https://www.alphaknockout.com
Mouse Exoc6 Knockout Project (CRISPR/Cas9)
Objective: To create a Exoc6 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Exoc6 gene (NCBI Reference Sequence: NM_175353 ; Ensembl: ENSMUSG00000053799 ) is located on Mouse chromosome 19. 22 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 22 (Transcript: ENSMUST00000066439). Exon 2~7 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: Homozygotes for a spontaneous mutation exhibit severe microcytic anemia, erythrocyte hyperchromia, and markedly increased levels of red cell protoporphyrin.
Exon 2 starts from about 4.23% of the coding region. Exon 2~7 covers 29.77% of the coding region. The size of effective KO region: ~8193 bp. The KO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele 5' gRNA region gRNA region 3'
1 2 3 4 5 6 7 22
Legends Exon of mouse Exoc6 Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 2000 bp section upstream of Exon 2 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 7 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(27.4% 548) | C(19.2% 384) | T(29.25% 585) | G(24.15% 483)
Note: The 2000 bp section upstream of Exon 2 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(21.85% 437) | C(22.35% 447) | T(35.3% 706) | G(20.5% 410)
Note: The 2000 bp section downstream of Exon 7 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.
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BLAT Search Results (up)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 2000 1 2000 2000 100.0% chr19 + 37568384 37570383 2000 browser details YourSeq 190 273 613 2000 89.6% chr15 - 53242973 53243257 285 browser details YourSeq 190 421 622 2000 97.6% chr11 - 80254012 80254221 210 browser details YourSeq 185 421 614 2000 98.0% chr5 + 150714877 150715077 201 browser details YourSeq 184 418 617 2000 97.0% chr1 + 182335498 182335697 200 browser details YourSeq 183 418 618 2000 96.5% chr2 + 97741211 97741421 211 browser details YourSeq 182 421 614 2000 97.5% chr5 - 139950800 139951001 202 browser details YourSeq 181 421 613 2000 97.5% chr15 - 8814004 8814204 201 browser details YourSeq 181 418 614 2000 96.9% chr6 + 128504439 128504649 211 browser details YourSeq 181 421 614 2000 96.9% chr4 + 136492749 136493129 381 browser details YourSeq 181 418 614 2000 96.9% chr11 + 69971098 69971295 198 browser details YourSeq 180 422 613 2000 97.4% chr5 - 144745962 144746161 200 browser details YourSeq 180 423 633 2000 92.1% chr5 - 139113082 139113288 207 browser details YourSeq 180 424 615 2000 97.4% chr16 - 29901460 29901659 200 browser details YourSeq 180 422 614 2000 96.9% chr12 - 28616328 28616524 197 browser details YourSeq 180 418 613 2000 96.9% chr9 + 21371245 21371451 207 browser details YourSeq 180 421 618 2000 94.4% chr5 + 30213681 30213875 195 browser details YourSeq 179 418 613 2000 96.5% chr1 - 42789255 42789467 213 browser details YourSeq 179 421 614 2000 94.3% chr1 - 28375997 28376186 190 browser details YourSeq 179 418 614 2000 96.4% chr8 + 107334717 107334915 199
Note: The 2000 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 2000 1 2000 2000 100.0% chr19 + 37578577 37580576 2000 browser details YourSeq 89 1564 1730 2000 83.2% chr10 - 123057160 123057321 162 browser details YourSeq 89 1532 1701 2000 79.9% chr8 + 86793976 86794150 175 browser details YourSeq 83 1529 1700 2000 86.3% chr7 + 126727927 126728097 171 browser details YourSeq 81 1509 1930 2000 75.5% chr10 - 62679948 62680251 304 browser details YourSeq 75 1515 1704 2000 75.7% chr10 + 30565861 30566056 196 browser details YourSeq 73 1203 1705 2000 71.3% chr8 - 79436486 79436887 402 browser details YourSeq 71 1589 1701 2000 87.4% chr10 - 121544424 121544542 119 browser details YourSeq 70 1589 1704 2000 82.3% chr1 - 172768901 172769010 110 browser details YourSeq 