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Mouse Trim27 Knockout Project (CRISPR/Cas9)

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Mouse Trim27 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Trim27 Knockout Project (CRISPR/Cas9) Objective: To create a Trim27 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Trim27 gene (NCBI Reference Sequence: NM_009054 ; Ensembl: ENSMUSG00000021326 ) is located on Mouse chromosome 13. 8 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 8 (Transcript: ENSMUST00000021761). Exon 2~7 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 gene trap allele exhibit exhibit increased potassium/calcium channel activity and TCR- stimulated calcium influx in Th1 and Th2 CD4 T cells. Mice homozygous for another gene trap allele exhibit decreased incidence of chemically-induced tumors. Exon 2 starts from about 27.36% of the coding region. Exon 2~7 covers 34.18% of the coding region. The size of effective KO region: ~9263 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 2 3 4 5 6 7 8 Legends Exon of mouse Trim27 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 1069 bp section upstream of Exon 2 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 783 bp section downstream of Exon 7 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(1069bp) | A(24.79% 265) | C(24.04% 257) | T(26.01% 278) | G(25.16% 269) Note: The 1069 bp section upstream of Exon 2 is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(783bp) | A(31.67% 248) | C(18.9% 148) | T(28.48% 223) | G(20.95% 164) Note: The 783 bp section downstream of Exon 7 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 1069 1 1069 1069 100.0% chr13 + 21180916 21181984 1069 browser details YourSeq 33 635 788 1069 97.2% chr1 - 161288550 161288706 157 browser details YourSeq 29 721 791 1069 96.8% chr10 + 115551441 115551559 119 browser details YourSeq 26 767 797 1069 96.5% chr11 + 8645031 8645065 35 browser details YourSeq 25 414 442 1069 80.8% chr3 - 111630976 111631001 26 browser details YourSeq 23 161 184 1069 100.0% chr11 + 66257481 66257505 25 browser details YourSeq 23 767 792 1069 96.2% chr10 + 61288936 61288964 29 browser details YourSeq 22 767 788 1069 100.0% chr12 - 62184215 62184236 22 browser details YourSeq 22 767 788 1069 100.0% chr10 - 111186010 111186031 22 browser details YourSeq 22 767 788 1069 100.0% chr10 + 16892361 16892382 22 browser details YourSeq 22 767 788 1069 100.0% chr1 + 72637136 72637157 22 browser details YourSeq 21 773 793 1069 100.0% chr8 - 53242451 53242471 21 browser details YourSeq 21 767 787 1069 100.0% chr1 - 128376371 128376391 21 browser details YourSeq 21 638 658 1069 100.0% chr10 + 32289872 32289892 21 browser details YourSeq 21 767 787 1069 100.0% chr1 + 79356881 79356901 21 browser details YourSeq 20 767 786 1069 100.0% chr12 - 3417177 3417196 20 browser details YourSeq 20 767 786 1069 100.0% chr10 - 117331242 117331261 20 Note: The 1069 bp section upstream of Exon 2 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 783 1 783 783 100.0% chr13 + 21191248 21192030 783 browser details YourSeq 48 494 615 783 87.5% chr10 + 39386715 39386834 120 browser details YourSeq 36 514 608 783 95.0% chr3 + 41640447 41640542 96 browser details YourSeq 31 496 536 783 87.9% chr10 + 30412763 30412803 41 browser details YourSeq 30 152 184 783 97.0% chr1 + 179300612 179300679 68 browser details YourSeq 28 549 591 783 86.7% chr19 - 26918944 26918984 41 browser details YourSeq 27 212 242 783 96.6% chr7 - 53283754 53283785 32 browser details YourSeq 26 496 529 783 78.6% chr6 - 23130310 23130338 29 browser details YourSeq 26 551 591 783 89.3% chr8 + 70829008 70829047 40 browser details YourSeq 25 215 242 783 84.7% chr3 + 75252591 75252616 26 browser details YourSeq 25 160 186 783 88.5% chr2 + 31525401 31525426 26 browser details YourSeq 24 496 529 783 70.4% chr1 - 69572195 69572221 27 browser details YourSeq 24 513 536 783 100.0% chr13 + 61683509 61683532 24 browser details YourSeq 23 155 179 783 96.0% chr10 + 22654928 