https://www.alphaknockout.com
Mouse Stard13 Knockout Project (CRISPR/Cas9)
Objective: To create a Stard13 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 5~6 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: 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. Exon 5~6 covers 45.2% of the coding region. The size of effective KO region: ~2909 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 5 6 14
Legends Exon of mouse Stard13 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 5 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 1072 bp section downstream of Exon 6 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(35.3% 706) | C(15.25% 305) | T(28.0% 560) | G(21.45% 429)
Note: The 2000 bp section upstream of Exon 5 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(1072bp) | A(29.2% 313) | C(20.15% 216) | T(27.52% 295) | G(23.13% 248)
Note: The 1072 bp section downstream of Exon 6 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% chr5 - 151063657 151065656 2000 browser details YourSeq 77 1415 1846 2000 94.5% chr14 - 30595435 30595874 440 browser details YourSeq 75 1431 1689 2000 82.8% chr14 - 110560144 110560364 221 browser details YourSeq 73 1329 1879 2000 72.5% chr10 + 99367321 99367594 274 browser details YourSeq 69 1650 1850 2000 91.4% chr1 - 41986302 41986544 243 browser details YourSeq 65 1436 1848 2000 70.3% chr14 + 116223732 116223828 97 browser details YourSeq 56 1761 1871 2000 77.0% chr11 + 68125891 68125970 80 browser details YourSeq 55 1728 1843 2000 82.6% chr6 - 106804035 106804139 105 browser details YourSeq 55 1506 1846 2000 67.2% chr13 - 46887261 46887353 93 browser details YourSeq 54 1752 1844 2000 75.4% chr11 - 40143502 40143574 73 browser details YourSeq 53 1761 1855 2000 84.2% chr14 + 116457081 116457170 90 browser details YourSeq 53 1633 1693 2000 96.6% chr12 + 115413984 115414044 61 browser details YourSeq 52 1638 1694 2000 98.2% chr12 - 96185447 96185503 57 browser details YourSeq 50 1782 1856 2000 93.2% chr5 + 151063801 151063875 75 browser details YourSeq 50 1763 1848 2000 80.8% chr11 + 18960264 18960341 78 browser details YourSeq 45 1508 1848 2000 61.6% chr10 - 60995312 60995374 63 browser details YourSeq 45 1430 1811 2000 58.9% chr13 + 27287175 27287225 51 browser details YourSeq 44 1624 1847 2000 65.4% chr10 - 111881125 111881175 51 browser details YourSeq 43 1763 1852 2000 92.2% chr1 - 33890794 33890898 105 browser details YourSeq 43 1763 1811 2000 95.9% chr11 + 39275000 39275054 55
Note: The 2000 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 1072 1 1072 1072 100.0% chr5 - 151059676 151060747 1072 browser details YourSeq 27 660 688 1072 89.3% chr1 + 72455335 72455362 28 browser details YourSeq 25 376 400 1072 100.0% chr13 + 29501873 29501897 25 browser details YourSeq 23 1011 1033 1072 100.0% chr5 + 9241796 9241818 23 browser details YourSeq 22 588 610 1072 100.0% chr14 - 54697836 54697859 24 browser details YourSeq 22 1012 1036 1072 95.9% chr11 + 101070998 101071026 29 browser details YourSeq 20 1012 1031 1072 100.0% chr1 + 100321103 100321122 20
Note: The 1072 bp section downstream of Exon 6 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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