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Mouse Arv1 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Arv1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Arv1 gene (NCBI Reference Sequence: NM_026855 ; Ensembl: ENSMUSG00000031982 ) is located on Mouse chromosome 8. 6 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 5 (Transcript: ENSMUST00000034463). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Arv1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-296L15 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygous KO causes female infertility, reduction in body weight, amount of white adipose tissue and plasma lipid levels and increase in adiponectin levels, food consumption, energy expenditure and activity levels.
Exon 3 starts from about 35.09% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 2953 bp, and the size of intron 3 for 3'-loxP site insertion: 2309 bp. The size of effective cKO region: ~654 bp. The cKO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele gRNA region 5' gRNA region 3'
1 3 6 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Arv1 Homology arm cKO region loxP site
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Overview of the Dot Plot Window size: 10 bp
Forward Reverse Complement
Sequence 12
Note: The sequence of homologous arms and cKO region 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 GC Content Distribution Window size: 300 bp
Sequence 12
Summary: Full Length(7154bp) | A(25.27% 1808) | C(22.24% 1591) | T(29.0% 2075) | G(23.48% 1680)
Note: The sequence of homologous arms and cKO region 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 3000 1 3000 3000 100.0% chr8 + 124725080 124728079 3000 browser details YourSeq 257 740 1036 3000 95.2% chr4 - 116790820 116791144 325 browser details YourSeq 257 728 1035 3000 95.8% chr10 + 4258685 4259291 607 browser details YourSeq 253 931 1690 3000 80.7% chr4 + 135290120 135290541 422 browser details YourSeq 244 739 1033 3000 95.2% chr4 + 59182670 59182968 299 browser details YourSeq 230 743 1035 3000 93.3% chr12 - 111197843 111198143 301 browser details YourSeq 210 729 1422 3000 88.8% chr11 - 97308250 97308707 458 browser details YourSeq 195 723 1037 3000 94.5% chr7 + 112860686 112861224 539 browser details YourSeq 187 809 1035 3000 93.9% chr13 + 3714752 3714997 246 browser details YourSeq 186 728 1036 3000 88.8% chr5 - 110631073 110631289 217 browser details YourSeq 185 728 1037 3000 88.3% chr19 + 8890159 8890365 207 browser details YourSeq 184 837 1037 3000 94.4% chr5 - 34522535 34522731 197 browser details YourSeq 183 843 1051 3000 95.6% chr10 - 5113710 5113919 210 browser details YourSeq 183 737 1036 3000 88.2% chr7 + 35538335 35538543 209 browser details YourSeq 182 837 1036 3000 95.5% chr2 - 156171484 156171683 200 browser details YourSeq 182 840 1037 3000 96.5% chr2 + 119129131 119129329 199 browser details YourSeq 179 842 1037 3000 96.5% chr2 - 128617201 128617443 243 browser details YourSeq 178 840 1037 3000 95.0% chr8 - 68058162 68058359 198 browser details YourSeq 178 836 1039 3000 95.5% chr3 - 88273537 88518871 245335 browser details YourSeq 178 732 1037 3000 89.3% chr2 - 125846516 125846764 249
Note: The 3000 bp section upstream of Exon 3 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 3000 1 3000 3000 100.0% chr8 + 124728734 124731733 3000 browser details YourSeq 136 144 1572 3000 87.1% chr5 - 127224689 127709149 484461 browser details YourSeq 130 1488 1638 3000 95.9% chr12 + 95922536 95922699 164 browser details YourSeq 125 1491 1637 3000 93.8% chr6 - 113646128 113646275 148 browser details YourSeq 124 1491 1637 3000 96.4% chr13 - 58613454 58613985 532 browser details YourSeq 123 1491 1637 3000 90.8% chr14 - 51933790 51933932 143 browser details YourSeq 123 1502 1729 3000 