https://www.alphaknockout.com
Mouse Cox5a Knockout Project (CRISPR/Cas9)
Objective: To create a Cox5a knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Cox5a gene (NCBI Reference Sequence: NM_007747 ; Ensembl: ENSMUSG00000000088 ) is located on Mouse chromosome 9. 5 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 4 (Transcript: ENSMUST00000000090). 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:
Exon 2 starts from about 20.32% of the coding region. Exon 2~3 covers 54.57% of the coding region. The size of effective KO region: ~1407 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 5
Legends Exon of mouse Cox5a 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 1306 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(29.55% 591) | C(19.4% 388) | T(29.2% 584) | G(21.85% 437)
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(1306bp) | A(26.8% 350) | C(21.13% 276) | T(31.78% 415) | G(20.29% 265)
Note: The 1306 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% chr9 + 57526957 57528956 2000 browser details YourSeq 208 334 1029 2000 89.1% chr7 - 80163253 80163561 309 browser details YourSeq 204 334 1031 2000 89.9% chr6 + 39415368 39415871 504 browser details YourSeq 203 834 1042 2000 99.1% chr10 - 76480725 76480935 211 browser details YourSeq 202 333 1032 2000 88.5% chr3 + 89466246 89466569 324 browser details YourSeq 200 834 1037 2000 99.6% chr10 - 128047230 128047509 280 browser details YourSeq 200 821 1037 2000 98.1% chr11 + 101520872 101521090 219 browser details YourSeq 200 835 1039 2000 99.1% chr10 + 80045312 80045520 209 browser details YourSeq 199 834 1079 2000 99.1% chr1 - 86539075 86539322 248 browser details YourSeq 199 821 1041 2000 95.3% chr14 + 34541430 34541646 217 browser details YourSeq 198 835 1035 2000 99.6% chr11 - 103521008 103521213 206 browser details YourSeq 198 833 1038 2000 98.6% chr1 - 180925548 180925756 209 browser details YourSeq 198 835 1037 2000 99.6% chr5 + 144724162 144724395 234 browser details YourSeq 197 835 1037 2000 99.1% chr9 - 44768000 44768206 207 browser details YourSeq 196 831 1040 2000 96.2% chr8 - 79686174 79686382 209 browser details YourSeq 196 834 1035 2000 99.1% chr8 - 11493369 11493587 219 browser details YourSeq 196 834 1037 2000 96.5% chr1 + 88696968 88697166 199 browser details YourSeq 195 834 1037 2000 98.1% chr9 + 65978531 65978738 208 browser details YourSeq 195 834 1393 2000 91.5% chr7 + 110167646 110168177 532 browser details YourSeq 194 834 1037 2000 98.1% chr3 - 95213139 95213342 204
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 1306 1 1306 1306 100.0% chr9 + 57530364 57531669 1306 browser details YourSeq 235 191 844 1306 92.8% chrX - 94400346 94401100 755 browser details YourSeq 226 295 868 1306 87.0% chr11 + 107116122 107116667 546 browser details YourSeq 209 288 803 1306 89.1% chr14 + 20830270 20830723 454 browser details YourSeq 201 302 868 1306 88.2% chr7 + 97129967 97130399 433 browser details YourSeq 191 279 928 1306 86.2% chr11 + 76270726 76271016 291 browser details YourSeq 190 148 484 1306 88.8% chr2 - 28869476 28869786 311 browser details YourSeq 190 215 482 1306 91.8% chr9 + 22419420 22419794 375 browser details YourSeq 188 215 488 1306 94.0% chr4 + 133564974 133565366 393 browser details YourSeq 187 300 549 1306 94.4% chr11 + 117582956 117583217 262 browser details YourSeq 184 289 891 1306 87.1% chr15 - 102125587 102125994 408 browser details YourSeq 180 304 917 1306 87.2% chr2 - 24883046 24883255 210 browser details YourSeq 177 283 504 1306 94.1% chr15 + 89194579 89195046 468 browser details YourSeq 174 281 482 1306 95.4% chr8 - 110994866 110995339 474 browser details YourSeq 174 288 482 1306 97.4% chr10 + 62918043 62918286 244 browser details YourSeq 173 287 482 1306 95.9% chr2 - 121523341 121523751 411 browser details YourSeq 173 287 484 1306 94.9% chr11 - 4851439 4851639 201 browser details YourSeq 173 294 483 1306 97.4% chr9 + 58590290 58590492 203 browser details YourSeq 173 288 484 1306 94.9% chr8 + 106208244 106208446 203 browser details YourSeq 173 294 504 1306 90.9% chr19 + 29525415 29525617 203
Note: The 1306 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: Cox5a cytochrome c oxidase subunit 5A [ Mus musculus (house mouse) ] Gene ID: 12858, updated on 12-Aug-2019
Gene summary
Official Symbol Cox5a provided by MGI Official Full Name cytochrome c oxidase subunit 5A provided by MGI Primary source MGI:MGI:88474 See related Ensembl:ENSMUSG00000000088 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 CcOX; AA959768 Expression Broad expression in duodenum adult (RPKM 1236.7), stomach adult (RPKM 854.8) and 26 other tissues See more Orthologs human all
Genomic context
Location: 9; 9 B See Cox5a in Genome Data Viewer Exon count: 6
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (57517328..57532427)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 9 NC_000075.5 (57369039..57380234)
Chromosome 9 - NC_000075.6
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Transcript information: This gene has 3 transcripts
Gene: Cox5a ENSMUSG00000000088
Description cytochrome c oxidase subunit 5A [Source:MGI Symbol;Acc:MGI:88474] Gene Synonyms CcOX Location Chromosome 9: 57,521,274-57,532,426 forward strand. GRCm38:CM001002.2 About this gene This gene has 3 transcripts (splice variants), 291 orthologues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Cox5a-201 ENSMUST00000000090.7 645 146aa ENSMUSP00000000090.6 Protein coding CCDS23223 P12787 TSL:1 GENCODE basic APPRIS P1
Cox5a-202 ENSMUST00000213678.1 1818 No protein - Retained intron - - TSL:1
Cox5a-203 ENSMUST00000214154.1 605 No protein - Retained intron - - TSL:2
31.15 kb Forward strand
57.52Mb 57.53Mb 57.54Mb Genes (Comprehensive set... Cox5a-202 >retained intron Fam219b-201 >protein coding
Cox5a-201 >protein coding Fam219b-202 >protein coding
Cox5a-203 >retained intron Fam219b-203 >retained intron
Contigs < AC164548.3
Genes < Gm26631-201lncRNA (Comprehensive set...
Regulatory Build
57.52Mb 57.53Mb 57.54Mb Reverse strand 31.15 kb
Regulation Legend CTCF Enhancer Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
RNA gene processed transcript
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Transcript: ENSMUST00000000090
11.15 kb Forward strand
Cox5a-201 >protein coding
ENSMUSP00000000... Low complexity (Seg) Superfamily Cytochrome c oxidase, subunit Va/VI superfamily Pfam Cytochrome c oxidase, subunit Va/VI
PANTHER PTHR14200:SF13
Cytochrome c oxidase, subunit Va/VI Gene3D Cytochrome c oxidase, subunit Va/VI superfamily
CDD Cytochrome c oxidase, subunit Va/VI
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend synonymous variant
Scale bar 0 20 40 60 80 100 120 146
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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