGGAGACATGTCATCTTTCATGAAGGT TCAGTGTCCTAGTTCCCTTCCCCCAGGCAAAACGACACGGGAGCAGGTCAGGGTTGCTCT GGGTAAAAGCCTGTAAGCCTAAGAGCTAATCCTGTACATGGCTCCTTTACCTACACACTG GGGATTTGACCTCTATCTCCACTCTCATTAATATGGGTGGCCTATTTGCTCTTATTAAAA GGATAGGGGGAGA Trans-nat-dsRNA 1153bp 98.4% Endo-siRNA-T10 TCTCCTGCTTTTTTACCAC

2/2 Endo-siRNA-T63 TCTCTCCTAGTTTGGGCCTT Slc38a6 (ENSMUST00000058139) mRNA/3’UTR Chr12/+ strand OUR DATA TCTCCCCCTTTTTCTTTTAATAAGAGCAAATAGGCCACCCATATTAATGAGAGTGGAGAT AGAGGTCAAATCCCCAGTGTGTAGGTAAAGGAGCCATGTACAGGATTAGCTCTTAGGCTT ACAGGCTTTTACCCAGAGCAACCCTGACCTGCTCCCGTGTCGTTTTGCCTGGGGGAAGGG AACTAGGACACTGAACCTTCATGAAAGATGACATGTCTCCCTAGAATAGGCTCATATATG CCGCAGAGCCTTTCCATTGCAGTGCTTAGCCTTGCAACTCTCTCGGGCTGCTGAAGCACA CTCACTCTATCCCGTGCAATGAGTCTAGCCTCATGGGATATAAGAGCTGAGTGGCCAGCG ACCTATTGCCTAAGCATAGATATATCAGGGGAAGCTCCATGTTCTAGTCCTGCAAGCGCC TGGGCAATAACCACCTTGTCTCTCCTAGTTTGGGCCTTAAGCTTACAGACCAATCAAAGA AGCAACACTAATCCACAGCAAAGTGTATCTCCAAATAATATTAATCCCACCCATTTTTTA AAGAAAGAAAATGCTGAGGAGATCCAATTGGGTAATCCTTTGGTCAGCGACAGGTCCAAG CGCGTGGAGTTGACCTGAAGTCTCAATTCCCGAAGGATCTGTTCAAATTCAGCCATCCAA TTCTGTAACATATACTGAAAAAGACTTTTTGACAAATTAGCTGTCCTAGTAAATTTAACA TACTGAATGGAAATAACACACAATCCCGGAAACTTTTGTTCACATCCCTGCTGAGTTATT TGTCATAATACATCTAGTTGTATCTGGACAAGATCTATGAGTTGATTAACCAGCATGAGA CCTCCCTGTATCTTGACATTAGCTGAGGCCTGTTCATCTATGACTGTAGTCACTGAGGCT GACAAAGTGTTAATGGTGTCAGTCGTCTGGACCTGTCCAGACAGAGCCAAGGCTGTCTGA ATTAAGGCCAAACCCAGTTCCTAGTTAGTGGTAAAAAAGCAGGAGAATACTTGAGCATTA TACATCACCGTCATTGGGAGTGGAAATGTCGACATTATCCCCCAACGCTGCTCTCTCTTT ATTATTGACGCCCTGGACATCACCAAGACGAGGGACATTAGTATTCCCTTGGTCAGTCTG GATTTTTCGGGTG IAPLTR1a_I_MM Endogenous Retrovirus OUR DATA CACCCGAAAAATCCAGACTGACCAAGGGAATACTGATGTCCCTCGTCTTGGTGATGTCCA GGGCGTCAATAATAAAGAGAGAGCAGCGTTGGGGGATAATGTCGACATTTCCACTCCCAA TGACGGTGATGTATAATGCTCAAGTATTCTCCTGCTTTTTTACCACTAACTAGGAACTGG GTTTGGCCTTGATTCAGACAGCCTTGGCTCTGTCTGGACAGGTCCAGACGACTGACACCA TTAACACTTTGTCAGCCTCAGTGACTACAGTCATAGATAAACAGGCCTCAGCTAATGTCA AGATACAGGGAGGTCTCATGCTGGTTAATCAACTCATAGATCTTGTCCAGATACAACTAG ATGTATTATGGCAAATAGCTCAGCTGGGATGTGAACAAAAGTTTCCGGGATTGTGTGTTA CTTCCATTCAGTATGTTAAATTTACTAGGGCAGCTAATTTGTCAAAAAGTCTTTTTCAGT ATATGTTACAGAATTGGACGGCTGAATTTGAACAGATCCTTCGGGAATTGAGACTTCAGG TCAACTCCACGCGCTTGGACCTGTCCCTGACCAAAGGATTACCCAATTGGATCTCCTCAG CATTTTCCTTCTTTAAAGAATGGGTGGGATTGATATTATTTGGAGATACACTTTGCTGTG GATTAGTGTTGCTTCTTTGATTGGTCTGTAAGCTTAAGGCCCAAACTAGGAGAGACAAGG TGGTTATTGCCCAGGCGCTTGCAGGACTAGAACATGGAGCTTCCCCTGATAATATCTATG CTTAGGCAATAGGTCGCTGGCCACTCAGCTCTTATATCCCATGAGGCTAGTCTCATTGCA CGGGATAGAGTGAGTGTGCTTCAGCAGCCCGAGAGAGTTGCACGGCTAAGCACTGCAGTA GAAGGGCTCTGCGGCATAATATGAGCCTATTCTAGGGAGACATGTCATCTTTCAAGAAGG TTGAGTGTCCAAGTGTCCTTCTCTCCAGGCAAAACGACACGGGAGCAGGTCAGGGTTGCT CTGGGTAAAAGCCTGTGAGCCTAAGAGCTAATCCTGTACATGGCTCCTTTACCTACACAC TGGGGATTTGACCTCTATCTCCACTCTCATTAATATGGGTGGCCTATTTGCTCTTATTAA AAGGAAAGGGGGAGA Trans-nat-dsRNA 1154bp 97.3% Endo-siRNA-T10 TCTCCTGCTTTTTTACCAC

