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Mouse Traf3ip3 Knockout Project (CRISPR/Cas9)

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Mouse Traf3ip3 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Traf3ip3 Knockout Project (CRISPR/Cas9) Objective: To create a Traf3ip3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Traf3ip3 gene (NCBI Reference Sequence: NM_153137 ; Ensembl: ENSMUSG00000037318 ) is located on Mouse chromosome 1. 16 exons are identified, with the ATG start codon in exon 3 and the TGA stop codon in exon 16 (Transcript: ENSMUST00000043550). Exon 3~8 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: Mice homozygous for a knock-out allele exhibit impaired single positive thymocyte development and increased gamma-delta T cell numbers. Exon 3 starts from the coding region. Exon 3~8 covers 45.81% of the coding region. The size of effective KO region: ~3789 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 6 7 8 16 Legends Exon of mouse Traf3ip3 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. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 8 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. 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(27.7% 554) | C(23.05% 461) | T(24.0% 480) | G(25.25% 505) 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(30.05% 601) | C(19.75% 395) | T(28.6% 572) | G(21.6% 432) Note: The 2000 bp section downstream of Exon 8 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% chr1 - 193198020 193200019 2000 browser details YourSeq 36 143 219 2000 97.4% chr13 - 114314355 114314878 524 browser details YourSeq 34 192 230 2000 97.3% chr6 + 129279066 129279109 44 browser details YourSeq 31 196 229 2000 97.0% chr3 - 138162419 138162876 458 browser details YourSeq 31 195 237 2000 87.9% chr4 + 106021188 106021228 41 browser details YourSeq 31 196 226 2000 100.0% chr14 + 74358367 74358397 31 browser details YourSeq 30 191 220 2000 100.0% chr9 + 102001666 102001695 30 browser details YourSeq 30 197 226 2000 100.0% chr18 + 38830390 38830419 30 browser details YourSeq 29 190 219 2000 100.0% chr6 - 51491091 51491121 31 browser details YourSeq 29 189 219 2000 90.0% chr11 + 32191351 32191380 30 browser details YourSeq 28 191 218 2000 100.0% chr7 - 24455434 24455461 28 browser details YourSeq 28 190 219 2000 89.7% chr6 - 120107813 120107841 29 browser details YourSeq 28 194 221 2000 100.0% chr6 - 91532105 91532132 28 browser details YourSeq 28 191 218 2000 100.0% chr5 - 133306350 133306377 28 browser details YourSeq 28 192 219 2000 100.0% chr11 - 4822039 4822066 28 browser details YourSeq 28 190 219 2000 89.7% chr8 + 25434366 25434394 29 browser details YourSeq 28 192 219 2000 100.0% chr5 + 151409836 151409863 28 browser details YourSeq 28 190 219 2000 89.7% chr5 + 128658979 128659007 29 browser details YourSeq 28 191 218 2000 100.0% chr17 + 5628641 5628668 28 browser details YourSeq 28 191 218 2000 100.0% chr13 + 101428646 101428673 28 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% chr1 - 193192289 193194288 2000 browser details YourSeq 318 1016 1769 2000 92.8% chr11 + 116962111 117131540 169430 browser details YourSeq 275 1378 1771 2000 90.6% chr3 + 88594981 88884426 289446 browser details YourSeq 268 1395 1769 2000 91.5% chr1 + 177698784 178313114 614331 browser details YourSeq 259 1390 1769 2000 91.0% chr15 + 85981177 85990636 9460 browser details YourSeq 243 1397 1768 2000 89.0% chr7 - 140999953 141000527 575 browser details YourSeq 242 1419 1774 2000 89.3% chr9 + 59792070 59792578 509 browser details YourSeq 240 1378 1768 2000 89.1% chr15 - 99007583 99008160 578 browser details YourSeq 220 1430 1769 2000 91.1% chr9 + 54561433 54561902 470 browser details YourSeq 206 1442 1760 