https://www.alphaknockout.com
Mouse Cnksr3 Knockout Project (CRISPR/Cas9)
Objective: To create a Cnksr3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Cnksr3 gene (NCBI Reference Sequence: NM_172546 ; Ensembl: ENSMUSG00000015202 ) is located on Mouse chromosome 10. 13 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 13 (Transcript: ENSMUST00000015346). Exon 2~4 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 3.18% of the coding region. Exon 2~4 covers 27.33% of the coding region. The size of effective KO region: ~7944 bp. The KO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele 5' gRNA region gRNA region 3'
1 2 3 4 13
Legends Exon of mouse Cnksr3 Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 2000 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 2000 bp section downstream of Exon 4 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(22.7% 454) | C(22.15% 443) | T(29.75% 595) | G(25.4% 508)
Note: The 2000 bp section upstream 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(2000bp) | A(22.4% 448) | C(21.55% 431) | T(35.7% 714) | G(20.35% 407)
Note: The 2000 bp section downstream of Exon 4 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.
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BLAT Search Results (up)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 2000 1 2000 2000 100.0% chr10 - 7160808 7162807 2000 browser details YourSeq 65 1440 1516 2000 92.3% chr7 - 139124628 139124704 77 browser details YourSeq 64 1443 1516 2000 93.3% chr9 - 46368520 46368593 74 browser details YourSeq 64 1441 1516 2000 92.2% chr16 - 31077102 31077177 76 browser details YourSeq 64 1443 1516 2000 93.3% chr14 + 41044777 41044850 74 browser details YourSeq 63 1444 1516 2000 93.2% chr5 + 112897242 112897314 73 browser details YourSeq 63 1442 1516 2000 92.0% chr14 + 118808121 118808195 75 browser details YourSeq 63 1440 1516 2000 88.2% chr1 + 76305205 76305280 76 browser details YourSeq 62 1445 1516 2000 93.1% chrX - 74852312 74852383 72 browser details YourSeq 62 1445 1516 2000 93.1% chr7 - 117825012 117825083 72 browser details YourSeq 62 1441 1516 2000 90.8% chr2 - 161046582 161046657 76 browser details YourSeq 62 1445 1516 2000 93.1% chr18 - 67446756 67446827 72 browser details YourSeq 62 1443 1516 2000 91.9% chr1 - 132699078 132699151 74 browser details YourSeq 62 1445 1516 2000 93.1% chrX + 74780727 74780798 72 browser details YourSeq 62 1441 1516 2000 90.8% chr8 + 127576594 127576669 76 browser details YourSeq 62 1438 1516 2000 89.8% chr8 + 74984392 74984470 79 browser details YourSeq 62 1445 1516 2000 93.1% chr17 + 34389294 34389365 72 browser details YourSeq 62 1443 1516 2000 91.9% chr15 + 8793146 8793219 74 browser details YourSeq 62 1445 1516 2000 93.1% chr14 + 51004061 51004132 72 browser details YourSeq 62 1444 1516 2000 93.2% chr1 + 62289922 62289995 74
Note: The 2000 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 2000 1 2000 2000 100.0% chr10 - 7150864 7152863 2000 browser details YourSeq 951 788 1844 2000 95.7% chr7 - 113663544 113664622 1079 browser details YourSeq 941 789 1844 2000 94.8% chr11 - 61229120 61230195 1076 browser details YourSeq 935 657 1844 2000 93.3% chr11 - 82686321 82687396 1076 browser details YourSeq 933 789 1844 2000 95.8% chr13 - 103286890 103353221 66332 browser details YourSeq 932 773 1844 2000 94.4% chr3 + 32840837 32842078 1242 browser details YourSeq 931 803 1844 2000 95.0% chr6 + 34837161 34838224 1064 browser details YourSeq 930 658 1844 2000 93.7% chr1 + 163026933 163028167 1235 browser details YourSeq 927 787 1844 2000 94.8% chr11 - 72236017 