1/2 Endo-siRNA-T65 AAATAAATAAATAAATCTTT Unc13d (ENSMUST00000106449) mRNA/3’UTR Chr11/- strand OUR DATA AGGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCTGAAGGTCCGAAGTT CAAATCCCAGCAACCACATGGTGGCTCACAACCACCCGTAATGAGATCTGATGCCCTCTTCTGG TGCGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATAAATCTTT Ppp1r16b (NM_153089, NM_001159662, ENSMUST00000052927, ENSMUST00000045503) mRNA/3’UTR Chr2/+ strand GEO/GDS606,409 AAAGATTTATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAG AGGGAGTCAGATCTCATTATGGGTGGTTGTAAGCCACCATGTGGTTGCTGGGATTTGAACTTCG AACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCACT Trans-nat-dsRNA 185bp 95.1%

2/2 Endo-siRNA-T65 AAATAAATAAATAAATCTTT Ehbp1l1 (NM_053252, NM_001114596, NM_001114597, NM_001114595) mRNA/3’UTR Chr19/- strand GEO/GDS607,410 GTAGGGGTGGAGAGATGGCTCAGCAGTTAAGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTC AATTCTCAGCAGTCACATGGTGGCTCACAACCATCTGTAATGGGATCCGATGCCCTATTCTGGT GTGTCTGAAGACAGCTACAGTGTACTTACATACATAAAATAAATAAATAAATCTTTAAA Padi2 (ENSMUST00000030765, NM_008812) mRNA/3’UTR Chr4/+ strand OUR DATA ATTAAAGATTTATTTATTTATTTTATGTATATGAGTACACTGCAGCTGTCTTCAGACACACCAG AAGAGGGCGTCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACT TAGGACCTCTGGGCGAGCAGTCAATGCTCTTAACCACTGAGCCATCTCTCCAGCCCCAG Trans-nat-dsRNA 187bp 89.8% Endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT Endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT

1/2 Endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT Ripply3 (ENSMUST00000023660, NM_133229) mRNA/3’UTR Chr16/+ strand GEO/GDS410 TCCCATTTTAAGAGTTCATTTGCAGGGCTGGAGAGATGGCTCAGCAGTTAAGAGCACTGACTGC TCTTCCAGAGGTCCTGAGTTCAATTCTCAGCAACCACATGGTGGCTCCCAACCATCCGTAATGA GATCTGATGCCCTCTTCTGGTGTATCTGAAGACAGCTACAGTGTGCTTATATAAATAACATAAA TAAAT Gm10389 (ENSMUST00000100773) mRNA/3’UTR Chr15/+ strand OUR DATA ATTTACTTATTTTATATATGTGAGTACACTGTAGCTATCTTCAGATACACCAGAAGAGGGCATC GGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTG GAAGAGCAGTCAGTGCTCTTAACTCTTGAGCCATCTCTCCAGCCCTATAAATGAAATTTTTAAA GGA Trans-nat-dsRNA 197bp 89.3% Endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT

2/2 Endo-siRNA-T66 CTCTTCCAGAGGTCCTGAGT Ifnar1 (NM_010508, ENSMUST00000023689, ENSMUST00000117748) mRNA/3’UTR Chr16/+ strand GEO/GDS607,401,410 AAAAAGAAACACCACGGGCTGGAGAGATGGCTCAGTGGTTAAGAACACTGACCACTCTTCCAGA GGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATAGGATCTGATG CCCCCTTCTGGTGTGTCTGAAGATAGCTACAGTGTATTCATATATAAAATAATAAATACATCCT TTTTTTTCT 0610040B10Rik (ENSMUST00000087782) mRNA/3’UTR Chr5/+ strand GEO/GDS606 AAAAAAAAAAAGATTTGTTTTATTTATTTTATGTGAGTCCAATGTCGCTGTCTCCAGACACACC AGAAGAGGGCATCAAATCCCATTACAGATGGTTGTGAGCCACCATATGGTTGGGGGGATTTGAA CTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCTAGCTA TTTTCTTTTT Trans-nat-dsRNA 202bp 84.9% Endo-siRNA-T57 TTCCAGAGGTCCTGAGTTCAATT

1/2 Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Mobkl3 (NM_025283, ENSMUST00000162364) mRNA/3’UTR Chr1/+ strand GEO/GDS606,409 AAGAATTTAAGTGCAGCCGGGCGGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGA GGCAGGTGGATTTCTGAGTTGGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGG CTACACAGAGAAACCCTGTCTCAGAAAACCAAAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAA AAAAAAAAAA Git2 (ENSMUST00000102579, ENSMUST00000112185, ENSMUST00000043283, ENSMUST00000112183) mRNA/3’UTR Chr5/- strand GEO/GDS606,409 TTATTTCTTGACATTTTTCTTTTCTTTTCTTTTCTTTTTTTTTTTTTTGGTTTTTCGAGACAAG GTTTCTCTGTGTAGCCCTGGCTGTCGTGGAACTCACTTTGTAGACCAGGCTGTCCTGGAACTCA GAAATCCACCTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGCGTACGCCACCACCGCCAGGCT TCATGACATTTTT Trans-nat-dsRNA 205bp 88.8% Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT

2/2 Endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC Bri3bp (NM_029752) mRNA/3’UTR Chr5/+ strand Our Data TTAAAAACTTCAACCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCTGGAGGCAGAGGCA GGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTAC ACAGAGAAACCCTGTCTCGAAAATCAAAAAAACAAAAAACAAAAAAAAATAAAACAAAACAAAA CAAA Ctcfl (ENSMUST00000094287, NM_001081387) mRNA/3’UTR Chr2/- strand OUR DATA TTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTTCT CTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATC CGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGTGCCACCACACCCGGCTGATATTT CTGA Trans-nat-dsRNA 196bp 91.8% Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC Endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG

1/2 Endo-siRNA-T70 TTAGTCAGGGTTCTCTAGAGTC Prkcq (ENSMUST00000114853) mRNA/3’UTR Chr2/+ strand GEO/GDS605,401 TGTATTAGTCAGGGTTCTCTAGAGTCACAGAACTTATGGACAGTCTCTAGATAGTAAAGGAATT TATTGATGACTTACAGTCGGCAGCCCAATTCCCAACAATTGTTCAGTCGCAGCTGTGAATGGAA GTCCAAGGATCTAGCAGTTACTCAGTCTCACGCAGCAAGCAGGCAAAGGAGCAAGAGCAAGAGC TAGACTCCCTTCTTCCAATGTCCTTATATTGTCTCCAGCAGAAGGTGT MERVL_LTR LTR Retrotransposon OUR DATA ACACCTTCTGCTGGAGACAATATAAGGACATTGGAAGAAGGGAGTCTAGCTCTTGCTCTTGTTC CTTCACCTGCTTGCTGCGTGAGACTGAGTAATTGCTAGATCTTTGGACTTCCATTCACAGCTGC GACTGAATCATTGTTGGGAATTGGGCTGCCAACTGTAAGTCATCAATAAATTCCTTTACTATCT AGAGACTATTCATAAGTTCTGTGACTCTAGAGAACCCTGACTAATACA Trans-nat-dsRNA 240bp 95.8%