91.9% chr10 + 63087754 63088350 597 browser details YourSeq 121 1491 1636 3000 89.4% chr2 + 104300845 104300976 132 browser details YourSeq 120 1406 1638 3000 84.4% chr4 + 136209855 136210011 157 browser details YourSeq 117 1494 1841 3000 84.5% chr11 + 20179696 20179817 122 browser details YourSeq 116 3 256 3000 86.0% chr5 - 126105730 126106062 333 browser details YourSeq 113 1491 1632 3000 92.7% chr1 - 84611164 84611316 153 browser details YourSeq 111 8 261 3000 87.3% chr12 + 80487273 80487534 262 browser details YourSeq 109 16 256 3000 86.0% chr15 + 35188744 35189051 308 browser details YourSeq 108 1491 1637 3000 89.4% chr17 + 31700896 31701041 146 browser details YourSeq 107 20 257 3000 86.3% chrX - 95674839 95675100 262 browser details YourSeq 107 1489 1636 3000 92.8% chr12 + 99598458 99598901 444 browser details YourSeq 104 8 255 3000 79.2% chr9 + 32001732 32001946 215 browser details YourSeq 103 1491 1618 3000 94.1% chr2 + 30704052 30704180 129 browser details YourSeq 102 1489 1608 3000 95.6% chr10 - 78301383 78301651 269
Note: The 3000 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: Arv1 ARV1 homolog, fatty acid homeostasis modulator [ Mus musculus (house mouse) ] Gene ID: 68865, updated on 24-Oct-2019
Gene summary
Official Symbol Arv1 provided by MGI Official Full Name ARV1 homolog, fatty acid homeostasis modulator provided by MGI Primary source MGI:MGI:1916115 See related Ensembl:ENSMUSG00000031982 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 AI461928; AW121084; 1110067L22Rik Expression Ubiquitous expression in thymus adult (RPKM 10.0), ovary adult (RPKM 7.3) and 28 other tissues See more Orthologs human all
Genomic context
Location: 8; 8 E2 See Arv1 in Genome Data Viewer
Exon count: 7
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (124722026..124742794)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 8 NC_000074.5 (127246039..127258023)
Chromosome 8 - NC_000074.6
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Transcript information: This gene has 3 transcripts
Gene: Arv1 ENSMUSG00000031982
Description ARV1 homolog, fatty acid homeostasis modulator [Source:MGI Symbol;Acc:MGI:1916115] Gene Synonyms 1110067L22Rik Location Chromosome 8: 124,722,139-124,734,123 forward strand. GRCm38:CM001001.2 About this gene This gene has 3 transcripts (splice variants), 195 orthologues, is a member of 1 Ensembl protein family and is associated with 27 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Arv1- ENSMUST00000034463.3 1165 266aa ENSMUSP00000034463.3 Protein coding CCDS22774 Q0VBH5 TSL:1 201 Q9D0U9 GENCODE basic APPRIS P1
Arv1- ENSMUST00000212959.1 937 149aa ENSMUSP00000148335.1 Protein coding - A0A1D5RLE6 CDS 5' 203 incomplete TSL:1
Arv1- ENSMUST00000212036.1 891 112aa ENSMUSP00000148475.1 Nonsense mediated - A0A1D5RLR4 TSL:1 202 decay
31.98 kb Forward strand 124.72Mb 124.73Mb 124.74Mb Genes (Comprehensive set... Arv1-201 >protein coding
Arv1-202 >nonsense mediated decay
Arv1-203 >protein coding
Contigs < AC151736.6 Genes < Ttc13-212protein coding < Fam89a-201protein coding (Comprehensive set...
< Ttc13-202protein coding
< Ttc13-210protein coding
< Ttc13-203protein coding
< Ttc13-201protein coding
< Ttc13-205retained intron
Regulatory Build
124.72Mb 124.73Mb 124.74Mb Reverse strand 31.98 kb
Regulation Legend CTCF Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript
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Transcript: ENSMUST00000034463
11.98 kb Forward strand
Arv1-201 >protein coding
ENSMUSP00000034... Transmembrane heli... Low complexity (Seg) Pfam Arv1 protein PANTHER PTHR14467:SF0
Arv1 protein
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 40 80 120 160 200 266
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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