72237093 1077 browser details YourSeq 927 803 1844 2000 95.4% chr16 + 35520715 35521770 1056 browser details YourSeq 926 787 1844 2000 94.4% chr9 - 74566371 74567452 1082 browser details YourSeq 925 801 1844 2000 94.6% chr4 - 40562576 40563646 1071 browser details YourSeq 924 792 1844 2000 94.4% chr5 - 103899287 103900366 1080 browser details YourSeq 923 756 1844 2000 94.1% chr10 - 37058562 37059671 1110 browser details YourSeq 923 790 1844 2000 94.2% chr6 + 89620684 89621756 1073 browser details YourSeq 921 787 1844 2000 94.3% chr10 - 14370792 14371872 1081 browser details YourSeq 921 803 1844 2000 94.7% chrX + 151216933 151217994 1062 browser details YourSeq 921 789 1844 2000 94.6% chr11 + 55954302 55955382 1081 browser details YourSeq 920 803 1844 2000 95.2% chr1 - 9836565 9837633 1069 browser details YourSeq 920 789 1844 2000 94.0% chr7 + 6845928 6847018 1091
Note: The 2000 bp section downstream of Exon 4 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Cnksr3 Cnksr family member 3 [ Mus musculus (house mouse) ] Gene ID: 215748, updated on 12-Aug-2019
Gene summary
Official Symbol Cnksr3 provided by MGI Official Full Name Cnksr family member 3 provided by MGI Primary source MGI:MGI:2674130 See related Ensembl:ENSMUSG00000015202 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 Magi1; BC024086; 6820402C05 Expression Ubiquitous expression in cerebellum adult (RPKM 8.5), bladder adult (RPKM 8.3) and 28 other tissues See more Orthologs human all
Genomic context
Location: 10; 10 A1 See Cnksr3 in Genome Data Viewer Exon count: 14
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (7119061..7212237, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (3134304..3227479)
Chromosome 10 - NC_000076.6
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Transcript information: This gene has 2 transcripts
Gene: Cnksr3 ENSMUSG00000015202
Description Cnksr family member 3 [Source:MGI Symbol;Acc:MGI:2674130] Gene Synonyms Magi1 Location Chromosome 10: 7,119,063-7,212,237 reverse strand. GRCm38:CM001003.2 About this gene This gene has 2 transcripts (splice variants), 103 orthologues, 6 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Cnksr3-201 ENSMUST00000015346.11 3447 555aa ENSMUSP00000015346.5 Protein coding CCDS56690 Q8BMA3 TSL:1 GENCODE basic APPRIS P1
Cnksr3-202 ENSMUST00000150282.1 2554 314aa ENSMUSP00000115863.1 Protein coding - Q8BMA3 TSL:1 GENCODE basic
113.17 kb Forward strand 7.12Mb 7.14Mb 7.16Mb 7.18Mb 7.20Mb 7.22Mb Contigs < AC161889.5 < AC099593.6
Genes (Comprehensive set... < Cnksr3-202protein coding
< Cnksr3-201protein coding
Regulatory Build
7.12Mb 7.14Mb 7.16Mb 7.18Mb 7.20Mb 7.22Mb Reverse strand 113.17 kb
Regulation Legend
CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
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Transcript: ENSMUST00000015346
< Cnksr3-201protein coding
Reverse strand 93.17 kb
ENSMUSP00000015... MobiDB lite Low complexity (Seg) Superfamily Sterile alpha motif/pointed domain superfamily PDZ superfamily
SMART Sterile alpha motif domain PDZ domain
Pfam CRIC domain PDZ domain Connector enhancer of kinase suppressor of ras 2
Sterile alpha motif domain PROSITE profiles Sterile alpha motif domain PDZ domain
CRIC domain PANTHER PTHR12844:SF43
PTHR12844 Gene3D 2.30.42.10
Sterile alpha motif/pointed domain superfamily CDD cd09511
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant splice region variant synonymous variant
Scale bar 0 60 120 180 240 300 360 420 480 555
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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