2000 87.3% chr5 - 109951991 110012810 60820 browser details YourSeq 180 1481 1763 2000 87.5% chr5 + 114974571 114975225 655 browser details YourSeq 169 1457 1770 2000 82.1% chr10 - 130578123 130578389 267 browser details YourSeq 167 1397 1658 2000 89.3% chr11 - 97189986 97190797 812 browser details YourSeq 161 1551 1769 2000 90.1% chr14 + 34318686 34319230 545 browser details YourSeq 158 1425 1716 2000 89.6% chr4 - 86864115 86864651 537 browser details YourSeq 152 1375 1773 2000 83.0% chr4 - 106771937 106772127 191 browser details YourSeq 151 1464 1772 2000 84.7% chr9 + 53674906 53675212 307 browser details YourSeq 151 1580 1769 2000 88.6% chr5 + 116051549 116051734 186 browser details YourSeq 150 1387 1769 2000 83.9% chr3 + 94888260 94888434 175 browser details YourSeq 148 1549 1769 2000 90.7% chr13 - 93680574 93680911 338 Note: The 2000 bp section downstream of Exon 8 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Traf3ip3 TRAF3 interacting protein 3 [ Mus musculus (house mouse) ] Gene ID: 215243, updated on 7-Sep-2019 Gene summary Official Symbol Traf3ip3 provided by MGI Official Full Name TRAF3 interacting protein 3 provided by MGI Primary source MGI:MGI:2441706 See related Ensembl:ENSMUSG00000037318 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 T3jam; AI115021; 6030423D04Rik Expression Biased expression in thymus adult (RPKM 26.7), spleen adult (RPKM 17.6) and 7 other tissuesS ee more Orthologs human all Genomic context Location: 1; 1 H6 See Traf3ip3 in Genome Data Viewer Exon count: 16 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (193175504..193201546, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (195001698..195027740, complement) Chromosome 1 - NC_000067.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 13 transcripts Gene: Traf3ip3 ENSMUSG00000037318 Description TRAF3 interacting protein 3 [Source:MGI Symbol;Acc:MGI:2441706] Gene Synonyms 6030423D04Rik Location Chromosome 1: 193,175,453-193,201,703 reverse strand. GRCm38:CM000994.2 About this gene This gene has 13 transcripts (splice variants), 174 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 10 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Traf3ip3- ENSMUST00000043550.10 2122 513aa ENSMUSP00000040977.4 Protein coding CCDS15634 G3X949 TSL:1 201 GENCODE basic APPRIS P2 Traf3ip3- ENSMUST00000192020.5 1854 513aa ENSMUSP00000141698.1 Protein coding CCDS15634 G3X949 TSL:5 212 GENCODE basic APPRIS P2 Traf3ip3- ENSMUST00000160302.3 675 147aa ENSMUSP00000142321.1 Protein coding - A0A0A6YY84 CDS 5' 204 incomplete TSL:2 Traf3ip3- ENSMUST00000162480.2 447 97aa ENSMUSP00000141669.1 Protein coding - A0A0A6YWS1 CDS 5' 210 incomplete TSL:5 Traf3ip3- ENSMUST00000159666.1 360 17aa ENSMUSP00000141938.1 Protein coding - A0A0A6YXD0 CDS 5' 202 incomplete TSL:3 Traf3ip3- ENSMUST00000161367.1 340 113aa ENSMUSP00000141358.1 Protein coding - A0A0A6YW19 CDS 5' and 3' 208 incomplete TSL:3 APPRIS ALT2 Traf3ip3- ENSMUST00000194278.5 2235 185aa ENSMUSP00000141661.1 Nonsense mediated - A0A0A6YWR4 TSL:5 213 decay Traf3ip3- ENSMUST00000161403.7 3372 No - Retained intron - - TSL:1 209 protein Traf3ip3- ENSMUST00000160332.7 1590 No - Retained intron - - TSL:1 205 protein Traf3ip3- ENSMUST00000159805.7 1289 No - Retained intron - - TSL:1 203 protein Traf3ip3- ENSMUST00000161151.2 706 No - lncRNA - - TSL:2 207 protein Traf3ip3- ENSMUST00000161145.7 496 No - lncRNA - - TSL:5 206 protein Traf3ip3- ENSMUST00000162905.1 373 No - lncRNA - - TSL:5 211 protein Page 7 of 9 https://www.alphaknockout.com 46.25 kb Forward strand 193.17Mb 193.18Mb 193.19Mb 193.20Mb 193.21Mb Genes Irf6-201 >protein coding A130010J15Rik-204 >protein coding Gm15872-201 >lncRNA
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