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Mouse Stard13 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Stard13 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Stard13 gene (NCBI Reference Sequence: NM_001163493 ; Ensembl: ENSMUSG00000016128 ) is located on Mouse chromosome 5. 14 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 14 (Transcript: ENSMUST00000062015). Exon 5 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Stard13 gene. 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: Mice homozygous for a knock-out allele exhibit small body size, decreased weight, and reduced adipose tissue. Mice homozygous for another knock-out allele exhibit increased angiogenesis in matrigel plugs and implanted tumors.
Exon 5 starts from about 11.43% of the coding region. The knockout of Exon 5 will result in frameshift of the gene. The size of intron 4 for 5'-loxP site insertion: 9644 bp, and the size of intron 5 for 3'-loxP site insertion: 1374 bp. The size of effective cKO region: ~1861 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'
1 5 6 14 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Stard13 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. Tandem repeats are found in the dot plot matrix. It may be difficult to construct this targeting vector.
Overview of the GC Content Distribution Window size: 300 bp
Sequence 12
Summary: Full Length(8361bp) | A(26.93% 2252) | C(21.76% 1819) | T(28.88% 2415) | G(22.43% 1875)
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% chr5 - 151063907 151066906 3000 browser details YourSeq 89 297 417 3000 95.1% chr10 + 111104734 111104874 141 browser details YourSeq 58 324 424 3000 92.7% chr11 + 70470663 70470773 111 browser details YourSeq 56 314 425 3000 80.4% chr11 - 38947717 38947798 82 browser details YourSeq 52 297 369 3000 81.7% chr10 + 111104842 111104903 62 browser details YourSeq 46 325 402 3000 92.4% chr13 + 73422700 73422901 202 browser details YourSeq 43 389 438 3000 94.0% chr14 - 38127840 38127890 51 browser details YourSeq 42 2579 2835 3000 63.3% chr14 + 81462945 81463056 112 browser details YourSeq 40 365 417 3000 91.4% chr14 - 21683547 21683598 52 browser details YourSeq 39 364 412 3000 93.4% chr19 + 45511737 45511786 50 browser details YourSeq 39 2899 2939 3000 92.5% chr10 + 90150678 90150717 40 browser details YourSeq 38 323 375 3000 82.0% chr13 - 93022944 93022994 51 browser details YourSeq 33 323 364 3000 88.6% chr14 - 21683503 21683542 40 browser details YourSeq 32 909 941 3000 100.0% chr12 - 75787096 75787135 40 browser details YourSeq 32 13 73 3000 91.9% chr13 + 61104186 61104247 62 browser details YourSeq 31 370 406 3000 94.5% chr12 + 15910956 15911008 53 browser details YourSeq 30 39 160 3000 96.9% chr13 - 57767745 57767866 122 browser details YourSeq 29 15 73 3000 94.0% chr12 - 93107035 93107094 60 browser details YourSeq 29 2651 2776 3000 54.6% chr11 + 91863238 91863287 50 browser details YourSeq 28 2868 2896 3000 100.0% chrX + 109880749 109880778 30
Note: The 3000 bp section upstream of Exon 5 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% chr5 - 151059046 151062045 3000 browser details YourSeq 112 580 748 3000 85.9% chr9 - 108072970 108073133 164 browser details YourSeq 106 597 752 3000 94.4% chr17 - 10993790 10993960 171 browser details YourSeq 106 586 765 3000 86.3% chr15 + 101806823 101806992 170 browser details YourSeq 104 584 750 3000 81.2% chr1 - 86741725 86741873 149 browser details YourSeq 101 617 841 3000 80.5% chr6 + 3238413 3238571 159 browser details YourSeq 95 598 738 3000 90.4% chr1 - 88554439 88554583 145 browser details YourSeq 93 593 766 3000 80.6% chr6 - 89127377 89127517 141 browser details YourSeq 91 605 752 3000 81.9% chr16 - 93111565 93111692 128 browser details YourSeq 86 666 800 3000 87.5% chr9 - 123992046 123992166 121 browser details YourSeq 85 632 752 3000 93.9% chr10 - 24706034 24706264 231 browser details YourSeq 85 637 744 3000 95.9% chr15 + 96902504 96902640 137 browser details YourSeq 83 617 747 3000 88.3% chr7 - 18857496 18857670 175 browser details YourSeq 82 666 761 3000 95.7% chr1 - 40848871 40849051 181 browser details YourSeq 82 661 765 3000 95.8% chr3 + 66809487 66809602 116 browser details YourSeq 81 643 752 3000 94.7% chr16 + 38733776 38733950 175 browser details YourSeq 80 588 714 3000 82.9% chr8 + 45065485 45065606 122 browser details YourSeq 79 593 712 3000 92.4% chr7 - 110605981 110606101 121 browser details YourSeq 77 597 757 3000 95.5% chr7 - 46383473 46383645 173 browser details YourSeq 77 666 764 3000 92.5% chr1 - 39864048 39864150 103
