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Mouse Napb Conditional Knockout Project (CRISPR/Cas9)

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Mouse Napb Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Napb Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Napb conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Napb gene (NCBI Reference Sequence: NM_019632 ; Ensembl: ENSMUSG00000027438 ) is located on Mouse chromosome 2. 11 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 11 (Transcript: ENSMUST00000028926). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Napb gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-81L23 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: Mice homozygous for a knock-out allele exhibit seizures, ataxia, abnormal synaptic vesicle priming, and premature death. Exon 2 starts from about 11.07% of the coding region. The knockout of Exon 2 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 19511 bp, and the size of intron 2 for 3'-loxP site insertion: 3241 bp. The size of effective cKO region: ~580 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 gRNA region 5' gRNA region 3' 1 2 11 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Napb Homology arm 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(7080bp) | A(27.1% 1919) | C(20.96% 1484) | T(28.31% 2004) | G(23.63% 1673) 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% chr2 - 148713005 148716004 3000 browser details YourSeq 200 2711 3000 3000 86.5% chr5 - 147622371 147622661 291 browser details YourSeq 197 2701 2994 3000 84.4% chr9 - 77861013 77861306 294 browser details YourSeq 189 2705 3000 3000 85.4% chr17 - 25710627 25710925 299 browser details YourSeq 186 2715 2994 3000 85.5% chr10 - 110875742 110876020 279 browser details YourSeq 184 2701 3000 3000 81.6% chr10 - 68340224 68340522 299 browser details YourSeq 178 2711 2987 3000 84.8% chr2 + 74625262 74625527 266 browser details YourSeq 175 2714 2994 3000 88.0% chr15 - 80032431 80032710 280 browser details YourSeq 175 2706 2985 3000 83.8% chr10 - 91248041 91248320 280 browser details YourSeq 175 2701 2989 3000 87.2% chr7 + 130841553 130841841 289 browser details YourSeq 171 2701 2988 3000 88.4% chr19 - 40252311 40252611 301 browser details YourSeq 171 2711 2988 3000 85.8% chr16 - 13534880 13535159 280 browser details YourSeq 171 2712 3000 3000 87.8% chr13 - 34809656 34809944 289 browser details YourSeq 170 2711 2972 3000 91.7% chr5 - 139292303 139843394 551092 browser details YourSeq 170 2711 2989 3000 88.3% chr15 + 36941349 36941624 276 browser details YourSeq 169 2715 2989 3000 84.4% chr10 + 70899326 70899587 262 browser details YourSeq 168 2704 2989 3000 83.4% chr13 - 49089546 49089833 288 browser details YourSeq 168 2714 2974 3000 81.8% chrX + 12530318 12530556 239 browser details YourSeq 166 2711 2989 3000 84.3% chr5 - 90970438 90970716 279 browser details YourSeq 166 2703 2989 3000 85.6% chr19 + 55373673 55373948 276 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% chr2 - 148709425 148712424 3000 browser details YourSeq 460 1135 1679 3000 95.0% chr15 + 70391513 70392225 713 browser details YourSeq 401 1206 1680 3000 93.2% chr14 + 94705974 94706695 722 browser details YourSeq 400 1246 1690 3000 95.7% chr12 + 17046059 17046509 451 browser details YourSeq 399 1246 1696 3000 94.5% chr1 - 163649866 163650340 475 browser details YourSeq 395 1246 1695 3000 93.1% chr11 + 106074379 106074825 447 browser details YourSeq 394 1246 1679 3000 95.9% chr5 - 105448169 105448607 439 browser details YourSeq 393 1246 1686 3000 95.2% chr6 + 106869249 106869703 455 browser details YourSeq 392 1248 1686 3000 95.9% chr12 + 40878540 40878994 455 browser details YourSeq 390 1246 1684 3000 95.0% chr16 - 41122124 41122575 