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Mouse Riox1 Knockout Project (CRISPR/Cas9)

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Mouse Riox1 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Riox1 Knockout Project (CRISPR/Cas9) Objective: To create a Riox1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Riox1 gene (NCBI Reference Sequence: NM_023633.3 ; Ensembl: ENSMUSG00000046791 ) is located on Mouse chromosome 12. 1 exon is identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 1 (Transcript: ENSMUST00000053744). Exon 1 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 activated in mesenchyme exhibit increased body length and weight, increased ossification with increased bone mass, bone mineral density, and volume, increased osteoblasts; and decrease osteoclasts. Exon 1 starts from about 0.06% of the coding region. Exon 1 covers 100.0% of the coding region. The size of effective KO region: ~1809 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 Legends Exon of mouse Riox1 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. 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 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(31.3% 626) | C(22.5% 450) | T(23.3% 466) | G(22.9% 458) 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(23.3% 466) | C(20.05% 401) | T(30.3% 606) | G(26.35% 527) 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% chr12 + 83948693 83950692 2000 browser details YourSeq 245 295 794 2000 83.2% chr2 - 158245415 158245872 458 browser details YourSeq 245 289 791 2000 83.2% chr17 + 32500904 32501402 499 browser details YourSeq 244 302 795 2000 84.7% chr2 + 103817133 103817621 489 browser details YourSeq 231 304 794 2000 86.7% chr12 - 54301686 54302173 488 browser details YourSeq 219 323 792 2000 82.4% chr11 + 109130333 109130791 459 browser details YourSeq 216 321 788 2000 82.3% chr6 + 83606452 83606909 458 browser details YourSeq 207 305 795 2000 82.7% chr7 + 27412022 27412478 457 browser details YourSeq 203 301 814 2000 84.9% chr6 - 49387005 49387565 561 browser details YourSeq 202 301 794 2000 82.4% chr7 - 127722484 127722969 486 browser details YourSeq 200 293 789 2000 88.6% chr11 - 67449349 67449843 495 browser details YourSeq 197 295 794 2000 86.2% chr1 + 193596281 193596754 474 browser details YourSeq 196 301 790 2000 83.9% chr5 + 97407098 97407540 443 browser details YourSeq 195 356 794 2000 81.7% chr18 - 34235113 34235519 407 browser details YourSeq 194 376 794 2000 86.5% chr9 - 32653318 32653728 411 browser details YourSeq 192 293 818 2000 83.9% chr16 - 20568922 20569381 460 browser details YourSeq 190 364 795 2000 85.2% chr16 + 95544403 95544842 440 browser details YourSeq 187 376 795 2000 85.1% chr9 + 62609685 62610087 403 browser details YourSeq 187 436 794 2000 86.5% chr5 + 24681579 24681930 352 browser details YourSeq 176 301 725 2000 83.0% chr18 - 45429213 45429629 417 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% chr12 + 83952502 83954501 2000 browser details YourSeq 224 568 1781 2000 93.2% chr15 + 58085815 58136081 50267 browser details YourSeq 200 605 1786 2000 91.3% chr11 + 77360114 77591344 231231 browser details YourSeq 159 1584 1782 2000 91.0% chr15 - 53107819 53108016 198 browser details YourSeq 149 1609 1778 2000 95.3% chr18 - 56651601 56651785 185 browser details YourSeq 147 1582 1780 2000 90.2% chr10 - 115346119 115346317 199 browser details YourSeq 144 1580 1783 2000 90.5% chr7 + 97347062 97347265 204 browser details YourSeq 140 1582 1780 2000 84.8% chr16 + 30497786 30497959 174 browser details YourSeq 140 1617 1782 2000 93.3% chr12 + 100685868 100686036 169 browser details YourSeq 138 1622 1799 2000 89.9% chr2 + 157226733 157226909 177 browser details YourSeq 137 1617 1780 2000 93.7% chr11 + 21897278 21897442 165 browser details YourSeq 134 1622 1781 2000 91.0% chr14 - 61032266 61032423 158 browser details YourSeq 133 1617 1781 2000 91.4% chr2 - 113062528 113062694 167 browser details YourSeq 133 1620 1781 2000 93.0% chr14 + 90248796 90248958 163 browser details YourSeq 132 1627 1783 2000 92.4% chr17 + 24247580 24247737 158 browser details YourSeq 130 1622 1780 2000 92.8% chr18 - 45895695 45895854 160 browser details YourSeq 130 1603 1781 2000 88.8% chr1 + 118620159 118620327 169 browser details YourSeq 127 1628 1780 2000 92.7% chr11 + 50181705 50181871 167 browser details YourSeq 126 1622 1785 2000 91.5% chr14 + 72641555 72641718 164 browser details YourSeq 125 526 696 2000 93.2% chr11 - 85399434 85399916 483 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: Riox1 ribosomal oxygenase 1 [ Mus musculus (house mouse) ] Gene ID: 71952, updated on 26-Jun-2020 Gene summary Official Symbol Riox1 provided by MGI Official Full Name ribosomal oxygenase 1 provided by MGI Primary source MGI:MGI:1919202 See related Ensembl:ENSMUSG00000046791 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 NO66; MAPJD; 2410016O06Rik Orthologs human all Genomic context Location: 12; 12 D1 See Riox1 in Genome Data Viewer Exon count: 1 Annotation release Status Assembly Chr Location 108.20200622 current GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (83950608..83952953) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 12 NC_000078.5 (85291558..85293903) Chromosome 12 - NC_000078.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 1 transcript Gene: Riox1 ENSMUSG00000046791 Description ribosomal oxygenase 1 [Source:MGI Symbol;Acc:MGI:1919202] Gene Synonyms 2410016O06Rik, NO66 Location Chromosome 12: 83,950,608-83,952,951 forward strand. GRCm38:CM001005.2 About this gene This gene has 1 transcript (splice variant), 231 orthologues, 1 paralogue and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Riox1-201 ENSMUST00000053744.8 2344 603aa ENSMUSP00000057984.7 Protein coding CCDS26033 Q9JJF3 TSL:NA GENCODE basic APPRIS P1 22.34 kb Forward strand 83.945Mb 83.950Mb 83.955Mb 83.960Mb Genes (Comprehensive set... Riox1-201 >protein coding Contigs < AC133183.3 Genes < Gm26571-204antisense < Heatr4-201protein coding (Comprehensive set... < Gm26571-203antisense < Gm26571-201antisense < Gm26571-205antisense < Gm26571-202antisense Regulatory Build 83.945Mb 83.950Mb 83.955Mb 83.960Mb Reverse strand 22.34 kb Regulation Legend CTCF Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding processed transcript Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000053744 2.34 kb Forward strand Riox1-201 >protein coding ENSMUSP00000057... MobiDB lite Low complexity (Seg) Superfamily SSF51197 SMART JmjC domain Pfam JmjC domain PROSITE profiles JmjC domain PANTHER JmjC domain-containing Gene3D 2.60.120.650 1.10.10.1500 1.10.10.1520 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 60 120 180 240 300 360 420 480 540 603 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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