2/2 Endo-siRNA-T70 TTAGTCAGGGTTCTCTAGAGTC Prkcq (ENSMUST00000114853) mRNA/3’UTR Chr2/+ strand GEO/GDS605,401 TGTATTAGTCAGGGTTCTCTAGAGTCACAGAACTTATGGACAGTCTCTAGATAGTAAAGGAATT TATTGATGACTTACAGTCGGCAGCCCAATTCCCAACAATTGTTCAGTCGCAGCTGTGAATGGAA GTCCAAGGATCTAGCAGTTACTCAGTCTCACGCAGCAAGCAGGCAAAGGAGCAAGAGCAAGAGC TAGACTCCCTTCTTCCAATGTCCTTATATTGTCTCCAGCAG Dcdc2c (ENSMUST00000020963) mRNA/3’UTR Chr12/- strand OUR DATA CTGCTGGAGACAATATAAGGACATTGGAAAAAGGGAGTCTAGCTCTTGCTCTTGCTCCTTCGCC TGCTTGCCGTGTGAGACTGAGTAACTGCTAGATCCTTGGACTTCCATTCACAGCTGCGACTGAA CAATTGTAAGGAATTGGGCTGCCGACTGTAAGTCATCAATAAATTCCTTTACTATCTAGAGACT ATCCATAAGTTCTGTGACTCTAGAGAACCCTGACTAATACA Trans-nat-dsRNA 233bp 97.0%

1/2 Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGG Tmod1 (ENSMUST00000107773, NM_021883) mRNA/3’UTR Chr4/+ strand 46127618-46128904 Our Data TTTGGAAGCGTGGTGAAACAATCTTTTATTTCCAATTTGATCGTAGCAACTCAGTAAAAAGAACACATAA TCATGATCTGTCAACCCCCACTTGAAACTTTGACATCAAGATTAAAGCTGCCAAATTGATTCCAGGATCA AACCCCCACCCCTAAGAATGAAAGACAAGCCACAGAATTTTCTAAGAGTCAGAAAGACACAGGATTCCTT TTGCCAGGTAAGATAAAGAGGGAGAAAAAGGCAATGGTGAATTTTCAAGTTTCAAAACCCACCACACCAG GCAACAGACATCCTTCTGAGTGCTGTGGGAACACCTGCGGGGTACTCATCTGCAGTCAGAAATCATTTCT TCTTTATTGAATTCCAACTTCATGATGGATGAAAACTTACAGCCGCTGGGCAGTGGTGGCACACGCCTTT AATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAG TTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAAAGGAAAAA AAAAGAAAACTTACAGCCACATAAAAACATCTTCCTATACCACAGTGGGCAATGGCTTATGTGAGATCAA CACCATTGGGTGAATTTCCAGTCCACCATGCCTGTGGTATTTAGCATGGCCCTGCTTACAGACACCAAGT GCCTGCCTGGTCATTTATGAGACAAATCAAATCACACAGAGCTCTTGCCTACAAACAAAGCCTCTAGAGG ACAGCAGAGTACAGCATCTTAATGGTAAGGAATTAGGAGATCCTGGCCAAACAACACACGGGATTACTCT GAAACCTAATCTTGGTGTTCCTACTGGATTTCCTTTTTTAACACCATGGGAGCCAGTAAAAATGTTCAAA TACACTGTTCTTGTGCCTTTTAATAGACCACAGTGCCAGTTAAACTAGTATTTTTGTTGTTTTGGGGAGT TATTTTCCTTAGGGATTCAGCCAATATTATAGTAATGATAAGGCTCAAAAGCTGTTGAGCATAGCCAGGG GGCTTCTGACTTAAGAGAAAGCCTGCACACCGAACTGTAACAGTATGGACAGTACAGGGTAACTAGAGGT GGCATCGGGGCCTCAGCACTGAGTGTCCACTGAGGCTGCACACGGGCCCAGGAGTGGCACCAAGCTGCAG GGACAGCCAGCCCCACTCAGCTTCTCCTTGAAACACAACTGCAGCTGCATTCTGCATCACTGGAAACTGC AAAATAATATTAAAGCCATTTGGTCTA Tstd2 (ENSMUST00000107772, NM_173033) mRNA/3’UTR Chr4/- strand 46127618-46128904 Our Data TAGACCAAATGGCTTTAATATTATTTTGCAGTTTCCAGTGATGCAGAATGCAGCTGCAGTTGTGTTTCAA GGAGAAGCTGAGTGGGGCTGGCTGTCCCTGCAGCTTGGTGCCACTCCTGGGCCCGTGTGCAGCCTCAGTG GACACTCAGTGCTGAGGCCCCGATGCCACCTCTAGTTACCCTGTACTGTCCATACTGTTACAGTTCGGTG TGCAGGCTTTCTCTTAAGTCAGAAGCCCCCTGGCTATGCTCAACAGCTTTTGAGCCTTATCATTACTATA ATATTGGCTGAATCCCTAAGGAAAATAACTCCCCAAAACAACAAAAATACTAGTTTAACTGGCACTGTGG TCTATTAAAAGGCACAAGAACAGTGTATTTGAACATTTTTACTGGCTCCCATGGTGTTAAAAAAGGAAAT CCAGTAGGAACACCAAGATTAGGTTTCAGAGTAATCCCGTGTGTTGTTTGGCCAGGATCTCCTAATTCCT TACCATTAAGATGCTGTACTCTGCTGTCCTCTAGAGGCTTTGTTTGTAGGCAAGAGCTCTGTGTGATTTG ATTTGTCTCATAAATGACCAGGCAGGCACTTGGTGTCTGTAAGCAGGGCCATGCTAAATACCACAGGCAT GGTGGACTGGAAATTCACCCAATGGTGTTGATCTCACATAAGCCATTGCCCACTGTGGTATAGGAAGATG TTTTTATGTGGCTGTAAGTTTTCTTTTTTTTTCCTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGGTTT CTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCC TGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCAGCGGCTGTAAGTTTTCATC CATCATGAAGTTGGAATTCAATAAAGAAGAAATGATTTCTGACTGCAGATGAGTACCCCGCAGGTGTTCC CACAGCACTCAGAAGGATGTCTGTTGCCTGGTGTGGTGGGTTTTGAAACTTGAAAATTCACCATTGCCTT TTTCTCCCTCTTTATCTTACCTGGCAAAAGGAATCCTGTGTCTTTCTGACTCTTAGAAAATTCTGTGGCT TGTCTTTCATTCTTAGGGGTGGGGGTTTGATCCTGGAATCAATTTGGCAGCTTTAATCTTGATGTCAAAG TTTCAAGTGGGGGTTGACAGATCATGATTATGTGTTCTTTTTACTGAGTTGCTACGATCAAATTGGAAAT AAAAGATTGTTTCACCACGCTTCCAAA Cis-nat-dsRNA 1287bp 100.0% Endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG

2/2 Endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT Tmed5 (ENSMUST00000002837, ENSMUST00000119437, NM_028876) mRNA/3’UTR Chr5/- strand OUR DATA GCCGGGCAGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCT GAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACC CTGTCTTGAAAAAACAAAAATAAAAATAAAAATAAACAAAAAAAAAAAAAAAAAGAAGAAAGAA AAGAAAAAAAGAAGAA Zbtb8a (ENSMUST00000030610, NM_028603) mRNA/3’UTR Chr4/- strand GEO/GDS606,409 TTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTGTTTTGTTTTGTTTTGTTTTGTTT TGTTTTTTCAAGACAGGGTTTCTCTGTATGGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCA GGCTGGCCTCAAATTCAGAAATCCACCTGCCTCTGCCTCCCAAGTCCTGGGATTAAAGGCGTGT GCCACCACCTCATGGC Trans-nat-dsRNA 208bp 89.6% Endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG Endo-siRNA-T19 TCACTTTGTAGACCAGGCTG Endo-siRNA-T59 GGCAGAGGCAGGTGGATTT

SI Dataset 1B-Predicted intramolecular dsRNAs

Hairpin-dsRNA (hp-dsRNA)

Format:

Transcript ID (Accession Number), Type/dsRNA Source Region, Expression Profile During Developing Testis (GEO/GDS or Our Data)

Sequences of two strands of dsRNA

Type of dsRNA (hp-dsRNA), dsRNA length, Percentage of Complementary Match of Two Strands endo-siRNAs in this dsRNA (ID, sequence)

Zfp933 (ENSMUST00000105718, NM_198619) mRNA/3’UTR Our Data GTGGTGGCGCACACCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGGGGATTTCTGAGTTCAA GGCCAGCCTGGTCTACAAAGTGAATGCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTG AAAAACCAAAAAAACAAACAAAC - GTTTGTTTGTTTGATTGATTTTCGAGACAGGGTTTCTCTGTGCAGCTCTGGCTGTCCTGAAACT CACTCTGTAGACCAGGCTGGCCTCGAACTTAGAGATCCACCTGCCTCTGCCTCCCGAGTGCTGG GATTAAAAGCGTGCGCCACCAT hp-dsRNA 151bp 88.1% endo-siRNA-T18 CACAGAGAAACCCTGTCTTG endo-siRNA-T22 TCTGAGTTCAAGGCCAGCCT endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC

Psmb11 (NM_175204) mRNA/3’UTR Our Data ctttaatcccagcactcagtaggcagcagcaggcggatttctgagttggaggccagcctggtct acagagtgagttccaggacagccagggctacacagagaaaccctgtcttgaaaaaccaaaccaa accaaac - gttttgttttgttttgtttttcgagacagggtttctctgtatagccctggctgtcctggaactc actttgtagaccaggttggcctcgatctcagaaattcacctgcctctgcctcccgagtgctggg attaaag hp-dsRNA 135bp 88.9% endo-siRNA-T18 CACAGAGAAACCCTGTCTTG endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC

Zfp459 (ENSMUST00000056470, NM_177811) mRNA/3’UTR Our Data TTTTGAGGCAGGTTTTTTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTG GCCTCAAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAAGCGTGTGCCAC CACGCCCGGCCCCTATGTGAGTTC - GAAAGTCACCAGAAGCTGGGTGGTGGTGGTGCACACCTTTAATCCCAGCACTTGGGAGGCAGAG GCAGGTGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACGGCCGGGGC TATACAGAGAAACCCTGTCTCAAAA hp-dsRNA 153bp 86.4% endo-siRNA-T19 TCACTTTGTAGACCAGGCTG endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG endo-siRNA-T59 GGCAGAGGCAGGTGGATTT endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

Car5b (ENSMUST00000033739, NM_181315) mRNA/3’UTR Our Data TTCTTTCTTTCTTTCTTTCTTTTTTTTTTTTGAGACAGGGTTTCTCTGTGTAGTCTTGGCTAGC CTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCACCTGTCTCTGCCTCCCA AGTGCTGGGATTAAAGGCGTGCGCCACCACGCTCAGCAGATTTACTT - GAGGAATCTGCCAGGCAGTGGTGGCGCACGGCTTTAATCCCAGCACTTGGGAGGCAGAGACAGG TGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACAC AGAGAAACCCTATCTCGGGGAAAAAGAAAAAAAAAAGGCAGAGGAA hp-dsRNA 175bp 86.4% endo-siRNA-T19 TCACTTTGTAGACCAGGCTG endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

Casc5 (ENSMUST00000028802) mRNA/3’UTR Our Data GCCAGGTGGTGGTGGTACACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCT GAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGATCAGCCCAGGCTATACAGAGAAACC CTGTCTTGAAAAACAAAAACAAAACAAACAAAAAT - GTTTTTATTTGTTTTGGTTTTTGGTTTTTCGAGACAGGATGTCTCTGTGTAGCCCTGGCTGTCC TGGAACTCACTTTGTAGACCAGGCTGGCCTTAAACTGAGAAATCTACCTGCCTCTGCCTTCCAA GTGCTGGGATTAAAGGCATGCGCCACCACTGCCTAGC hp-dsRNA 165bp 84.2% endo-siRNA-T19 TCACTTTGTAGACCAGGCTG endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

Iws1 (NM_173441) mRNA/3’UTR GEO/GDS409,606 gcctggtgtggtgacacacacctttaatctcagcatttgggagggagaagaaggctgacctctg agttcatgaccagcctggcctacagagtgagttccaggacagccagggctacacagagaaaccc tgtcttttaaaaagagagagaga - tttgtttttgtttttttgagacagggtttctctctatagccctggctgtcctggaactcacttt gtagaccaggctggcctcgaactcagaaatccgcctgcctctggctcctgagtgctgggattaa aggtgtgcaccaccacgcccggt hp-dsRNA 151bp 78.8% endo-siRNA-T19 TCACTTTGTAGACCAGGCTG endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC

AC158558.2 (ENSMUST00000016274) mRNA/3’UTR Our Data TTTCTGTATTGCTCTGGATGTCCTGGAACTTGCTCTATAGACCAGGCTGGCCTAGAACCTAGAG ATCCACCTACTACTGTCTACTGAGCACTGGGATCAAAGGTGTGCATCACCTCTGCCCAGCAGCT ATGGG - TCTTTTTTGCTGGGCGTGGTGAAGCACGCCTTTAATCCCAGCACTCAGGAGGCAGAGGCAGGCA GATTTCTGAGTTCAAGGCCAGCCTGATCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAG AGA hp-dsRNA 133bp 74.4% endo-siRNA-T22 TCTGAGTTCAAGGCCAGCCT endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC

A830018L16Rik (ENSMUST00000135014, NM_001160371) mRNA/3’UTR Our Data TTTTTTTTTCAGAACAGATTTTCTCTGTGTAGTCCTAGATGTCCTGGAACTCACTCTGTTGACC AGGCTGACCTTGAGCTCAGAGATCCACCTGCCTCTACTTCCTAAGTGTTGGGATTAAAGGTGTG GACCACC - GGTGGAACACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCAGATTTCTGAGTTCGAGG CCAGCCTGGTCTACAAAATGAGCTCCAGGACAGCCAGGACTACAAAGAGAAACCCTGTCTCGAA AAACAAA hp-dsRNA 135bp 80.7% endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

Zfp874b (NM_001076791) mRNA/3’UTR Our Data ttttttttttttttttggttttttcaagacagggtttctctttatagccctgactgtcctggaa ctcactttgtataccaggctggcctcgaactcaaaaatccgcctgcctctgcctcccgagtgct gggattaaaggcgtgcgccaccacacccggctctttcctgttttgatac gtgttaagagaaagcatggagtcaggcatggtggcgcacacctttagtcccagtacttgggagg cagaggcaggtgaatttctgagttcgaggccagcctggtctacagaatgagttccaggacagcc aaggctacacagagaaatcctgtctcgaaaaaccaaaaaaaaaaaaaaaa hp-dsRNA 178bp 83.2% endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

A630055G03Rik (NM_001162932) mRNA/3’UTR Our Data tttgttttttgttgtttttcgagacagggtttctctgtatagccctggctgtcctggaattcac tttttagaccaggctggcctcgaactcagaaatccgcctgcctctgcctccccagtgctgggat taaaggcgtgcgccaccacacccggccctagtaacattttttg taaaaaataaagagagccaggtggtggtagcgcacgcctttaatcccagggaggcagaagcagg cggatttctgagttcgaggccagcctggtctacaaagtgagttccaggacagccagggctacac agagaaaccctgtctcgaaaaacaaataaataaa hp-dsRNA 171bp 86.0% endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

9030025P20Rik (ENSMUST00000081476) mRNA/3’UTR Our Data CGAGACAGGGTTTCTCAGTATAGCTGTGGGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGG CCTCGAACTCAGAAATCCGCCTGCTTCTGCCTCCCAAGTGGTGGGATTAAAGGCGTGCGCCACC ACGCCTGGCTCTGAGACTACTTCTTA - TAAGATTAAGTGTTGGGCCGGGTGGTGGTGGCCCATGCCTTTAATCCCAGCACTTGGGAGGCAG AGGAAGGAGGATTTCTGAGTTTGAGGCCAGCCTGGTCTACAAAGTGAGTGCCAGGACAGCCAGG GCTACACAGAGAAACCCTGTCTTG hp-dsRNA 154bp 81.8% endo-siRNA-T18 CACAGAGAAACCCTGTCTTG endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC

Slfn5 (NM_183201) mRNA/3’UTR Our Data tttgtcatttgctttaggtctctgtatagccctggctgtcctggaactcactctgtagaccagg ctggcctcgaactcagaaatccacctgcctctgcctcccgagtgctgggattaaaggcatgtgc caccac gtgatggcacacacctttaaccccagaactcagaaggcagaggcaggtggatctctgagttgga ggccagcctggtttacagagtgagttctaggacatctaaggttatacagaaaacccctgtctca aaaagcaaa hp-dsRNA 137bp 81.0% endo-siRNA-T32 TCACTCTGTAGACCAGGCTGGC

D730040F13Rik (ENSMUST00000068792, ENSMUST00000107609) mRNA/3’UTR GEO/GDS401,605 GGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCCAGAGTTC AGATCCCAGCAACCACATGGTGGCTCACAACCATCCGCAACAAGATCTGACTCCCTCTTCTGGA GTGTCTGAGGACAGCTACAGTGTACTTACATATATTAATAAAATAAATCTTTAAAAAAAAAAAA AAAAAAAAGA

