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Mouse Adamtsl4 Knockout Project (CRISPR/Cas9)

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Mouse Adamtsl4 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Adamtsl4 Knockout Project (CRISPR/Cas9) Objective: To create a Adamtsl4 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Adamtsl4 gene (NCBI Reference Sequence: NM_001301705 ; Ensembl: ENSMUSG00000015850 ) is located on Mouse chromosome 3. 18 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 18 (Transcript: ENSMUST00000117782). Exon 2~18 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 0.03% of the coding region. Exon 2~18 covers 100.0% of the coding region. The size of effective KO region: ~8638 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 8 11 12 13 14 15 16 17 18 Legends Exon of mouse Adamtsl4 Knockout region Page 2 of 8 https://www.alphaknockout.com 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. Page 3 of 8 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(22.5% 450) | C(27.95% 559) | T(21.5% 430) | G(28.05% 561) Note: The 2000 bp section upstream of start 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. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(21.0% 420) | C(27.7% 554) | T(26.1% 522) | G(25.2% 504) 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. Page 4 of 8 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr3 - 95685476 95687475 2000 browser details YourSeq 31 315 357 2000 97.0% chr19 + 40992000 40992454 455 browser details YourSeq 22 314 336 2000 100.0% chr9 + 33447023 33447046 24 browser details YourSeq 21 317 337 2000 100.0% chr17 - 84817421 84817441 21 browser details YourSeq 21 195 215 2000 100.0% chr12 - 3856641 3856661 21 browser details YourSeq 21 549 569 2000 100.0% chr5 + 68069756 68069776 21 browser details YourSeq 21 1651 1671 2000 100.0% chr15 + 34464846 34464866 21 browser details YourSeq 20 314 333 2000 100.0% chr9 - 73558199 73558218 20 browser details YourSeq 20 319 338 2000 100.0% chr11 + 14021634 14021653 20 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% chr3 - 95674836 95676835 2000 browser details YourSeq 128 1697 1987 2000 89.6% chr2 + 133582751 133583083 333 browser details YourSeq 105 1731 1997 2000 90.0% chr16 + 31295502 31295838 337 browser details YourSeq 97 1711 1990 2000 90.0% chr19 - 11823216 11823498 283 browser details YourSeq 88 1733 1997 2000 92.4% chr8 + 121686111 121686381 271 browser details YourSeq 85 1725 1990 2000 92.1% chr6 - 54471161 54471468 308 browser details YourSeq 83 1703 1990 2000 88.7% chr7 - 64547980 64548317 338 browser details YourSeq 83 1726 1990 2000 92.8% chr10 + 43125754 43126037 284 browser details YourSeq 81 1764 1990 2000 90.8% chr7 - 128046081 128046356 276 browser details YourSeq 81 1756 1990 2000 91.9% chr14 + 27026906 27027147 242 browser details YourSeq 80 1703 1943 2000 88.4% chr10 + 95512578 95512846 269 browser details YourSeq 79 1736 1989 2000 88.6% chr19 - 34516751 34517040 290 browser details YourSeq 75 1726 1990 2000 90.5% chr15 - 12311306 12311576 271 browser details YourSeq 72 1733 1974 2000 88.3% chr14 + 31518515 31518783 269 browser details YourSeq 69 1874 1990 2000 85.6% chr4 + 141441100 141441211 112 browser details YourSeq 69 1756 1956 2000 92.6% chr18 + 11790258 11790463 206 browser details YourSeq 65 1759 1990 2000 89.2% chr5 - 127639046 127639302 257 browser details YourSeq 65 1731 1823 2000 93.5% chr19 + 21087250 21087356 107 browser details YourSeq 65 1697 1794 2000 91.1% chr14 + 36794665 36794762 98 browser details YourSeq 63 1756 1990 2000 91.9% chr4 - 129378880 129379145 266 Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found. Page 5 of 8 https://www.alphaknockout.com Gene and protein information: Adamtsl4 ADAMTS-like 4 [ Mus musculus (house mouse) ] Gene ID: 229595, updated on 12-Aug-2019 Gene summary Official Symbol Adamtsl4 provided by MGI Official Full Name ADAMTS-like 4 provided by MGI Primary source MGI:MGI:2389008 See related Ensembl:ENSMUSG00000015850 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 Tsrc1; ADAMTSL-4 Summary The protein encoded by this gene is a member of the ADAMTS superfamily of secreted proteins, which contain a Expression metalloprotease domain at the N-terminus and a C-terminal ancillary domain. ADAMTS-like proteins lack protease activity and resemble the ancillary domain of ADAMTS proteins. ADAMTS-like proteins have been implicated in regulation of the extracellular matrix. The encoded protein contains 7 thrombospondin type 1 repeats, a conserved extracellular domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014] Orthologs Broad expression in lung adult (RPKM 18.4), bladder adult (RPKM 18.2) and 17 other tissues See more human all Genomic context Location: 3; 3 F2.1 See Adamtsl4 in Genome Data Viewer Exon count: 19 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (95676201..95687927, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (95480127..95491781, complement) Chromosome 3 - NC_000069.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 5 transcripts Gene: Adamtsl4 ENSMUSG00000015850 Description ADAMTS-like 4 [Source:MGI Symbol;Acc:MGI:2389008] Gene Synonyms Tsrc1 Location Chromosome 3: 95,676,201-95,687,917 reverse strand. GRCm38:CM000996.2 About this gene This gene has 5 transcripts (splice variants), 130 orthologues, 25 paralogues, is a member of 1 Ensembl protein family and is associated with 10 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Adamtsl4-202 ENSMUST00000117782.7 4036 1036aa ENSMUSP00000113424.1 Protein coding CCDS17618 Q80T21 TSL:1 GENCODE basic APPRIS P1 Adamtsl4-201 ENSMUST00000015994.3 3856 1036aa ENSMUSP00000015994.3 Protein coding CCDS17618 Q80T21 TSL:1 GENCODE basic APPRIS P1 Adamtsl4-204 ENSMUST00000148854.1 452 70aa ENSMUSP00000120844.1 Protein coding - D3Z0T6 CDS 3' incomplete TSL:3 Adamtsl4-203 ENSMUST00000124410.1 403 No protein - lncRNA - - TSL:3 Adamtsl4-205 ENSMUST00000151054.1 288 No protein - lncRNA - - TSL:3 31.72 kb Forward strand 95.67Mb 95.68Mb 95.69Mb Contigs < AC092479.16 Genes < Adamtsl4-202protein coding (Comprehensive set... < Adamtsl4-201protein coding < Adamtsl4-205lncRNA < Adamtsl4-204protein coding < Adamtsl4-203lncRNA Regulatory Build 95.67Mb 95.68Mb 95.69Mb Reverse strand 31.72 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 Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000117782 < Adamtsl4-202protein coding Reverse strand 11.72 kb ENSMUSP00000113... MobiDB lite Low complexity (Seg) Cleavage site (Sign... Superfamily Thrombospondin type-1 (TSP1) repeat superfamily SMART Thrombospondin type-1 (TSP1) repeat Pfam ADAM-TS Spacer 1 PLAC Thrombospondin type-1 (TSP1) repeat PROSITE profiles Thrombospondin type-1 (TSP1) repeat PLAC PANTHER PTHR13723 PTHR13723:SF144 Gene3D 2.60.120.830 Thrombospondin type-1 (TSP1) repeat superfamily All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 100 200 300 400 500 600 700 800 900 1036 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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