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Mouse Rabac1 Knockout Project (CRISPR/Cas9)

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Mouse Rabac1 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Rabac1 Knockout Project (CRISPR/Cas9) Objective: To create a Rabac1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Rabac1 gene (NCBI Reference Sequence: NM_010261 ; Ensembl: ENSMUSG00000003380 ) is located on Mouse chromosome 7. 5 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 5 (Transcript: ENSMUST00000076961). Exon 1~5 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 1 starts from about 0.18% of the coding region. Exon 1~5 covers 100.0% of the coding region. The size of effective KO region: ~2657 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 3 4 5 Legends Exon of mouse Rabac1 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(25.65% 513) | C(27.7% 554) | T(25.3% 506) | G(21.35% 427) 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(24.65% 493) | C(26.35% 527) | T(22.45% 449) | G(26.55% 531) 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% chr7 - 24972583 24974582 2000 browser details YourSeq 98 3 147 2000 80.6% chr10 + 126146270 126146408 139 browser details YourSeq 95 3 136 2000 84.7% chr3 - 83003775 83003907 133 browser details YourSeq 89 2 134 2000 83.5% chr4 - 103181280 103181412 133 browser details YourSeq 88 7 144 2000 82.6% chr8 - 128708275 128708410 136 browser details YourSeq 88 1 134 2000 82.9% chr4 - 118327394 118327527 134 browser details YourSeq 88 2 121 2000 89.4% chr11 - 62109451 62109573 123 browser details YourSeq 88 2 131 2000 87.1% chr1 - 157422345 157422537 193 browser details YourSeq 87 2 132 2000 84.3% chr14 - 20983029 20983161 133 browser details YourSeq 86 14 129 2000 85.3% chr2 - 132207057 132207171 115 browser details YourSeq 85 2 134 2000 85.4% chr12 - 25151378 25151509 132 browser details YourSeq 85 14 143 2000 83.1% chrX + 7636566 7636697 132 browser details YourSeq 84 2 134 2000 88.5% chr7 - 126222317 126222448 132 browser details YourSeq 84 7 143 2000 82.9% chr11 - 6197536 6197676 141 browser details YourSeq 84 8 131 2000 83.9% chr4 + 118966270 118966393 124 browser details YourSeq 83 1 121 2000 84.9% chr18 - 32076461 32076582 122 browser details YourSeq 83 5 134 2000 82.2% chr5 + 128062550 128062681 132 browser details YourSeq 83 2 126 2000 83.8% chr11 + 120637935 120638060 126 browser details YourSeq 82 21 125 2000 89.6% chr12 - 54809763 54814142 4380 browser details YourSeq 82 8 121 2000 86.0% chr11 - 102966181 102966294 114 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% chr7 - 24967924 24969923 2000 browser details YourSeq 272 237 1652 2000 92.0% chr10 - 63000526 63327033 326508 browser details YourSeq 138 265 871 2000 84.5% chr10 - 44023490 44287514 264025 browser details YourSeq 115 237 491 2000 86.2% chr10 + 128403396 128403794 399 browser details YourSeq 108 239 900 2000 87.5% chr11 + 96564165 96898566 334402 browser details YourSeq 102 240 481 2000 84.9% chr11 - 85175090 85175332 243 browser details YourSeq 101 236 478 2000 85.9% chr8 - 25502961 25503526 566 browser details YourSeq 98 232 479 2000 84.1% chr7 - 34318815 34319190 376 browser details YourSeq 95 239 478 2000 77.9% chr8 - 121845959 121846172 214 browser details YourSeq 95 391 1107 2000 78.8% chr6 + 72639364 72639930 567 browser details YourSeq 90 235 478 2000 81.2% chr1 - 160861625 160861912 288 browser details YourSeq 83 241 478 2000 84.5% chr11 + 57699822 57700193 372 browser details YourSeq 81 235 480 2000 85.9% chr1 - 91432401 91432701 301 browser details YourSeq 79 237 482 2000 85.1% chr12 + 102298612 102298929 318 browser details YourSeq 75 265 482 2000 89.4% chr9 + 44269215 44269701 487 browser details YourSeq 74 284 482 2000 90.3% chr11 + 20364331 20751636 387306 browser details YourSeq 73 786 895 2000 86.2% chr17 + 29114493 29114603 111 browser details YourSeq 65 402 482 2000 93.3% chr14 + 34215295 34215376 82 browser details YourSeq 63 788 878 2000 86.3% chr5 + 128372364 128372461 98 browser details YourSeq 61 237 308 2000 98.5% chr7 - 28190176 28190247 72 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: Rabac1 Rab acceptor 1 (prenylated) [ Mus musculus (house mouse) ] Gene ID: 14470, updated on 12-Aug-2019 Gene summary Official Symbol Rabac1 provided by MGI Official Full Name Rab acceptor 1 (prenylated) provided by MGI Primary source MGI:MGI:1201692 See related Ensembl:ENSMUSG00000003380 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 PRA1; Gbpap1; prenylin; 2310040I06Rik Expression Ubiquitous expression in lung adult (RPKM 327.7), adrenal adult (RPKM 305.5) and 28 other tissues See more Orthologs human all Genomic context Location: 7; 7 A3 See Rabac1 in Genome Data Viewer Exon count: 5 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (24969750..24972728, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 7 NC_000073.5 (25754769..25757747, complement) Chromosome 7 - NC_000073.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 6 transcripts Gene: Rabac1 ENSMUSG00000003380 Description Rab acceptor 1 (prenylated) [Source:MGI Symbol;Acc:MGI:1201692] Gene Synonyms 2310040I06Rik, Gbpap1, PRA1, prenylin Location Chromosome 7: 24,969,752-24,972,754 reverse strand. GRCm38:CM001000.2 About this gene This gene has 6 transcripts (splice variants), 163 orthologues, is a member of 1 Ensembl protein family and is associated with 6 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Rabac1-201 ENSMUST00000076961.8 899 185aa ENSMUSP00000076227.7 Protein coding CCDS20968 Q9Z0S9 TSL:1 GENCODE basic APPRIS P1 Rabac1-203 ENSMUST00000205871.1 986 226aa ENSMUSP00000146042.1 Protein coding - A0A0U1RPM3 TSL:1 GENCODE basic Rabac1-202 ENSMUST00000205771.1 599 No protein - Retained intron - - TSL:1 Rabac1-204 ENSMUST00000206222.1 583 No protein - Retained intron - - TSL:2 Rabac1-206 ENSMUST00000206941.1 530 No protein - lncRNA - - TSL:2 Rabac1-205 ENSMUST00000206868.1 473 No protein - lncRNA - - TSL:3 23.00 kb Forward strand 24.96Mb 24.97Mb 24.98Mb Contigs AC125468.5 > Genes (Comprehensive set... < Rabac1-201protein coding < Atp1a3-201protein coding < Rabac1-204retained intron < Atp1a3-202protein coding < Rabac1-203protein coding < Atp1a3-205protein coding < Rabac1-205lncRNA < Rabac1-206lncRNA < Mir7046-201miRNA < Rabac1-202retained intron Regulatory Build 24.96Mb 24.97Mb 24.98Mb Reverse strand 23.00 kb Regulation Legend CTCF Enhancer Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding processed transcript RNA gene Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000076961 < Rabac1-201protein coding Reverse strand 3.00 kb ENSMUSP00000076... Transmembrane heli... Pfam Prenylated rab acceptor PRA1 PANTHER PTHR19317:SF0 Prenylated rab acceptor PRA1 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant splice region variant synonymous variant Scale bar 0 20 40 60 80 100 120 140 160 185 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
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