452 browser details YourSeq 390 1246 1695 3000 93.8% chrX + 6700549 6701013 465 browser details YourSeq 389 1246 1681 3000 94.8% chr14 - 123574060 123574496 437 browser details YourSeq 389 1246 1691 3000 94.0% chrX + 62442230 62442687 458 browser details YourSeq 389 1246 1680 3000 95.0% chr8 + 104843494 104843941 448 browser details YourSeq 388 1247 1691 3000 93.3% chrX - 6954514 6954957 444 browser details YourSeq 388 1246 1693 3000 93.2% chrX + 59218514 59218960 447 browser details YourSeq 387 1246 1689 3000 93.9% chr6 - 39864607 39865058 452 browser details YourSeq 387 1246 1684 3000 94.4% chr2 - 20265628 20266069 442 browser details YourSeq 387 1246 1685 3000 95.0% chr6 + 46909485 46909938 454 browser details YourSeq 387 1246 1676 3000 95.2% chr6 + 45601925 45602367 443 Note: The 3000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Napb N-ethylmaleimide sensitive fusion protein attachment protein beta [ Mus musculus (house mouse) ] Gene ID: 17957, updated on 12-Aug-2019 Gene summary Official Symbol Napb provided by MGI Official Full Name N-ethylmaleimide sensitive fusion protein attachment protein beta provided by MGI Primary source MGI:MGI:104562 See related Ensembl:ENSMUSG00000027438 Gene type protein coding RefSeq status PROVISIONAL Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as I47; E161; Brp14; SNARE; b-SNAP Expression Biased expression in frontal lobe adult (RPKM 69.4), cortex adult (RPKM 55.9) and 5 other tissues See more Orthologs human all Genomic context Location: 2; 2 G3 See Napb in Genome Data Viewer Exon count: 11 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (148693985..148732425, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (148520393..148558156, complement) Chromosome 2 - NC_000068.7 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 3 transcripts Gene: Napb ENSMUSG00000027438 Description N-ethylmaleimide sensitive fusion protein attachment protein beta [Source:MGI Symbol;Acc:MGI:104562] Gene Synonyms Brp14, E161, I47, SNARE, b-SNAP Location Chromosome 2: 148,693,985-148,732,467 reverse strand. GRCm38:CM000995.2 About this gene This gene has 3 transcripts (splice variants), 262 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 7 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Napb- ENSMUST00000028926.12 4412 298aa ENSMUSP00000028926.6 Protein coding CCDS16842 P28663 TSL:1 201 GENCODE basic APPRIS P1 Napb- ENSMUST00000136513.1 4311 115aa ENSMUSP00000120979.1 Nonsense mediated - D6RHL2 TSL:5 202 decay Napb- ENSMUST00000140647.1 3087 No - Retained intron - - TSL:2 203 protein 58.48 kb Forward strand 148.69Mb 148.70Mb 148.71Mb 148.72Mb 148.73Mb 148.74Mb Genes Gzf1-201 >protein coding (Comprehensive set... Gzf1-202 >protein coding Gzf1-203 >lncRNA Contigs AL928638.7 > AL844519.9 > Genes (Comprehensive set... < Napb-202nonsense mediated decay < Napb-201protein coding < Napb-203retained intron Regulatory Build 148.69Mb 148.70Mb 148.71Mb 148.72Mb 148.73Mb 148.74Mb Reverse strand 58.48 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding processed transcript RNA gene Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000028926 < Napb-201protein coding Reverse strand 38.48 kb ENSMUSP00000028... Low complexity (Seg) Coiled-coils (Ncoils) Superfamily Tetratricopeptide-like helical domain superfamily Prints NSF attachment protein Pfam PF14938 PANTHER PTHR13768:SF12 NSF attachment protein Gene3D Tetratricopeptide-like helical domain superfamily CDD NSF attachment protein All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend stop gained missense variant splice region variant synonymous variant Scale bar 0 40 80 120 160 200 240 298 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
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