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Mouse Parp16 Knockout Project (CRISPR/Cas9)

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Mouse Parp16 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Parp16 Knockout Project (CRISPR/Cas9) Objective: To create a Parp16 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Parp16 gene (NCBI Reference Sequence: NM_177460 ; Ensembl: ENSMUSG00000032392 ) is located on Mouse chromosome 9. 7 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 7 (Transcript: ENSMUST00000069000). Exon 3~5 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 3 starts from about 18.12% of the coding region. Exon 3~5 covers 53.52% of the coding region. The size of effective KO region: ~7788 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 3 4 5 7 Legends Exon of mouse Parp16 Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 3 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 5 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 9 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(22.6% 452) | C(22.4% 448) | T(30.6% 612) | G(24.4% 488) Note: The 2000 bp section upstream of Exon 3 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(29.0% 580) | C(22.6% 452) | T(22.75% 455) | G(25.65% 513) Note: The 2000 bp section downstream of Exon 5 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 4 of 9 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr9 + 65224054 65226053 2000 browser details YourSeq 158 964 1149 2000 93.1% chr12 + 31058981 31059169 189 browser details YourSeq 154 968 1149 2000 92.9% chr8 - 80690233 80690424 192 browser details YourSeq 154 962 1149 2000 91.4% chr8 - 36581995 36582186 192 browser details YourSeq 154 973 1149 2000 93.8% chr8 + 86700315 86700493 179 browser details YourSeq 152 723 1135 2000 80.9% chr7 - 5004915 5005177 263 browser details YourSeq 151 978 1149 2000 94.2% chr8 + 34515380 34515553 174 browser details YourSeq 151 892 1148 2000 91.8% chr10 + 78707915 78708349 435 browser details YourSeq 150 961 1149 2000 91.3% chr8 + 107352280 107352469 190 browser details YourSeq 149 967 1147 2000 91.7% chr2 - 30034262 30034442 181 browser details YourSeq 149 961 1135 2000 93.1% chr10 - 63473647 63473821 175 browser details YourSeq 149 499 1149 2000 79.9% chr15 + 73541357 73541953 597 browser details YourSeq 149 968 1469 2000 90.8% chr12 + 28917449 28918021 573 browser details YourSeq 148 977 1149 2000 93.1% chr1 + 45798709 45798883 175 browser details YourSeq 147 973 1149 2000 91.9% chr9 - 31162447 31162622 176 browser details YourSeq 147 976 1149 2000 92.6% chr5 + 140431728 140431903 176 browser details YourSeq 146 968 1150 2000 91.6% chr1 - 191344372 191344554 183 browser details YourSeq 144 973 1465 2000 81.9% chr5 - 116384267 116384438 172 browser details YourSeq 144 974 1150 2000 90.8% chr10 + 40373517 40373688 172 browser details YourSeq 143 968 1149 2000 89.6% chr2 - 167312018 167312201 184 Note: The 2000 bp section upstream of Exon 3 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr9 + 65233842 65235841 2000 browser details YourSeq 263 177 521 2000 92.9% chr11 + 103757078 103757504 427 browser details YourSeq 263 177 521 2000 95.3% chr1 + 80400192 80400809 618 browser details YourSeq 259 178 526 2000 92.8% chr12 - 111568111 111568452 342 browser details YourSeq 259 177 523 2000 90.0% chr13 + 73715387 73715706 320 browser details YourSeq 258 177 536 2000 92.1% chr14 + 47400741 47401085 345 browser details YourSeq 255 177 519 2000 95.8% chr4 - 152057305 152057657 353 browser details YourSeq 255 177 518 2000 94.8% chrX + 106172748 106173102 355 browser details YourSeq 252 177 526 2000 91.9% chr10 + 7668881 7669214 334 browser details YourSeq 250 177 523 2000 90.0% chr16 - 93915857 93916184 328 browser