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Mouse Oxld1 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Oxld1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Oxld1 gene (NCBI Reference Sequence: NM_025560 ; Ensembl: ENSMUSG00000039670 ) is located on Mouse chromosome 11. 2 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 2 (Transcript: ENSMUST00000044007). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Oxld1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-463A13 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:
Exon 2 covers 65.67% of the coding region. Start codon is in exon 1, and stop codon is in exon 2. The size of intron 1 for 5'-loxP site insertion: 650 bp. The size of effective cKO region: ~1307 bp. The cKO 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'
2 1 1 2 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Homology arm Exon of mouse Ccdc137 Exon of mouse Oxld1 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(6896bp) | A(27.04% 1865) | C(26.0% 1793) | T(22.32% 1539) | G(24.64% 1699)
Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. Significant high GC-content regions are found. It may be difficult to construct this targeting vector.
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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% chr11 - 120457413 120460412 3000 browser details YourSeq 370 147 2282 3000 89.0% chr10 + 44169938 44170396 459 browser details YourSeq 302 756 2994 3000 92.2% chr1 + 151095276 151472391 377116 browser details YourSeq 253 1102 1456 3000 90.5% chr18 + 56679959 56680453 495 browser details YourSeq 232 1136 1468 3000 92.7% chr1 - 93833531 93834246 716 browser details YourSeq 229 1113 1428 3000 87.8% chr4 + 98770492 98770798 307 browser details YourSeq 200 1123 1385 3000 90.4% chr9 + 121726762 121727015 254 browser details YourSeq 191 1123 1394 3000 93.3% chr5 + 103251209 103251608 400 browser details YourSeq 184 1103 1393 3000 92.6% chr14 + 55570294 55570599 306 browser details YourSeq 176 1142 1420 3000 85.1% chr17 + 29860752 29861012 261 browser details YourSeq 173 1135 1357 3000 94.9% chr7 + 80890281 80890668 388 browser details YourSeq 172 1120 1379 3000 88.8% chr6 - 124765069 124765648 580 browser details YourSeq 160 766 1236 3000 90.0% chr4 + 116969212 116969830 619 browser details YourSeq 159 784 1236 3000 86.1% chr15 + 98573663 98573969 307 browser details YourSeq 153 1124 1411 3000 88.1% chr9 - 64940117 64940613 497 browser details YourSeq 147 784 1244 3000 83.5% chr17 + 28755473 28755790 318 browser details YourSeq 146 1166 1456 3000 88.9% chr5 - 115763390 115834965 71576 browser details YourSeq 145 1279 1468 3000 92.9% chr8 - 113060903 113061102 200 browser details YourSeq 145 784 1263 3000 81.2% chr13 + 97033249 97033550 302 browser details YourSeq 142 1281 1467 3000 90.9% chr19 + 47022388 47022580 193
Note: The 3000 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 3000 1 3000 3000 100.0% chr11 - 120453767 120456766 3000 browser details YourSeq 288 667 1006 3000 93.9% chr5 + 65742898 65743541 644 browser details YourSeq 287 674 1006 3000 94.8% chr6 - 125298380 125298732 353 browser details YourSeq 285 682 1006 3000 94.5% chr5 - 31025840 31026209 370 browser details YourSeq 284 679 1007 3000 94.1% chr5 + 130255743 130256293 551 browser details YourSeq 281 669 1006 3000 94.9% chr6 + 38379084 38528239 149156 browser details YourSeq 273 674 1006 3000 93.4% chr16 + 32968358 32968761 404 browser details YourSeq 271 674 995 3000 93.7% chr11 - 53834483 53834879 397 browser details YourSeq 270 669 997 3000 93.9% chr8 + 33698938 33699383 446 browser details YourSeq 268 680 1003 3000 92.5% chr1 + 86412321 86412971 651 browser details YourSeq 263 666 1029 3000 93.5% chr6 + 72168019 72326813 