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Mouse Uqcrq Knockout Project (CRISPR/Cas9)

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Mouse Uqcrq Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Uqcrq Knockout Project (CRISPR/Cas9) Objective: To create a Uqcrq knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Uqcrq gene (NCBI Reference Sequence: NM_025352 ; Ensembl: ENSMUSG00000044894 ) is located on Mouse chromosome 11. 2 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 2 (Transcript: ENSMUST00000061326). Exon 1~2 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 1 starts from about 0.41% of the coding region. Exon 1~2 covers 100.0% of the coding region. The size of effective KO region: ~1629 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 Legends Exon of mouse Uqcrq 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. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. 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(27.7% 554) | C(26.1% 522) | T(23.7% 474) | G(22.5% 450) 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(28.15% 563) | C(22.2% 444) | T(26.95% 539) | G(22.7% 454) 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% chr11 - 53430690 53432689 2000 browser details YourSeq 39 1 265 2000 97.7% chr14 + 31626746 31627130 385 browser details YourSeq 37 1 55 2000 78.1% chr3 - 90185120 90185165 46 browser details YourSeq 37 183 264 2000 93.1% chr5 + 99629441 99629524 84 browser details YourSeq 36 1 54 2000 80.0% chr4 + 41086070 41086116 47 browser details YourSeq 36 1 50 2000 77.8% chr18 + 10230006 10230050 45 browser details YourSeq 35 1 50 2000 77.8% chr5 + 65323146 65323191 46 browser details YourSeq 30 1 40 2000 77.2% chr2 + 3237976 3238010 35 browser details YourSeq 29 1 40 2000 80.7% chr19 - 46807818 46807852 35 browser details YourSeq 29 121 155 2000 91.5% chrX + 60559514 60559548 35 browser details YourSeq 28 160 193 2000 91.2% chr7 - 5049554 5049587 34 browser details YourSeq 28 1 28 2000 100.0% chr15 - 38098548 38098575 28 browser details YourSeq 26 1 28 2000 96.5% chrX - 120935576 120935603 28 browser details YourSeq 26 1 26 2000 100.0% chr4 - 19632487 19632512 26 browser details YourSeq 26 1 26 2000 100.0% chr2 - 144539909 144539934 26 browser details YourSeq 26 1 26 2000 100.0% chr17 - 32469417 32469442 26 browser details YourSeq 26 1 26 2000 100.0% chr11 - 85356195 85356220 26 browser details YourSeq 26 130 155 2000 100.0% chr9 + 66873002 66873027 26 browser details YourSeq 26 1 28 2000 96.5% chr4 + 101414374 101414401 28 browser details YourSeq 26 1 28 2000 96.5% chr16 + 44017265 44017292 28 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% chr11 - 53427059 53429058 2000 browser details YourSeq 175 1077 1603 2000 85.5% chr5 + 144950950 144951294 345 browser details YourSeq 161 1045 1600 2000 83.0% chr11 + 95787665 95787964 300 browser details YourSeq 156 1050 1623 2000 81.6% chr15 - 8454955 8455226 272 browser details YourSeq 154 1101 1623 2000 81.5% chr2 + 34853172 34853566 395 browser details YourSeq 152 1051 1601 2000 82.8% chr18 - 56759485 56759860 376 browser details YourSeq 143 1690 1890 2000 94.5% chr19 - 21622029 21622237 209 browser details YourSeq 129 1078 1601 2000 84.4% chr14 + 26529020 26529482 463 browser details YourSeq 121 1075 1578 2000 87.7% chr7 - 29416332 29416833 502 browser details YourSeq 120 1054 1696 2000 82.3% chr10 + 95920828 95921458 631 browser details YourSeq 117 1050 1574 2000 92.8% chr13 + 110438072 110438605 534 browser details YourSeq 116 1075 1262 2000 90.3% chr14 - 50832625 50832815 191 browser details YourSeq 114 