details YourSeq 248 195 537 2000 91.6% chr1 + 181191179 181191495 317 browser details YourSeq 242 177 525 2000 93.0% chr9 - 110414541 110415073 533 browser details YourSeq 239 183 532 2000 84.6% chr16 - 14322938 14323252 315 browser details YourSeq 237 177 507 2000 94.8% chr8 - 17270857 17271249 393 browser details YourSeq 224 178 518 2000 94.8% chr11 + 70516858 70517286 429 browser details YourSeq 212 295 538 2000 97.0% chr4 + 136011950 136012381 432 browser details YourSeq 209 241 520 2000 96.0% chr2 - 152424220 152424795 576 browser details YourSeq 208 319 547 2000 93.7% chr13 + 44929208 44929430 223 browser details YourSeq 207 177 520 2000 91.1% chr14 + 52093357 52093666 310 browser details YourSeq 206 303 538 2000 96.5% chr10 - 95535699 95536151 453 Note: The 2000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Parp16 poly (ADP-ribose) polymerase family, member 16 [ Mus musculus (house mouse) ] Gene ID: 214424, updated on 12-Aug-2019 Gene summary Official Symbol Parp16 provided by MGI Official Full Name poly (ADP-ribose) polymerase family, member 16 provided by MGI Primary source MGI:MGI:2446133 See related Ensembl:ENSMUSG00000032392 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as ARTD15; C79952; PARP-16; BC055447 Expression Ubiquitous expression in adrenal adult (RPKM 11.5), ovary adult (RPKM 5.0) and 28 other tissues See more Orthologs human all Genomic context Location: 9; 9 C See Parp16 in Genome Data Viewer Exon count: 7 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (65214652..65239220) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (65062497..65087026) Chromosome 9 - NC_000075.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 5 transcripts Gene: Parp16 ENSMUSG00000032392 Description poly (ADP-ribose) polymerase family, member 16 [Source:MGI Symbol;Acc:MGI:2446133] Location Chromosome 9: 65,195,353-65,239,224 forward strand. GRCm38:CM001002.2 About this gene This gene has 5 transcripts (splice variants), 200 orthologues, 2 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Parp16- ENSMUST00000213396.1 2518 322aa ENSMUSP00000150318.1 Protein coding CCDS23286 Q7TMM8 TSL:1 202 GENCODE basic APPRIS P1 Parp16- ENSMUST00000069000.8 2482 322aa ENSMUSP00000070098.7 Protein coding CCDS23286 Q7TMM8 TSL:1 201 GENCODE basic APPRIS P1 Parp16- ENSMUST00000216702.1 1643 322aa ENSMUSP00000149927.1 Protein coding CCDS23286 Q7TMM8 TSL:1 205 GENCODE basic APPRIS P1 Parp16- ENSMUST00000216486.1 1714 237aa ENSMUSP00000150997.1 Nonsense mediated - A0A1L1SV38 TSL:1 204 decay Parp16- ENSMUST00000213766.1 1445 No - Retained intron - - TSL:NA 203 protein Page 7 of 9 https://www.alphaknockout.com 63.87 kb Forward strand 65.19Mb 65.20Mb 65.21Mb 65.22Mb 65.23Mb 65.24Mb Genes (Comprehensive set... Igdcc3-201 >protein coding Parp16-205 >protein coding Igdcc3-203 >protein coding Parp16-201 >protein coding Parp16-204 >nonsense mediated decay Parp16-202 >protein coding Parp16-203 >retained intron Contigs AC110235.13 > Genes < Gm25313-201snRNA (Comprehensive set... < Rnu5g-201snRNA Regulatory Build 65.19Mb 65.20Mb 65.21Mb 65.22Mb 65.23Mb 65.24Mb Reverse strand 63.87 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript RNA gene Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000069000 24.53 kb Forward strand Parp16-201 >protein coding ENSMUSP00000070... Transmembrane heli... Low complexity (Seg) Superfamily SSF56399 Pfam PARP16 N-terminal domain Poly(ADP-ribose) polymerase, catalytic domain PROSITE profiles Poly(ADP-ribose) polymerase, catalytic domain PANTHER PTHR21328:SF2 PTHR21328 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 40 80 120 160 200 240 280 322 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 9 of 9.
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