https://www.alphaknockout.com
Mouse Cox7a2l Knockout Project (CRISPR/Cas9)
Objective: To create a Cox7a2l knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Cox7a2l gene (NCBI Reference Sequence: NM_001159529 ; Ensembl: ENSMUSG00000024248 ) is located on Mouse chromosome 17. 4 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 4 (Transcript: ENSMUST00000167741). Exon 2~3 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 an allele encoding the short isoform exhibit higher succinate or pyruvate and malate-driven respiration rates with failure of an additive effect of pyruvate and malate in fed mice or an increase in succinate respiration in fasted mice.
Exon 2 starts from about 18.16% of the coding region. Exon 2~3 covers 49.25% of the coding region. The size of effective KO region: ~298 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
Legends Exon of mouse Cox7a2l 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. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats.
Overview of the Dot Plot (down) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 1193 bp section downstream of Exon 3 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(23.95% 479) | C(22.9% 458) | T(29.15% 583) | G(24.0% 480)
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(1193bp) | A(23.55% 281) | C(19.78% 236) | T(32.61% 389) | G(24.06% 287)
Note: The 1193 bp section downstream of Exon 3 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% chr17 - 83504229 83506228 2000 browser details YourSeq 199 355 611 2000 95.9% chr4 - 83341112 83341581 470 browser details YourSeq 196 421 998 2000 90.9% chr7 - 30802683 30803162 480 browser details YourSeq 195 396 614 2000 94.1% chr1 + 173383761 173383965 205 browser details YourSeq 194 355 611 2000 96.3% chr4 - 129296934 129297454 521 browser details YourSeq 192 371 607 2000 98.5% chrX - 60636291 60636578 288 browser details YourSeq 191 370 611 2000 97.1% chr9 - 106259412 106259715 304 browser details YourSeq 191 348 608 2000 97.1% chr12 - 76258084 76258744 661 browser details YourSeq 190 422 611 2000 100.0% chr2 + 60494900 60495089 190 browser details YourSeq 189 422 874 2000 88.3% chr5 - 105765605 105765856 252 browser details YourSeq 188 423 610 2000 100.0% chr2 - 18088188 18088375 188 browser details YourSeq 187 421 611 2000 99.0% chr17 - 60461811 60462001 191 browser details YourSeq 187 422 614 2000 98.5% chr1 - 171873700 171873892 193 browser details YourSeq 187 422 617 2000 98.0% chr5 + 144081756 144081963 208 browser details YourSeq 186 422 611 2000 99.0% chr5 - 103641491 103641680 190 browser details YourSeq 186 421 610 2000 99.0% chrX + 166055876 166056065 190 browser details YourSeq 186 421 614 2000 98.0% chr7 + 41454155 41454348 194 browser details YourSeq 186 422 611 2000 99.0% chr2 + 70997981 70998170 190 browser details YourSeq 185 422 610 2000 99.0% chr7 - 57101389 57101577 189 browser details YourSeq 185 422 779 2000 91.1% chr12 - 86182885 86183216 332
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 1193 1 1193 1193 100.0% chr17 - 83502738 83503930 1193 browser details YourSeq 217 898 1184 1193 96.2% chr3 + 94617387 94617822 436 browser details YourSeq 203 890 1120 1193 94.0% chr13 + 63501819 63502043 225 browser details YourSeq 198 900 1120 1193 97.2% chr8 + 70627404 70627628 225 browser details YourSeq 196 894 1108 1193 95.8% chr15 - 102125773 102125989 217 browser details YourSeq 196 901 1120 1193 94.6% chr9 + 49058030 49058241 212 browser details YourSeq 195 896 1105 1193 97.2% chr10 - 77872537 77872768 232 browser details YourSeq 193 894 1101 1193 96.7% chr2 + 153453855 153454067 213 browser details YourSeq 192 868 1088 1193 97.6% chr1 + 132010058 132010495 438 browser details YourSeq 191 894 1136 1193 91.6% chr12 + 55074049 55074257 209 browser details YourSeq 189 894 1096 1193 97.1% chr4 + 123024714 123024926 213 browser details YourSeq 188 899 1098 1193 97.5% chr6 - 30001892 30002402 511 browser details YourSeq 188 894 1088 1193 98.5% chr1 - 136702229 136702424 196 browser details YourSeq 188 894 1096 1193 96.6% chr11 + 73491895 73492107 213 browser details YourSeq 187 894 1088 1193 97.0% chr19 - 11938550 11938743 194 browser details YourSeq 187 894 1088 1193 97.0% chr12 - 54671868 54672061 194 browser details YourSeq 187 900 1097 1193 97.5% chr4 + 99537248 99537454 207 browser details YourSeq 187 896 1096 1193 97.0% chr3 + 95725459 95725666 208 browser details YourSeq 187 894 1088 1193 97.0% chr2 + 29878654 29878847 194 browser details YourSeq 187 894 1088 1193 97.0% chr11 + 7726805 7726998 194
Note: The 1193 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Cox7a2l cytochrome c oxidase subunit 7A2 like [ Mus musculus (house mouse) ] Gene ID: 20463, updated on 27-Aug-2019
Gene summary
Official Symbol Cox7a2l provided by MGI Official Full Name cytochrome c oxidase subunit 7A2 like provided by MGI Primary source MGI:MGI:106015 See related Ensembl:ENSMUSG00000024248 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 EB1; SIG81; COX7AR; COX7RP; SIG-81; Silg81 Expression Ubiquitous expression in bladder adult (RPKM 103.0), heart adult (RPKM 81.6) and 28 other tissues See more Orthologs human all
Genomic context
Location: 17; 17 E4 See Cox7a2l in Genome Data Viewer Exon count: 4
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (83501917..83514333, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (83901257..83913673, complement)
Chromosome 17 - NC_000083.6
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Transcript information: This gene has 4 transcripts
Gene: Cox7a2l ENSMUSG00000024248
Description cytochrome c oxidase subunit 7A2 like [Source:MGI Symbol;Acc:MGI:106015] Gene Synonyms COX7AR, COX7RP, EB1, SIG-81, SIG81 Location Chromosome 17: 83,501,918-83,517,330 reverse strand. GRCm38:CM001010.2 About this gene This gene has 4 transcripts (splice variants), 240 orthologues, 2 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
Cox7a2l- ENSMUST00000167741.8 1129 134aa ENSMUSP00000131584.1 Protein coding CCDS50194 E9PZS8 TSL:1 202 GENCODE basic
Cox7a2l- ENSMUST00000025095.8 1076 111aa ENSMUSP00000025095.7 Protein coding CCDS28995 Q3UDK5 TSL:1 201 Q61387 GENCODE basic APPRIS P1
Cox7a2l- ENSMUST00000235085.1 903 No - Retained - - - 204 protein intron
Cox7a2l- ENSMUST00000234258.1 592 No - lncRNA - - - 203 protein
35.41 kb Forward strand 83.50Mb 83.51Mb 83.52Mb Contigs < AC164634.3 Genes (Comprehensive set... < Cox7a2l-201protein coding
< Cox7a2l-202protein coding
< Cox7a2l-204retained intron
< Cox7a2l-203lncRNA
Regulatory Build
83.50Mb 83.51Mb 83.52Mb Reverse strand 35.41 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000167741
< Cox7a2l-202protein coding
Reverse strand 12.40 kb
ENSMUSP00000131... Transmembrane heli... Superfamily Cytochrome c oxidase, subunit VIIa superfamily PIRSF Cytochrome c oxidase subunit VIIa-related, mitochondrial PANTHER Cytochrome c oxidase subunit VIIa-related, mitochondrial
Cytochrome c oxidase subunit VIIa, metazoa Gene3D Cytochrome c oxidase, subunit VIIa superfamily CDD Cytochrome c oxidase subunit VIIa, metazoa
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend inframe insertion missense variant splice region variant synonymous variant
Scale bar 0 20 40 60 80 100 134
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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