1049 1266 2000 84.7% chr10 + 112919878 112920078 201 browser details YourSeq 113 1075 1474 2000 79.0% chr18 - 60034696 60034879 184 browser details YourSeq 112 1041 1231 2000 92.5% chr7 - 118632429 118632626 198 browser details YourSeq 110 1098 1603 2000 80.4% chr5 + 143492257 143492455 199 browser details YourSeq 109 1050 1261 2000 83.9% chr4 + 31818966 31819163 198 browser details YourSeq 107 1050 1263 2000 82.0% chr13 + 35642361 35642559 199 browser details YourSeq 104 1052 1262 2000 89.3% chr13 - 62836274 62836486 213 browser details YourSeq 103 1050 1200 2000 89.8% chr1 - 78291204 78689947 398744 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: Uqcrq ubiquinol-cytochrome c reductase, complex III subunit VII [ Mus musculus (house mouse) ] Gene ID: 22272, updated on 11-Sep-2019 Gene summary Official Symbol Uqcrq provided by MGI Official Full Name ubiquinol-cytochrome c reductase, complex III subunit VII provided by MGI Primary source MGI:MGI:107807 See related Ensembl:ENSMUSG00000044894 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 Qpc; QP-C; Uqcrb; c1502; 9.5kDa; AA959903; 1100001F06Rik; 1500040F11Rik; 5830407L17Rik Expression Ubiquitous expression in duodenum adult (RPKM 291.7), liver adult (RPKM 266.1) and 28 other tissues See more Orthologs human all Genomic context Location: 11; 11 B1.3 See Uqcrq in Genome Data Viewer Exon count: 2 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (53427922..53430831, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (53242450..53244333, complement) Chromosome 11 - NC_000077.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 4 transcripts Gene: Uqcrq ENSMUSG00000044894 Description ubiquinol-cytochrome c reductase, complex III subunit VII [Source:MGI Symbol;Acc:MGI:107807] Gene Synonyms 1100001F06Rik, 1500040F11Rik, 5830407L17Rik, QP-C, Qpc, c1502 Location Chromosome 11: 53,427,922-53,430,831 reverse strand. GRCm38:CM001004.2 About this gene This gene has 4 transcripts (splice variants), 203 orthologues, is a member of 1 Ensembl protein family and is associated with 3 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Uqcrq-201 ENSMUST00000061326.4 1521 82aa ENSMUSP00000053145.4 Protein coding CCDS36151 Q9CQ69 TSL:1 GENCODE basic APPRIS P1 Uqcrq-203 ENSMUST00000109021.3 405 82aa ENSMUSP00000104649.3 Protein coding CCDS36151 Q9CQ69 TSL:1 GENCODE basic APPRIS P1 Uqcrq-202 ENSMUST00000109019.7 504 37aa ENSMUSP00000104647.1 Protein coding - I7HPX6 TSL:2 GENCODE basic Uqcrq-204 ENSMUST00000156503.1 375 No protein - lncRNA - - TSL:2 22.91 kb Forward strand 53.42Mb 53.43Mb 53.44Mb Genes Aff4-201 >protein coding Gdf9-203 >lncRNA (Comprehensive set... Gdf9-202 >lncRNA Gdf9-201 >protein coding Contigs AL592489.13 > Genes < Leap2-201protein coding < Uqcrq-201protein coding (Comprehensive set... < Uqcrq-204lncRNA < Uqcrq-203protein coding < Uqcrq-202protein coding Regulatory Build 53.42Mb 53.43Mb 53.44Mb Reverse strand 22.91 kb Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding RNA gene Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000061326 < Uqcrq-201protein coding Reverse strand 2.91 kb ENSMUSP00000053... Superfamily Cytochrome b-c1 complex subunit 8 superfamily Pfam Cytochrome b-c1 complex subunit 8 PANTHER Cytochrome b-c1 complex subunit 8 Gene3D Cytochrome b-c1 complex subunit 8 superfamily All sequence SNPs/i... Sequence variants (dbSNP and all other sources) R Y Variant Legend splice region variant synonymous variant Scale bar 0 8 16 24 32 40 48 56 64 72 82 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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