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Mouse Fcho2 Knockout Project (CRISPR/Cas9)

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Mouse Fcho2 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Fcho2 Knockout Project (CRISPR/Cas9) Objective: To create a Fcho2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Fcho2 gene (NCBI Reference Sequence: NM_172591 ; Ensembl: ENSMUSG00000041685 ) is located on Mouse chromosome 13. 26 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 26 (Transcript: ENSMUST00000040340). Exon 3~5 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 3 starts from about 5.19% of the coding region. Exon 3~5 covers 15.25% of the coding region. The size of effective KO region: ~7005 bp. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 3 4 5 26 Legends Exon of mouse Fcho2 Knockout region Page 2 of 9 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 Exon 3 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 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. Page 3 of 9 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(27.75% 555) | C(18.9% 378) | T(31.8% 636) | G(21.55% 431) Note: The 2000 bp section upstream of Exon 3 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(29.85% 597) | C(18.7% 374) | T(33.95% 679) | G(17.5% 350) Note: The 2000 bp section downstream 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. Page 4 of 9 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% chr13 - 98796368 98798367 2000 browser details YourSeq 156 1733 1902 2000 95.8% chr2 + 30734988 30735156 169 browser details YourSeq 152 1741 1918 2000 92.4% chr6 - 116124756 116124931 176 browser details YourSeq 152 1734 1910 2000 93.2% chr15 + 62054286 62054462 177 browser details YourSeq 152 1741 1918 2000 95.3% chr10 + 88755912 88756094 183 browser details YourSeq 150 1733 1909 2000 92.1% chr8 - 32809203 32809373 171 browser details YourSeq 150 1734 1900 2000 92.3% chr18 - 77042804 77042958 155 browser details YourSeq 150 1733 1900 2000 95.8% chr1 + 179565239 179573650 8412 browser details YourSeq 148 1737 1904 2000 93.1% chr6 + 120218626 120218789 164 browser details YourSeq 147 1733 1900 2000 93.4% chr6 - 100546629 100546795 167 browser details YourSeq 147 1739 1902 2000 92.9% chr19 + 60941620 60941772 153 browser details YourSeq 144 1733 1902 2000 89.6% chr16 - 33911170 33911331 162 browser details YourSeq 144 1744 1907 2000 95.0% chr14 - 49152515 49152686 172 browser details YourSeq 143 1733 1900 2000 91.0% chr3 - 116876551 116876716 166 browser details YourSeq 143 1733 1906 2000 93.0% chr11 - 119002431 119002611 181 browser details YourSeq 143 1735 1899 2000 92.2% chr3 + 33850284 33850439 156 browser details YourSeq 143 1733 1901 2000 91.2% chr11 + 11903674 11903835 162 browser details YourSeq 142 1735 1899 2000 92.4% chr16 - 55637545 55637705 161 browser details YourSeq 142 1735 1902 2000 93.9% chr2 + 75732666 75732836 171 browser details YourSeq 142 1745 1902 2000 96.8% chr17 + 74543251 74543416 166 Note: The 2000 bp section upstream of Exon 3 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% chr13 - 98787363 98789362 2000 browser details YourSeq 176 1532 1773 2000 92.3% chr16 + 17602270 17602570 301 browser details YourSeq 166 1570 1780 2000 91.2% chr4 - 133174626 133175142 517 browser details YourSeq 164 1113 1754 2000 82.9% chr9 - 44665910 44666387 478 browser details YourSeq 163 1572 1776 2000 88.1% chr17 - 29645026 29645218 193 browser details YourSeq 162 1572 1757 2000 94.6% chr8 + 84221045 84221452 408 browser details YourSeq 161 1572 1758 2000 94.1% chr11 - 86998875 87061458 62584 browser details YourSeq 161 1567 1766 2000 91.7% chr7 + 112394352 112394551 200 browser details YourSeq 161 1508 1744 2000 94.0% chr3 + 116498720 116499149 430 browser details YourSeq 160 1506 1747 2000 94.1% chr1 - 165381726 