TCTTTTTTCTTGCTTTTTTTTTTAAAGATTTATTTATTACTATATGTAAGTACACGGTAGCTGT CTTCAGACACACCAGAAGAGAGCATCTGATCCCATTACAGATGGTTGTGAACCACCATGTGGTT GCTGGGATTTGAACTCAGGACCTTCAGAAGAGCAGTCATTTCTCTTACCCACTGAGCCATCTCT CCAGCCCCC hp-dsRNA 202bp 87.2% endo-siRNA-T4 GCTCTTCCGAAGGTCCAGAGT

Gen1 (ENSMUST00000052581) mRNA/3’UTR Our Data GGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTTGAACT CAGAAATCTGCCTGGCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCACCACCACGCCCGGC - GCCAGGCGTGGCAACACACACCTTTAATCCTAGCATTTGGAAGGCAAAGGCAAGTGGATCTCTG AATTCAAGGCTGGCCTGGTAGATAGAGCTAATTCCAGGACAGCCAGGGCTACACATAATTCCC hp-dsRNA 128bp 75.0% endo-siRNA-T19 TCACTTTGTAGACCAGGCTG endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC

Bri3bp (NM_029752) mRNA/3’UTR Our Data Cagaggcaggcggatttctgagttcgaggccagcctggtctacagagtgagttccaggacagcc agggctacacagagaaaccctgtctcgaaaatcaaaaaaacaaaaaacaaaaaaaaataaaaca aaacaa - ttgtttgtttgtttgtttgtttgtttgtttttctttttgaggcagggtctctctacatagccct ggctgtcctgcaactctctgtgtaaaccaggctgccctctaacttgcagagatccacctgcctc tg hp-dsRNA 134bp 78.7% endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T37 TCCAGGACAGCCAGGGCTACAC endo-siRNA-T69 CTACACAGAGAAACCCTGTCTC endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT

Zfp353 (NM_153096) mRNA/ 5’UTR + 3’UTR Our Data Tctaataggcctgcctttatatgttacttgacctttttaccttactgcttttaatattctgtct ttatttagtgcatttttggttctgattattatgtgttgggaggaatttcttttctggtccagtc tatttggagttctgtaggcttcttgtatgttcatgggcatatctttctttaggttagggaagtt ttcttctataattttgctgaagatatttgctggccctttaagttgaaaatcttcattctcatgt actcctattatctgtaggtttagtcttctcagtgggtcttggatttcctgaatgttttgagtta ggatctttttgcattttgcattttcttcaattgttatgtccatgctctctatagaatcttctgc atctgatattctctcttccatctcttgtattctgttgctgatgctcagatctatgattcctgat ttctttcctaggatttctatatccagagttgtctccctttgcgttttctttattgttcctactt ccatttttagatcttggatgtttttgtgcaattctgtcacgtgtttggtaatgttttcctgt - gcaggaaaacacagccaaacaggtaatggaaatgaacaaaaccatactagaactaaaaagggaa gtagacacagtaaagaaaacccaaagcgaggcaacgctggagatagaaaccctaggaaagagat ctggaaccatagatgcgagcatcagcaacagaatacaagaaatggaagagagaatctcaggtgc agaagattccatagagaacatcgacacaacagtcaaaaaaaatacaaaatgcaaaaggatccta actcaaaacatccaggaaatccaggacacaatgagaagaccaaacctacagataataggaattg atgagaatgaagattttcaacttaaagggccagctaatatcttcaacaaaataatagaagaaaa cttcccaaacataaagaaagagatgcccatgatcatacaagaagcctacagaactccaaataga ctggaccagaaaagaaattcctcccgacacataataatcagaacaacaaatgcactaaataatg atagaatatttaaagcagtaagggagaaaggtcaagtaacatataaaggaaggcctatcaga hp-dsRNA 574bp 88.3% endo-siRNA-T50 TCTGTAGGCTTCTTGTATG

Dhrs7b (ENSMUST00000108718) mRNA/3’UTR GEO/GDS401,605 GGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAGCTCCCTCTGTAGACCAGCCTGGCCTCAAACTC AAGAGATCTGCCTGCCTCTGCCTCCAGAGTGTGGGGGATTAAAGGCGTGCGCCACCACCATCAA GC - GCTGGGTAGTGGTGGCACACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCAGATTTCT GAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACCCAGAGAAACC hp-dsRNA 130bp 87.7% endo-siRNA-T26 TCTGAGTTCGAGGCCAGCCTG endo-siRNA-T41 CTGTGTAGCCCTGGCTGTCCTGG endo-siRNA-T71 CTGAGTTCGAGGCCAGCCTGGT