22654952 25 browser details YourSeq 22 154 175 783 100.0% chr7 - 44718591 44718612 22 browser details YourSeq 22 508 529 783 100.0% chr2 - 61666516 61666537 22 browser details YourSeq 22 508 529 783 100.0% chr19 - 34888695 34888716 22 browser details YourSeq 22 508 529 783 100.0% chr19 - 30254630 30254651 22 browser details YourSeq 22 508 529 783 100.0% chr17 - 26725941 26725962 22 browser details YourSeq 22 508 531 783 95.9% chr1 - 93494890 93494913 24 Note: The 783 bp section downstream of Exon 7 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Trim27 tripartite motif-containing 27 [ Mus musculus (house mouse) ] Gene ID: 19720, updated on 12-Aug-2019 Gene summary Official Symbol Trim27 provided by MGI Official Full Name tripartite motif-containing 27 provided by MGI Primary source MGI:MGI:97904 See related Ensembl:ENSMUSG00000021326 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 Rfp; Gm19403; AW538890 Expression Ubiquitous expression in ovary adult (RPKM 33.3), adrenal adult (RPKM 32.0) and 28 other tissues See more Orthologs human all Genomic context Location: 13 A2; 13 7.67 cM See Trim27 in Genome Data Viewer Exon count: 10 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (21179450..21194723) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 13 NC_000079.5 (21271828..21284726) Chromosome 13 - NC_000079.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 7 transcripts Gene: Trim27 ENSMUSG00000021326 Description tripartite motif-containing 27 [Source:MGI Symbol;Acc:MGI:97904] Gene Synonyms Rfp Location Chromosome 13: 21,179,445-21,194,724 forward strand. GRCm38:CM001006.2 About this gene This gene has 7 transcripts (splice variants), 152 orthologues, 73 paralogues, is a member of 1 Ensembl protein family and is associated with 12 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Trim27- ENSMUST00000222544.1 4312 513aa ENSMUSP00000152730.1 Protein coding CCDS36607 Q62158 TSL:5 206 GENCODE basic APPRIS P1 Trim27- ENSMUST00000021761.12 4204 513aa ENSMUSP00000021761.5 Protein coding CCDS36607 Q62158 TSL:1 201 GENCODE basic APPRIS P1 Trim27- ENSMUST00000223065.1 2046 314aa ENSMUSP00000152179.1 Protein coding - A0A1Y7VKW0 TSL:1 207 GENCODE basic Trim27- ENSMUST00000221464.1 1400 337aa ENSMUSP00000152230.1 Protein coding - A0A1Y7VJ13 TSL:5 205 GENCODE basic Trim27- ENSMUST00000139287.3 683 61aa ENSMUSP00000115397.3 Nonsense mediated - F6U3T5 CDS 5' 204 decay incomplete TSL:5 Trim27- ENSMUST00000124052.2 1750 No - Retained intron - - TSL:NA 202 protein Trim27- ENSMUST00000124794.1 439 No - Retained intron - - TSL:3 203 protein Page 7 of 9 https://www.alphaknockout.com 35.28 kb Forward strand 21.17Mb 21.18Mb 21.19Mb 21.20Mb Genes (Comprehensive set... Trim27-206 >protein coding Trim27-201 >protein coding Trim27-202 >retained intron Trim27-204 >nonsense mediated decay Trim27-207 >protein coding Trim27-205 >protein coding Trim27-203 >retained intron Contigs < AC138330.4 Genes < Gm47806-201lncRNA (Comprehensive set... Regulatory Build 21.17Mb 21.18Mb 21.19Mb 21.20Mb Reverse strand 35.28 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding Ensembl protein coding Non-Protein Coding processed transcript RNA gene Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000021761 14.79 kb Forward strand Trim27-201 >protein coding ENSMUSP00000021... Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF57850 SSF57845 Concanavalin A-like lectin/glucanase domain superfamily SMART Zinc finger, RING-type SPRY-associated B-box-type zinc finger SPRY domain Prints Zinc finger, B-box, chordata Butyrophylin-like, SPRY domain Pfam PF15227 B-box-type zinc finger SPRY domain SPRY-associated PROSITE profiles Zinc finger, RING-type B30.2/SPRY domain B-box-type zinc finger PROSITE patterns Zinc finger, RING-type, conserved site PANTHER PTHR24103:SF362 PTHR24103 Gene3D Zinc finger, RING/FYVE/PHD-type 2.60.120.920 3.30.40.200 CDD cd16594 B-box-type zinc finger TRIM27, PRY/SPRY domain All sequence SNPs/i..
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