Note: The 3000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Stard13 StAR-related lipid transfer (START) domain containing 13 [ Mus musculus (house mouse) ] Gene ID: 243362, updated on 12-Aug-2019
Gene summary
Official Symbol Stard13 provided by MGI Official Full Name StAR-related lipid transfer (START) domain containing 13 provided by MGI Primary source MGI:MGI:2385331 See related Ensembl:ENSMUSG00000016128 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 DLC2; GT650 Expression Broad expression in lung adult (RPKM 12.8), bladder adult (RPKM 6.2) and 23 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 G3 See Stard13 in Genome Data Viewer
Exon count: 19
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (151037515..151428200, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (151840090..151992768, complement)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 10 transcripts
Gene: Stard13 ENSMUSG00000016128
Description StAR-related lipid transfer (START) domain containing 13 [Source:MGI Symbol;Acc:MGI:2385331] Gene Synonyms DLC2, GT650 Location Chromosome 5: 151,037,510-151,233,836 reverse strand. GRCm38:CM000998.2 About this gene This gene has 10 transcripts (splice variants), 233 orthologues, 3 paralogues, is a member of 1 Ensembl protein family and is associated with 13 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Stard13-202 ENSMUST00000110483.8 5662 1113aa ENSMUSP00000106109.2 Protein coding CCDS19890 Q923Q2 TSL:1 GENCODE basic APPRIS P3
Stard13-201 ENSMUST00000062015.14 5526 1132aa ENSMUSP00000053232.8 Protein coding CCDS51710 F8WIY7 TSL:1 GENCODE basic APPRIS ALT2
Stard13-208 ENSMUST00000202111.3 3373 995aa ENSMUSP00000144056.1 Protein coding - A0A0J9YU82 TSL:5 GENCODE basic
Stard13-203 ENSMUST00000126770.1 457 111aa ENSMUSP00000122468.1 Protein coding - D3Z5Y1 CDS 3' incomplete TSL:3
Stard13-204 ENSMUST00000129088.7 449 129aa ENSMUSP00000116705.1 Protein coding - D3Z418 CDS 3' incomplete TSL:3
Stard13-206 ENSMUST00000146814.4 2480 No protein - Retained intron - - TSL:1
Stard13-207 ENSMUST00000201680.3 644 No protein - lncRNA - - TSL:3
Stard13-205 ENSMUST00000141117.7 442 No protein - lncRNA - - TSL:3
Stard13-209 ENSMUST00000202385.3 251 No protein - lncRNA - - TSL:3
Stard13-210 ENSMUST00000202866.1 243 No protein - lncRNA - - TSL:5
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216.33 kb Forward strand 151.05Mb 151.10Mb 151.15Mb 151.20Mb Contigs AC163219.3 > AC109614.9 > Genes (Comprehensive set... < Stard13-202protein coding
< Stard13-201protein coding
< Stard13-208protein coding
< Stard13-207lncRNA
< Stard13-209lncRNA < Stard13-210lncRNA
< Gm42906-201protein coding
< Stard13-204protein coding
< Stard13-205lncRNA
< Stard13-206retained intron
< Stard13-203protein coding
Regulatory Build
151.05Mb 151.10Mb 151.15Mb 151.20Mb Reverse strand 216.33 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 processed transcript
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Transcript: ENSMUST00000062015
< Stard13-201protein coding
Reverse strand 152.57 kb
ENSMUSP00000053... MobiDB lite Low complexity (Seg) Superfamily Sterile alpha motif/pointed domain superfamily SSF55961
Rho GTPase activation protein SMART Rho GTPase-activating protein domain
START domain Pfam Sterile alpha motif domain Rho GTPase-activating protein domain
START domain PROSITE profiles START domain
Rho GTPase-activating protein domain PANTHER PTHR12659:SF6
PTHR12659 Gene3D Rho GTPase activation protein START-like domain superfamily
CDD cd09592 cd04375
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend stop gained missense variant synonymous variant
Scale bar 0 100 200 300 400 500 600 700 800 900 1000 1132
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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