158795 browser details YourSeq 261 699 1029 3000 90.2% chr10 - 80091087 80091401 315 browser details YourSeq 242 682 1006 3000 92.5% chr11 - 87432041 87432344 304 browser details YourSeq 239 674 963 3000 93.2% chr5 - 123387669 123387967 299 browser details YourSeq 216 667 985 3000 93.6% chr8 - 94197195 94197733 539 browser details YourSeq 216 681 968 3000 93.3% chr11 - 87396657 87397171 515 browser details YourSeq 211 667 909 3000 94.6% chr7 - 92653851 92654503 653 browser details YourSeq 208 695 1008 3000 92.6% chr14 - 73338261 73338717 457 browser details YourSeq 205 679 966 3000 94.8% chr7 + 49591291 49591880 590 browser details YourSeq 204 663 921 3000 93.6% chr16 + 16919083 16919602 520
Note: The 3000 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: Oxld1 oxidoreductase like domain containing 1 [ Mus musculus (house mouse) ] Gene ID: 66431, updated on 14-Aug-2019
Gene summary
Official Symbol Oxld1 provided by MGI Official Full Name oxidoreductase like domain containing 1 provided by MGI Primary source MGI:MGI:1913681 See related Ensembl:ENSMUSG00000039670 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 1810049H13Rik Expression Ubiquitous expression in adrenal adult (RPKM 28.4), kidney adult (RPKM 16.4) and 28 other tissues See more Orthologs human all
Genomic context
Location: 11; 11 E2 See Oxld1 in Genome Data Viewer
Exon count: 2
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (120456601..120458070, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (120317918..120319377, complement)
Chromosome 11 - NC_000077.6
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Transcript information: This gene has 2 transcripts
Gene: Oxld1 ENSMUSG00000039670
Description oxidoreductase like domain containing 1 [Source:MGI Symbol;Acc:MGI:1913681] Gene Synonyms 1810049H13Rik Location Chromosome 11: 120,456,606-120,458,068 reverse strand. GRCm38:CM001004.2 About this gene This gene has 2 transcripts (splice variants), 162 orthologues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Oxld1- ENSMUST00000044007.2 813 201aa ENSMUSP00000036860.2 Protein CCDS25735 B2RVP3 TSL:1 201 coding Q9CR10 GENCODE basic APPRIS P2
Oxld1- ENSMUST00000137632.1 372 124aa ENSMUSP00000135197.1 Protein - H3BK04 CDS 5' and 3' 202 coding incomplete TSL:1 APPRIS ALT2
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21.46 kb Forward strand 120.450Mb 120.455Mb 120.460Mb 120.465Mb Genes Tspan10-201 >protein coding Ccdc137-201 >protein coding Hgs-201 >protein coding (Comprehensive set...
Ccdc137-205 >lncRNA Ccdc137-204 >lncRNA Hgs-202 >protein coding
Ccdc137-202 >retained intron Hgs-204 >protein coding
Ccdc137-206 >protein coding Hgs-205 >lncRNA
Ccdc137-207 >protein coding
Ccdc137-208 >lncRNA
Ccdc137-203 >retained intron
Contigs AL669855.20 > Genes (Comprehensive set... < Pde6g-202lncRNA < Oxld1-201protein coding < Arl16-208lncRNA
< Pde6g-203lncRNA < Oxld1-202protein coding < Arl16-201protein coding
< Pde6g-201protein coding < Arl16-203lncRNA
< Arl16-207lncRNA
< Arl16-204lncRNA
< Arl16-210lncRNA
< Arl16-211lncRNA
< Arl16-205lncRNA
< Arl16-202lncRNA
< Arl16-209lncRNA
< Arl16-206lncRNA
Regulatory Build
120.450Mb 120.455Mb 120.460Mb 120.465Mb Reverse strand 21.46 kb
Regulation Legend CTCF Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding merged Ensembl/Havana
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000044007
< Oxld1-201protein coding
Reverse strand 1.46 kb
ENSMUSP00000036... MobiDB lite Low complexity (Seg) Pfam Oxidoreductase-like, N-terminal PANTHER Oxidoreductase-like domain-containing protein 1
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 20 40 60 80 100 120 140 160 180 201
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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