https://www.alphaknockout.com
Mouse Ctnnal1 Knockout Project (CRISPR/Cas9)
Objective: To create a Ctnnal1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Ctnnal1 gene (NCBI Reference Sequence: NM_018761 ; Ensembl: ENSMUSG00000038816 ) is located on Mouse chromosome 4. 19 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 19 (Transcript: ENSMUST00000045142). 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: Mice homozygous for a targeted disruption of this gene are viable and fertile and exhibit no overt phenotypes or defects in hematopoiesis and hematopoietic stem cell function.
Exon 2 starts from about 6.34% of the coding region. Exon 2 covers 8.66% of the coding region. The size of effective KO region: ~190 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 19
Legends Exon of mouse Ctnnal1 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 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(26.25% 525) | C(20.7% 414) | T(31.5% 630) | G(21.55% 431)
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(26.2% 524) | C(21.2% 424) | T(27.3% 546) | G(25.3% 506)
Note: The 2000 bp section downstream 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.
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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% chr4 - 56848000 56849999 2000 browser details YourSeq 191 406 1389 2000 85.6% chr6 - 30200741 30201669 929 browser details YourSeq 187 847 1407 2000 83.8% chr17 - 45744218 45744490 273 browser details YourSeq 182 834 1407 2000 84.2% chr2 + 167051884 167052277 394 browser details YourSeq 177 834 1398 2000 91.7% chr12 - 72726045 73129617 403573 browser details YourSeq 176 849 1409 2000 83.9% chr7 + 49581171 49581451 281 browser details YourSeq 175 834 1407 2000 84.4% chr17 - 87527540 87527804 265 browser details YourSeq 167 849 1405 2000 82.7% chr4 - 129438629 129438902 274 browser details YourSeq 158 861 1401 2000 84.3% chr5 - 137774531 137774962 432 browser details YourSeq 152 861 1404 2000 82.0% chr4 - 94553851 94554096 246 browser details YourSeq 151 846 1386 2000 79.5% chr7 - 45606613 45606829 217 browser details YourSeq 143 1059 1411 2000 86.0% chr14 + 52980950 52981234 285 browser details YourSeq 143 1059 1411 2000 86.0% chr14 + 53292089 53292374 286 browser details YourSeq 140 834 1328 2000 91.3% chr2 + 154434127 154434701 575 browser details YourSeq 130 854 1398 2000 82.7% chr1 + 192172969 192173300 332 browser details YourSeq 128 737 974 2000 90.0% chr1 - 165627679 165627938 260 browser details YourSeq 128 1267 1417 2000 92.7% chr1 + 78633854 78634004 151 browser details YourSeq 125 1267 1409 2000 92.3% chr15 + 82287560 82287701 142 browser details YourSeq 124 1249 1408 2000 87.5% chrX + 151099069 151099224 156 browser details YourSeq 123 1267 1417 2000 90.8% chr4 - 46357220 46357370 151
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% chr4 - 56845810 56847809 2000 browser details YourSeq 84 648 806 2000 87.5% chr1 + 21374584 21374751 168 browser details YourSeq 83 656 805 2000 89.6% chr1 + 60177797 60177955 159 browser details YourSeq 80 646 785 2000 87.1% chr6 - 118901501 118901636 136 browser details YourSeq 78 254 793 2000 77.9% chr16 + 17027969 17028419 451 browser details YourSeq 77 658 784 2000 91.5% chr14 + 37692165 37692313 149 browser details YourSeq 75 421 791 2000 89.5% chr8 + 44381154 44381652 499 browser details YourSeq 72 706 806 2000 89.3% chr16 + 49790386 49790492 107 browser details YourSeq 70 657 805 2000 93.6% chr14 - 12902427 12902576 150 browser details YourSeq 68 656 785 2000 89.6% chr11 + 50313894 50314030 137 browser details YourSeq 67 657 805 2000 81.9% chr17 - 31446498 31446627 130 browser details YourSeq 67 658 785 2000 89.5% chr12 - 5047491 5047629 139 browser details YourSeq 66 656 805 2000 89.7% chr15 + 83257716 83257864 149 browser details YourSeq 63 716 805 2000 90.2% chr11 + 19724366 19724462 97 browser details YourSeq 61 668 774 2000 95.6% chr5 + 106381619 106381741 123 browser details YourSeq 61 645 760 2000 93.0% chr17 + 74404231 74404356 126 browser details YourSeq 59 730 820 2000 90.5% chr10 + 48353848 48353983 136 browser details YourSeq 58 660 752 2000 94.0% chr18 - 35952680 35952776 97 browser details YourSeq 58 419 746 2000 94.0% chr12 + 55402718 55403269 552 browser details YourSeq 58 657 776 2000 94.1% chr11 + 105301304 105301436 133
