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Mouse Psca Conditional Knockout Project (CRISPR/Cas9)

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Mouse Psca Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Psca Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Psca conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Psca gene (NCBI Reference Sequence: NM_028216 ; Ensembl: ENSMUSG00000022598 ) is located on Mouse chromosome 15. 3 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 3 (Transcript: ENSMUST00000023265). Exon 2~3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Psca gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-429N15 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 null mice are viable and fertile and show no significant differences in spontaneous or radiation- induced primary epithelial tumor formation relative to wild-type littermates. Exon 2~3 covers 85.91% of the coding region. Start codon is in exon 1, and stop codon is in exon 3. The size of intron 1 for 5'-loxP site insertion: 1114 bp. The size of effective cKO region: ~1799 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Homology arm Exon of mouse Psca cKO region loxP site Page 2 of 7 https://www.alphaknockout.com 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(7074bp) | A(24.85% 1758) | C(26.79% 1895) | T(21.37% 1512) | G(26.99% 1909) 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. Page 3 of 7 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr15 + 74712772 74715771 3000 browser details YourSeq 65 805 879 3000 89.1% chr8 - 4222421 4222493 73 browser details YourSeq 58 804 889 3000 79.5% chr9 + 31556339 31556409 71 browser details YourSeq 56 806 882 3000 81.6% chr1 - 36970828 36970899 72 browser details YourSeq 54 826 916 3000 96.7% chr11 - 17180785 17181094 310 browser details YourSeq 52 823 884 3000 93.5% chr1 - 12884583 12884647 65 browser details YourSeq 51 811 886 3000 93.3% chr4 + 64406803 64406880 78 browser details YourSeq 49 771 854 3000 92.8% chr2 - 110530303 110530644 342 browser details YourSeq 44 837 888 3000 94.2% chr15 + 76938352 76938405 54 browser details YourSeq 43 844 890 3000 97.9% chr6 + 93911076 93911138 63 browser details YourSeq 42 832 888 3000 86.6% chr3 + 148483304 148483359 56 browser details YourSeq 40 827 878 3000 77.8% chr14 - 20210821 20210866 46 browser details YourSeq 30 848 893 3000 74.3% chr3 + 84284439 84284477 39 browser details YourSeq 28 855 882 3000 100.0% chr17 + 60847419 60847446 28 browser details YourSeq 26 857 882 3000 100.0% chr18 - 82719921 82719946 26 browser details YourSeq 24 854 879 3000 96.2% chr16 - 72843586 72843611 26 browser details YourSeq 24 858 883 3000 96.2% chr15 + 18645111 18645136 26 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% chr15 + 74716596 74719595 3000 browser details YourSeq 197 866 1226 3000 92.0% chr13 - 3928776 4033425 104650 browser details YourSeq 154 855 1202 3000 85.2% chrX + 105918115 105918398 284 browser details YourSeq 150 866 1202 3000 94.8% chr12 - 84626518 84627111 594 browser details YourSeq 142 866 1229 3000 86.3% chr4 - 117180873 117181141 269 browser details YourSeq 139 1072 1241 3000 96.1% chr4 + 138920312 138920487 176 browser details YourSeq 136 1072 1229 3000 97.3% chr12 + 112901125 112901284 160 browser details YourSeq 135 1073 1226 3000 96.0% chr11 + 70839135 70839319 185 browser details YourSeq 134 1065 1229 3000 94.7% chr7 + 30795785 30795956 172 browser details YourSeq 132 1072 1225 3000 91.8% chr7 - 24489425 24489573 149 browser details YourSeq 131 1073 1229 3000 94.1% chr15 - 57474973 57475130 158 browser details YourSeq 130 1072 1229 3000 93.5% chr7 + 99722028 99722187 160 browser details YourSeq 130 1072 1226 3000 94.6% chr15 + 35211083 35211240 158 browser details YourSeq 129 1072 1224 3000 95.2% chr5 - 100330196 100330361 166 browser details YourSeq 129 1073 1229 3000 96.5% chr2 - 112494867 112495025 159 browser details YourSeq 129 1071 1274 3000 90.2% chr10 + 13219528 13219853 326 browser details YourSeq 129 1073 1229 3000 94.0% chr1 + 138957458 138958018 561 browser details YourSeq 128 1071 1226 3000 92.4% chr5 - 29779729 29779882 154 browser details YourSeq 128 1071 1226 3000 90.7% chr4 - 148084884 148085037 154 browser details YourSeq 128 991 1225 3000 83.5% chr15 + 62100287 62100456 170 Note: The 3000 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Psca prostate stem cell antigen [ Mus musculus (house mouse) ] Gene ID: 72373, updated on 10-Oct-2019 Gene summary Official Symbol Psca provided by MGI Official Full Name prostate stem cell antigen provided by MGI Primary source MGI:MGI:1919623 See related Ensembl:ENSMUSG00000022598 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 2210408B04Rik Expression Restricted expression toward stomach adult (RPKM 11209.1) See more Orthologs human all Genomic context Location: 15; 15 D3 See Psca in Genome Data Viewer Exon count: 3 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (74714839..74717065) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (74545269..74547495) Chromosome 15 - NC_000081.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 1 transcript Gene: Psca ENSMUSG00000022598 Description prostate stem cell antigen [Source:MGI Symbol;Acc:MGI:1919623] Gene Synonyms 2210408B04Rik Location Chromosome 15: 74,714,839-74,717,069 forward strand. GRCm38:CM001008.2 About this gene This gene has 1 transcript (splice variant), 100 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 4 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Psca-201 ENSMUST00000023265.4 860 123aa ENSMUSP00000023265.3 Protein coding CCDS27526 P57096 TSL:1 GENCODE basic APPRIS P1 22.23 kb Forward strand 74.705Mb 74.710Mb 74.715Mb 74.720Mb 74.725Mb Genes (Comprehensive set... 4933427E11Rik-201 >lncRNA Psca-201 >protein coding Gm28976-201 >processed pseudogene 4933427E11Rik-202 >lncRNA Them6-201 >protein coding Contigs AC118022.12 > Genes < Jrk-201protein coding < Slurp1-202protein coding (Comprehensive set... < Slurp1-201protein coding Regulatory Build 74.705Mb 74.710Mb 74.715Mb 74.720Mb 74.725Mb Reverse strand 22.23 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding pseudogene RNA gene Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000023265 2.23 kb Forward strand Psca-201 >protein coding ENSMUSP00000023... Low complexity (Seg) Cleavage site (Sign... Superfamily SSF57302 SMART Ly-6 antigen/uPA receptor-like Pfam Ly-6 antigen/uPA receptor-like PROSITE patterns CD59 antigen, conserved site PANTHER PTHR16983:SF1 PTHR16983 Gene3D 2.10.60.10 CDD cd00117 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 20 40 60 80 100 123 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
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