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Mouse Cd300c Knockout Project (CRISPR/Cas9)

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Mouse Cd300c Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Cd300c Knockout Project (CRISPR/Cas9) Objective: To create a Cd300c knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Cd300c gene (NCBI Reference Sequence: NM_001368239 ; Ensembl: ENSMUSG00000058728 ) is located on Mouse chromosome 11. 4 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 4 (Transcript: ENSMUST00000092466). 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 9.02% of the coding region. Exon 2 covers 52.4% of the coding region. The size of effective KO region: ~360 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 4 Legends Exon of mouse Cd300c 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 360 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 360 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(360bp) | A(27.78% 100) | C(22.5% 81) | T(25.0% 90) | G(24.72% 89) Note: The 360 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(360bp) | A(27.78% 100) | C(22.22% 80) | T(24.72% 89) | G(25.28% 91) Note: The 360 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 360 1 360 360 100.0% chr11 - 114959554 114959913 360 browser details YourSeq 168 53 280 360 86.9% chr11 - 115000705 115000932 228 browser details YourSeq 129 126 280 360 91.7% chr11 + 114893364 114893518 155 browser details YourSeq 35 182 231 360 90.5% chr11 - 115035215 115035264 50 browser details YourSeq 35 182 231 360 90.5% chr11 - 115045861 115045910 50 browser details YourSeq 25 208 239 360 96.3% chr14 - 14683819 14683857 39 browser details YourSeq 25 20 48 360 88.9% chr1 - 139251786 139251813 28 browser details YourSeq 24 86 116 360 79.4% chr1 + 105918983 105919011 29 browser details YourSeq 23 151 177 360 92.6% chr6 + 132573765 132573791 27 browser details YourSeq 23 151 177 360 92.6% chr6 + 132602060 132602086 27 browser details YourSeq 21 142 162 360 100.0% chr7 - 63747100 63747120 21 browser details YourSeq 20 59 80 360 95.5% chr6 - 89048671 89048692 22 browser details YourSeq 20 218 239 360 95.5% chr18 + 64330101 64330122 22 browser details YourSeq 20 217 236 360 100.0% chr14 + 78375017 78375036 20 browser details YourSeq 20 23 42 360 100.0% chr11 + 55206353 55206372 20 browser details YourSeq 20 119 138 360 100.0% chr1 + 147633053 147633072 20 Note: The 360 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 360 1 360 360 100.0% chr11 - 114959556 114959915 360 browser details YourSeq 168 55 282 360 86.9% chr11 - 115000705 115000932 228 browser details YourSeq 143 18 282 360 91.9% chr11 + 114893254 114893518 265 browser details YourSeq 35 184 233 360 90.5% chr11 - 115035215 115035264 50 browser details YourSeq 35 184 233 360 90.5% chr11 - 115045861 115045910 50 browser details YourSeq 25 22 50 360 88.9% chr1 - 139251786 139251813 28 browser details YourSeq 21 144 164 360 100.0% chr7 - 63747100 63747120 21 browser details YourSeq 21 77 97 360 100.0% chr12 + 93563691 93563711 21 browser details YourSeq 20 85 104 360 100.0% chr5 - 5104268 5104287 20 browser details YourSeq 20 219 238 360 100.0% chr14 + 78375017 78375036 20 browser details YourSeq 20 25 44 360 100.0% chr11 + 55206353 55206372 20 browser details YourSeq 20 121 140 360 100.0% chr1 + 147633053 147633072 20 Note: The 360 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: Cd300c CD300C molecule [ Mus musculus (house mouse) ] Gene ID: 387565, updated on 4-Dec-2019 Gene summary Official Symbol Cd300c provided by MGI Official Full Name CD300C molecule provided by MGI Primary source MGI:MGI:3032626 See related Ensembl:ENSMUSG00000058728 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as Clm6 Expression Biased expression in spleen adult (RPKM 2.6), mammary gland adult (RPKM 1.2) and 5 other tissues See more Orthologs human all Genomic context Location: 11; 11 E2 See Cd300c in Genome Data Viewer Exon count: 4 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (114956105..114960507, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (114817592..114821731, complement) Chromosome 11 - NC_000077.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 3 transcripts Gene: Cd300c ENSMUSG00000058728 Description CD300C molecule [Source:MGI Symbol;Acc:MGI:3032626] Gene Synonyms Clm6 Location Chromosome 11: 114,956,116-114,969,157 reverse strand. GRCm38:CM001004.2 About this gene This gene has 3 transcripts (splice variants), 214 orthologues, 17 paralogues, is a member of 1 Ensembl protein family and is associated with 4 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Cd300c-202 ENSMUST00000092466.12 700 229aa ENSMUSP00000090123.6 Protein coding - D3Z6G7 TSL:5 GENCODE basic APPRIS ALT2 Cd300c-201 ENSMUST00000061637.3 690 229aa ENSMUSP00000052647.3 Protein coding - F7C5I0 TSL:5 GENCODE basic APPRIS P5 Cd300c-203 ENSMUST00000106580.2 638 No protein - Processed transcript - - TSL:3 33.04 kb Forward strand 114.95Mb 114.96Mb 114.97Mb Contigs AL607025.21 > Genes < Cd300c-203processed transcript (Comprehensive set... < Cd300c-202protein coding < Cd300c-201protein coding Regulatory Build 114.95Mb 114.96Mb 114.97Mb Reverse strand 33.04 kb Regulation Legend CTCF Open Chromatin Promoter Flank Gene Legend Protein Coding Ensembl protein coding Non-Protein Coding processed transcript Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000092466 < Cd300c-202protein coding Reverse strand 4.15 kb ENSMUSP00000090... Transmembrane heli... Low complexity (Seg) Cleavage site (Sign... Superfamily Immunoglobulin-like domain superfamily SMART Immunoglobulin subtype Pfam Immunoglobulin V-set domain PROSITE profiles Immunoglobulin-like domain PANTHER PTHR11860 PTHR11860:SF93 Gene3D Immunoglobulin-like fold CDD cd05716 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend frameshift variant missense variant splice region variant synonymous variant Scale bar 0 20 40 60 80 100 120 140 160 180 200 229 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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