165382055 330 browser details YourSeq 160 1574 1776 2000 92.2% chr13 + 55123995 55124510 516 browser details YourSeq 159 1572 1774 2000 87.7% chr3 - 95939725 95939910 186 browser details YourSeq 159 1555 1757 2000 90.8% chr7 + 92378282 92378490 209 browser details YourSeq 159 1573 1777 2000 91.2% chr11 + 54669647 54670291 645 browser details YourSeq 157 1572 1779 2000 91.1% chr3 + 88423144 88423502 359 browser details YourSeq 157 1571 1778 2000 87.3% chr13 + 12604991 12605182 192 browser details YourSeq 156 1572 1757 2000 91.8% chr19 - 9021901 9022085 185 browser details YourSeq 156 1556 1740 2000 90.0% chr16 + 94617127 94617305 179 browser details YourSeq 156 1572 1757 2000 91.8% chr15 + 99663617 99663801 185 browser details YourSeq 156 1571 1757 2000 92.0% chr13 + 62748512 62748699 188 Note: The 2000 bp section downstream of Exon 5 is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Fcho2 FCH domain only 2 [ Mus musculus (house mouse) ] Gene ID: 218503, updated on 10-Oct-2019 Gene summary Official Symbol Fcho2 provided by MGI Official Full Name FCH domain only 2 provided by MGI Primary source MGI:MGI:3505790 See related Ensembl:ENSMUSG00000041685 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 AA387320; 5832424M12Rik Expression Ubiquitous expression in bladder adult (RPKM 10.4), placenta adult (RPKM 8.8) and 28 other tissues See more Orthologs human all Genomic context Location: 13; 13 D1 See Fcho2 in Genome Data Viewer Exon count: 26 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (98723406..98816577, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 13 NC_000079.5 (99493361..99585404, complement) Chromosome 13 - NC_000079.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 12 transcripts Gene: Fcho2 ENSMUSG00000041685 Description FCH domain only 2 [Source:MGI Symbol;Acc:MGI:3505790] Gene Synonyms 5832424M12Rik Location Chromosome 13: 98,723,403-98,815,449 reverse strand. GRCm38:CM001006.2 About this gene This gene has 12 transcripts (splice variants), 210 orthologues, 5 paralogues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Fcho2- ENSMUST00000040340.15 5122 809aa ENSMUSP00000042959.8 Protein coding CCDS56897 Q3UQN2 TSL:1 201 GENCODE basic APPRIS P1 Fcho2- ENSMUST00000224992.1 2964 395aa ENSMUSP00000153477.1 Protein coding - A0A286YDL7 GENCODE 208 basic Fcho2- ENSMUST00000179563.7 1586 414aa ENSMUSP00000137422.1 Protein coding - J3QPQ1 TSL:5 204 GENCODE basic Fcho2- ENSMUST00000109403.1 1523 394aa ENSMUSP00000105030.1 Protein coding - Q3UQN2 TSL:5 203 GENCODE basic Fcho2- ENSMUST00000225840.1 944 281aa ENSMUSP00000153040.1 Protein coding - A0A286YCL2 CDS 3' 211 incomplete Fcho2- ENSMUST00000099277.11 4979 356aa ENSMUSP00000096883.5 Nonsense mediated - F6RG68 TSL:5 202 decay Fcho2- ENSMUST00000223634.1 3221 No - Retained intron - - - 205 protein Fcho2- ENSMUST00000225945.1 2764 No - Retained intron - - - 212 protein Fcho2- ENSMUST00000225318.1 2437 No - Retained intron - - - 210 protein Fcho2- ENSMUST00000225094.1 1927 No - Retained intron - - - 209 protein Fcho2- ENSMUST00000224416.1 407 No - Retained intron - - - 207 protein Fcho2- ENSMUST00000224231.1 744 No - lncRNA - - - 206 protein Page 7 of 9 https://www.alphaknockout.com 112.05 kb Forward strand 98.72Mb 98.74Mb 98.76Mb 98.78Mb 98.80Mb 98.82Mb Genes Gm47550-201 >TEC Gm47551-201 >lncRNA (Comprehensive set... Gm18134-201 >processed pseudogene Contigs AC129085.6 > Genes (Comprehensive set... < Gm9465-201lncRNA < Fcho2-205retained intron < Fcho2-211protein coding < Fcho2-201protein coding < Fcho2-202nonsense mediated decay < Fcho2-210retained intron < Fcho2-209retained intron < Fcho2-212retained intron < Fcho2-204protein coding < Fcho2-208protein coding < Fcho2-203protein coding < Fcho2-206lncRNA < D130062J10Rik-201lncRNA <
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