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Mouse Cass4 Knockout Project (CRISPR/Cas9)

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Mouse Cass4 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Cass4 Knockout Project (CRISPR/Cas9) Objective: To create a Cass4 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Cass4 gene (NCBI Reference Sequence: NM_001080820 ; Ensembl: ENSMUSG00000074570 ) is located on Mouse chromosome 2. 7 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 7 (Transcript: ENSMUST00000109136). Exon 2 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 2 starts from about 1.53% of the coding region. Exon 2 covers 17.54% of the coding region. The size of effective KO region: ~337 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 7 Legends Exon of mouse Cass4 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 423 bp section 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 423 bp section 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. Page 3 of 8 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(423bp) | A(21.99% 93) | C(32.39% 137) | T(17.49% 74) | G(28.13% 119) Note: The 423 bp section of Exon 2 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(423bp) | A(22.22% 94) | C(32.62% 138) | T(17.26% 73) | G(27.9% 118) Note: The 423 bp section of Exon 2 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 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 423 1 423 423 100.0% chr2 + 172416122 172416544 423 browser details YourSeq 35 66 204 423 66.7% chr11 - 31642183 31642276 94 browser details YourSeq 30 284 320 423 94.3% chr7 + 139619760 139620016 257 browser details YourSeq 26 365 393 423 96.5% chr14 - 84552735 84552766 32 browser details YourSeq 25 175 200 423 100.0% chr2 - 25371146 25371181 36 browser details YourSeq 23 196 224 423 77.0% chr3 - 95685496 95685521 26 browser details YourSeq 23 388 413 423 96.0% chr5 + 142625863 142625891 29 browser details YourSeq 23 172 197 423 96.2% chr19 + 47813145 47813179 35 browser details YourSeq 21 87 107 423 100.0% chr8 - 69398851 69398871 21 browser details YourSeq 21 52 72 423 100.0% chr11 - 45204213 45204233 21 browser details YourSeq 20 308 327 423 100.0% chr17 + 12894161 12894180 20 browser details YourSeq 20 188 207 423 100.0% chr12 + 11392046 11392065 20 Note: The 423 bp section 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 423 1 423 423 100.0% chr2 + 172416120 172416542 423 browser details YourSeq 35 68 206 423 66.7% chr11 - 31642183 31642276 94 browser details YourSeq 30 286 322 423 94.3% chr7 + 139619760 139620016 257 browser details YourSeq 27 148 182 423 96.6% chr6 + 52913579 52914063 485 browser details YourSeq 23 198 226 423 77.0% chr3 - 95685496 95685521 26 browser details YourSeq 23 174 199 423 96.2% chr19 + 47813145 47813179 35 browser details YourSeq 22 291 313 423 100.0% chr1 + 25470591 25470616 26 browser details YourSeq 21 89 109 423 100.0% chr8 - 69398851 69398871 21 browser details YourSeq 21 54 74 423 100.0% chr11 - 45204213 45204233 21 browser details YourSeq 21 101 122 423 100.0% chr11 - 35492510 35492532 23 browser details YourSeq 20 307 326 423 100.0% chr14 - 120170297 120170316 20 browser details YourSeq 20 310 329 423 100.0% chr17 + 12894161 12894180 20 browser details YourSeq 20 190 209 423 100.0% chr12 + 11392046 11392065 20 Note: The 423 bp section of Exon 2 is BLAT searched against the genome. No significant similarity is found. Page 5 of 8 https://www.alphaknockout.com Gene and protein information: Cass4 Cas scaffolding protein family member 4 [ Mus musculus (house mouse) ] Gene ID: 320664, updated on 24-Oct-2019 Gene summary Official Symbol Cass4 provided by MGI Official Full Name Cas scaffolding protein family member 4 provided by MGI Primary source MGI:MGI:2444482 See related Ensembl:ENSMUSG00000074570 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 F730031O20Rik Expression Broad expression in lung adult (RPKM 2.2), thymus adult (RPKM 1.6) and 20 other tissues See more Orthologs human all Genomic context Location: 2; 2 H3 See Cass4 in Genome Data Viewer Exon count: 8 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (172393644..172433757) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (172219294..172258360) Chromosome 2 - NC_000068.7 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 4 transcripts Gene: Cass4 ENSMUSG00000074570 Description Cas scaffolding protein family member 4 [Source:MGI Symbol;Acc:MGI:2444482] Gene Synonyms F730031O20Rik Location Chromosome 2: 172,393,794-172,433,757 forward strand. GRCm38:CM000995.2 About this gene This gene has 4 transcripts (splice variants), 191 orthologues, 3 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Cass4-202 ENSMUST00000103073.8 3600 778aa ENSMUSP00000099362.2 Protein coding CCDS71205 A0A0R4J199 TSL:1 GENCODE basic APPRIS ALT2 Cass4-203 ENSMUST00000109136.2 2702 804aa ENSMUSP00000104764.2 Protein coding CCDS38347 Q08EC4 TSL:1 GENCODE basic APPRIS P3 Cass4-201 ENSMUST00000099061.8 3731 685aa ENSMUSP00000096660.2 Protein coding - Q08EC4 TSL:1 GENCODE basic Cass4-204 ENSMUST00000228775.1 2629 780aa ENSMUSP00000154073.1 Protein coding - Q08EC4 GENCODE basic APPRIS ALT2 59.96 kb Forward strand 172.39Mb 172.40Mb 172.41Mb 172.42Mb 172.43Mb 172.44Mb Genes (Comprehensive set... Cass4-201 >protein coding Rtf2-202 >retained intron Cass4-202 >protein coding Rtf2-201 >protein coding Cass4-203 >protein coding Cass4-204 >protein coding Contigs AL833787.8 > Genes < Gm14455-201lncRNA (Comprehensive set... Regulatory Build 172.39Mb 172.40Mb 172.41Mb 172.42Mb 172.43Mb 172.44Mb Reverse strand 59.96 kb Regulation Legend CTCF Enhancer Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding processed transcript Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000109136 38.96 kb Forward strand Cass4-203 >protein coding ENSMUSP00000104... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SH3-like domain superfamily SMART SH3 domain Pfam SH3 domain Serine rich protein interaction domain CAS family, C-terminal PROSITE profiles SH3 domain PANTHER Cas scaffolding protein family member 4 CAS family Gene3D 2.30.30.40 1.20.120.230 CAS, serine rich four helix bundle domain superfamily CDD Cas scaffolding protein family member 4, SH3 domain All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 80 160 240 320 400 480 560 640 720 804 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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