Note: The 2000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Ctnnal1 catenin (cadherin associated protein), alpha-like 1 [ Mus musculus (house mouse) ] Gene ID: 54366, updated on 12-Aug-2019
Gene summary
Official Symbol Ctnnal1 provided by MGI Official Full Name catenin (cadherin associated protein), alpha-like 1 provided by MGI Primary source MGI:MGI:1859649 See related Ensembl:ENSMUSG00000038816 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 ACRP; C86009; Catnal1; AI616177; AW545119 Expression Broad expression in bladder adult (RPKM 18.0), CNS E11.5 (RPKM 7.9) and 21 other tissues See more Orthologs human all
Genomic context
Location: 4; 4 B3 See Ctnnal1 in Genome Data Viewer Exon count: 20
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (56810935..56865375, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (56823807..56878083, complement)
Chromosome 4 - NC_000070.6
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Transcript information: This gene has 9 transcripts
Gene: Ctnnal1 ENSMUSG00000038816
Description catenin (cadherin associated protein), alpha-like 1 [Source:MGI Symbol;Acc:MGI:1859649] Gene Synonyms ACRP, Catnal1 Location Chromosome 4: 56,810,935-56,865,188 reverse strand. GRCm38:CM000997.2 About this gene This gene has 9 transcripts (splice variants), 203 orthologues, 5 paralogues, is a member of 1 Ensembl protein family and is associated with 1 phenotype. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Ctnnal1-201 ENSMUST00000045142.14 3664 731aa ENSMUSP00000036487.8 Protein coding CCDS18200 O88327 TSL:1 GENCODE basic APPRIS P1
Ctnnal1-202 ENSMUST00000107612.2 850 219aa ENSMUSP00000103237.2 Protein coding - B1AZA7 TSL:3 GENCODE basic
Ctnnal1-203 ENSMUST00000127908.7 3795 No protein - lncRNA - - TSL:5
Ctnnal1-206 ENSMUST00000134754.7 1956 No protein - lncRNA - - TSL:1
Ctnnal1-209 ENSMUST00000154511.1 740 No protein - lncRNA - - TSL:3
Ctnnal1-204 ENSMUST00000131231.1 654 No protein - lncRNA - - TSL:3
Ctnnal1-208 ENSMUST00000136308.1 622 No protein - lncRNA - - TSL:2
Ctnnal1-207 ENSMUST00000134915.1 565 No protein - lncRNA - - TSL:3
Ctnnal1-205 ENSMUST00000132764.1 297 No protein - lncRNA - - TSL:3
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74.25 kb Forward strand
Genes Abitram-204 >retained intron (Comprehensive set...
Abitram-201 >protein coding
Abitram-202 >nonsense mediated decay
Abitram-203 >nonsense mediated decay
Contigs AL929577.9 >
Genes (Comprehensive set... < Elp1-201protein coding< Ctnnal1-201protein coding < Tmem245-201protein coding
< Ctnnal1-204lncRNA < Ctnnal1-203lncRNA < Ctnnal1-202protein coding
< Ctnnal1-207lncRNA< Ctnnal1-206lncRNA
< Ctnnal1-208lncRNA < Ctnnal1-205lncRNA
< Ctnnal1-209lncRNA
Regulatory Build
Reverse strand 74.25 kb
Regulation Legend
CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000045142
< Ctnnal1-201protein coding
Reverse strand 54.25 kb
ENSMUSP00000036... Low complexity (Seg) Coiled-coils (Ncoils) Superfamily Alpha-catenin/vinculin-like superfamily Prints Alpha-catenin Pfam Vinculin/alpha-catenin PANTHER Alpha-catulin 1 Gene3D 1.20.120.230
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant splice region variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 731
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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