https://www.alphaknockout.com
Mouse Atp5g3 Knockout Project (CRISPR/Cas9)
Objective: To create a Atp5g3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Atp5g3 gene (NCBI Reference Sequence: NM_001301721 ; Ensembl: ENSMUSG00000018770 ) is located on Mouse chromosome 2. 5 exons are identified, with the ATG start codon in exon 2 and the TAA stop codon in exon 5 (Transcript: ENSMUST00000111996). Exon 2~5 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 0.24% of the coding region. Exon 2~5 covers 100.0% of the coding region. The size of effective KO region: ~2396 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 5
Legends Exon of mouse Atp5g3 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 start codon 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 stop codon 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(27.95% 559) | C(23.35% 467) | T(23.55% 471) | G(25.15% 503)
Note: The 2000 bp section upstream of start codon is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(30.5% 610) | C(19.05% 381) | T(25.8% 516) | G(24.65% 493)
Note: The 2000 bp section downstream of stop codon 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% chr2 - 73910994 73912993 2000 browser details YourSeq 175 427 792 2000 88.7% chr1 + 131984080 131984477 398 browser details YourSeq 170 433 786 2000 83.2% chr5 - 142156061 142156401 341 browser details YourSeq 170 427 791 2000 87.4% chr16 - 18693079 18693423 345 browser details YourSeq 170 442 783 2000 90.5% chr13 + 48990563 49285617 295055 browser details YourSeq 169 479 786 2000 89.0% chr1 + 153141936 153142243 308 browser details YourSeq 167 428 783 2000 88.7% chr10 - 43347745 43348099 355 browser details YourSeq 164 430 785 2000 87.9% chr10 + 61119153 61119653 501 browser details YourSeq 163 481 774 2000 84.9% chr8 - 86817246 86817528 283 browser details YourSeq 163 461 774 2000 85.1% chr5 - 129453483 129453780 298 browser details YourSeq 161 479 786 2000 82.8% chr7 + 122935658 122943964 8307 browser details YourSeq 161 481 786 2000 85.6% chr1 + 190732200 190732496 297 browser details YourSeq 160 421 725 2000 87.4% chr9 + 55056635 55056944 310 browser details YourSeq 158 461 786 2000 81.0% chr3 - 65762415 65762725 311 browser details YourSeq 158 479 793 2000 90.4% chr18 - 74055491 74055899 409 browser details YourSeq 153 479 797 2000 90.0% chr1 - 154892509 154892841 333 browser details YourSeq 152 473 786 2000 89.4% chr12 + 70005283 70005613 331 browser details YourSeq 152 487 791 2000 84.0% chr1 + 63404875 63405160 286 browser details YourSeq 151 422 791 2000 80.5% chr4 - 83172961 83173231 271 browser details YourSeq 151 465 783 2000 83.1% chr16 - 18188497 18188796 300
Note: The 2000 bp section upstream of start codon 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% chr2 - 73906596 73908595 2000 browser details YourSeq 304 507 1867 2000 91.1% chr4 - 154009302 154069083 59782 browser details YourSeq 303 514 1869 2000 91.8% chr14 - 45367760 45496755 128996 browser details YourSeq 205 596 1985 2000 92.6% chr5 - 121217264 121344277 127014 browser details YourSeq 165 973 1985 2000 91.6% chr3 + 88690579 88715776 25198 browser details YourSeq 141 514 670 2000 93.2% chr6 + 144916732 144916878 147 browser details YourSeq 140 606 1123 2000 93.2% chr4 + 132412850 132413369 520 browser details YourSeq 140 514 676 2000 92.7% chr4 + 120292742 120292893 152 browser details YourSeq 137 510 1026 2000 80.9% chr3 + 95252506 95252753 248 browser details YourSeq 136 507 672 2000 88.9% chr11 + 60429879 60430032 154 browser details YourSeq 136 510 680 2000 90.5% chr10 + 67317342 67317491 150 browser details YourSeq 134 514 666 2000 95.1% chr19 + 10516337 10516487 151 browser details YourSeq 132 507 659 2000 91.0% chr4 - 150020662 150020806 145 browser details YourSeq 132 506 676 2000 91.0% chr6 + 48390476 48390644 169 browser details YourSeq 132 507 669 2000 90.8% chr4 + 48237645 48237802 158 browser details YourSeq 131 506 1062 2000 81.1% chr16 + 96072611 96072897 287 browser details YourSeq 130 978 1123 2000 95.2% chr11 - 79732765 79732914 150 browser details YourSeq 129 510 654 2000 92.0% chr18 - 22898719 22898854 136 browser details YourSeq 129 514 674 2000 90.4% chr17 + 69248227 69248381 155 browser details YourSeq 128 514 659 2000 92.0% chr14 + 101852052 101852188 137
Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Atp5g3 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9) [ Mus musculus (house mouse) ] Gene ID: 228033, updated on 12-Aug-2019
Gene summary
Official Symbol Atp5g3 provided by MGI Official Full Name ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9) provided by MGI Primary source MGI:MGI:2442035 See related Ensembl:ENSMUSG00000018770 Gene type protein coding RefSeq status REVIEWED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as Atp5mc3; 6030447M23 Summary The protein encoded by this gene is a subunit of mitochondrial membrane ATP synthase, the enzyme that catalyzes ATP Expression synthesis during oxidative phosphorylation. This gene encodes subunit 9, which is present in multiple copies in the transmembrane part of the ATP synthase complex. Phenotype and gene expression profiles suggest correlations between this gene and alcoholism- and obesity-related phenotypes. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Sep 2014] Orthologs Ubiquitous expression in heart adult (RPKM 896.5), kidney adult (RPKM 502.3) and 27 other tissues See more human all
Genomic context
Location: 2; 2 C3 See Atp5g3 in Genome Data Viewer Exon count: 6
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (73908447..73912464, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (73746507..73749351, complement)
Chromosome 2 - NC_000068.7
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Transcript information: This gene has 5 transcripts
Gene: Atp5g3 ENSMUSG00000018770
Description ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9) [Source:MGI Symbol;Acc:MGI:2442035] Location Chromosome 2: 73,908,447-73,911,326 reverse strand. GRCm38:CM000995.2 About this gene This gene has 5 transcripts (splice variants), 172 orthologues, 2 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Atp5g3-202 ENSMUST00000111996.7 723 141aa ENSMUSP00000107627.1 Protein coding CCDS16136 P56384 Q14BC2 TSL:2 GENCODE basic APPRIS P1
Atp5g3-201 ENSMUST00000018914.2 714 141aa ENSMUSP00000018914.2 Protein coding CCDS16136 P56384 Q14BC2 TSL:1 GENCODE basic APPRIS P1
Atp5g3-204 ENSMUST00000142768.7 862 No protein - lncRNA - - TSL:2
Atp5g3-203 ENSMUST00000131045.1 791 No protein - lncRNA - - TSL:2
Atp5g3-205 ENSMUST00000155474.1 770 No protein - lncRNA - - TSL:2
22.88 kb Forward strand
73.90Mb 73.91Mb 73.92Mb Contigs AL844581.7 >
Genes (Comprehensive set... < Atp5g3-201protein coding
< Atp5g3-202protein coding
< Atp5g3-204lncRNA
< Atp5g3-203lncRNA
< Atp5g3-205lncRNA
Regulatory Build
73.90Mb 73.91Mb 73.92Mb Reverse strand 22.88 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
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Transcript: ENSMUST00000111996
< Atp5g3-202protein coding
Reverse strand 2.88 kb
ENSMUSP00000107... Transmembrane heli... Low complexity (Seg) Superfamily F/V-ATP synthase subunit C superfamily Prints ATP synthase, F0 complex, subunit C Pfam V-ATPase proteolipid subunit C-like domain
PROSITE patterns ATP synthase, F0 complex, subunit C, DCCD-binding site
PANTHER ATP synthase, F0 complex, subunit C
PTHR10031:SF31 HAMAP ATP synthase, F0 complex, subunit C Gene3D F1F0 ATP synthase subunit C superfamily CDD cd18182
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 20 40 60 80 100 120 141
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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