69 1622 1715 2000 88.0% chr1 - 7049863 7049968 106 browser details YourSeq 68 1626 1710 2000 92.6% chr17 + 47755562 47755646 85 browser details YourSeq 68 1589 1700 2000 80.5% chr1 + 175842201 175842305 105 browser details YourSeq 65 1622 1704 2000 89.2% chr10 - 13410516 13410598 83 browser details YourSeq 64 1622 1704 2000 89.2% chr10 - 91165741 91166283 543 browser details YourSeq 64 958 1044 2000 94.5% chr4 + 155842215 155842365 151 browser details YourSeq 63 1407 1704 2000 69.8% chr6 - 35084444 35084519 76 browser details YourSeq 63 1621 1705 2000 87.1% chr12 - 108430373 108430457 85 browser details YourSeq 63 1615 1704 2000 85.6% chr10 - 121299356 121472083 172728 browser details YourSeq 63 1592 1690 2000 88.9% chr4 + 63462564 63462667 104 browser details YourSeq 62 1636 1705 2000 95.8% chr10 - 71445658 71446095 438
Note: The 2000 bp section downstream of Exon 7 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Exoc6 exocyst complex component 6 [ Mus musculus (house mouse) ] Gene ID: 107371, updated on 10-Oct-2019
Gene summary
Official Symbol Exoc6 provided by MGI Official Full Name exocyst complex component 6 provided by MGI Primary source MGI:MGI:1351611 See related Ensembl:ENSMUSG00000053799 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 hbd; Sec15; msec15; Sec15l1; AW413330; C430002C19; 4833405E05Rik Expression Ubiquitous expression in placenta adult (RPKM 12.6), liver E14 (RPKM 11.8) and 28 other tissues See more Orthologs human all
Genomic context
Location: 19 C2; 19 32.32 cM See Exoc6 in Genome Data Viewer Exon count: 23
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (37536763..37684052)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 19 NC_000085.5 (37624908..37757743)
Chromosome 19 - NC_000085.6
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Transcript information: This gene has 3 transcripts
Gene: Exoc6 ENSMUSG00000053799
Description exocyst complex component 6 [Source:MGI Symbol;Acc:MGI:1351611] Gene Synonyms 4833405E05Rik, Sec15, Sec15l1, hbd, msec15 Location Chromosome 19: 37,520,879-37,684,059 forward strand. GRCm38:CM001012.2 About this gene This gene has 3 transcripts (splice variants), 210 orthologues, 1 paralogue, is a member of 1 Ensembl protein family and is associated with 33 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Exoc6-201 ENSMUST00000066439.7 3543 804aa ENSMUSP00000064332.6 Protein coding CCDS29779 Q3U9D6 TSL:1 GENCODE basic APPRIS P2
Exoc6-203 ENSMUST00000238954.1 3728 811aa ENSMUSP00000158866.1 Protein coding - - GENCODE basic APPRIS ALT2
Exoc6-202 ENSMUST00000238817.1 2692 802aa ENSMUSP00000159143.1 Protein coding - - GENCODE basic APPRIS ALT2
183.18 kb Forward strand 37.52Mb 37.54Mb 37.56Mb 37.58Mb 37.60Mb 37.62Mb 37.64Mb 37.66Mb 37.68Mb Genes (Comprehensive set... Exoc6-203 >protein coding
Exoc6-201 >protein coding
Exoc6-202 >protein coding
Cyp26c1-201 >protein coding
Contigs < AC101542.19 < AC110212.12 Regulatory Build
37.52Mb 37.54Mb 37.56Mb 37.58Mb 37.60Mb 37.62Mb 37.64Mb 37.66Mb 37.68Mb Reverse strand 183.18 kb
Regulation Legend
CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
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Transcript: ENSMUST00000066439
133.64 kb Forward strand
Exoc6-201 >protein coding
ENSMUSP00000064... Low complexity (Seg) Pfam Exocyst complex component EXOC6/Sec15
PIRSF Exocyst complex component EXOC6/Sec15
PANTHER PTHR12702:SF2
Exocyst complex component EXOC6/Sec15 Gene3D Exocyst complex component EXOC6/Sec15, C-terminal, domain 1
Exocyst complex component EXOC6/Sec15, C-terminal, domain 2
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant splice region variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 804
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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