https://www.alphaknockout.com
Mouse Exoc2 Knockout Project (CRISPR/Cas9)
Objective: To create a Exoc2 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Exoc2 gene (NCBI Reference Sequence: NM_025588 ; Ensembl: ENSMUSG00000021357 ) is located on Mouse chromosome 13. 28 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 28 (Transcript: ENSMUST00000021785). Exon 2~3 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 2 starts from the coding region. Exon 2~3 covers 10.64% of the coding region. The size of effective KO region: ~2655 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 28
Legends Exon of mouse Exoc2 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 3 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(29.8% 596) | C(15.85% 317) | T(35.8% 716) | G(18.55% 371)
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(29.65% 593) | C(17.45% 349) | T(34.35% 687) | G(18.55% 371)
Note: The 2000 bp section downstream 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.
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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% chr13 - 30940728 30942727 2000 browser details YourSeq 48 564 734 2000 90.0% chr13 - 112692022 112692192 171 browser details YourSeq 47 713 769 2000 91.3% chr12 - 31571230 31571286 57 browser details YourSeq 47 707 768 2000 88.8% chr10 + 52034612 52034674 63 browser details YourSeq 45 702 786 2000 75.5% chr7 - 25041334 25041409 76 browser details YourSeq 45 708 768 2000 91.0% chr13 - 48018202 48018262 61 browser details YourSeq 43 714 762 2000 93.9% chr2 - 106590396 106590444 49 browser details YourSeq 43 344 472 2000 82.1% chr17 - 42780811 42780941 131 browser details YourSeq 40 707 768 2000 82.3% chr8 - 95410365 95410426 62 browser details YourSeq 40 710 757 2000 91.7% chr1 - 181250347 181250394 48 browser details YourSeq 39 709 769 2000 82.0% chr12 - 102348264 102348324 61 browser details YourSeq 38 709 768 2000 81.7% chr10 - 76869492 76869551 60 browser details YourSeq 38 573 616 2000 97.6% chr14 + 70262318 70262492 175 browser details YourSeq 38 713 789 2000 91.4% chr14 + 67190965 67191427 463 browser details YourSeq 37 347 494 2000 90.3% chr1 + 78170370 78170516 147 browser details YourSeq 36 678 722 2000 92.9% chrX - 75802998 75803043 46 browser details YourSeq 36 704 746 2000 93.1% chr13 - 34000990 34001033 44 browser details YourSeq 35 344 472 2000 92.5% chr4 - 63192045 63192173 129 browser details YourSeq 35 715 756 2000 94.9% chr11 + 70181390 70181431 42 browser details YourSeq 33 709 747 2000 92.4% chr15 + 36572610 36572648 39
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% chr13 - 30936116 30938115 2000 browser details YourSeq 65 821 1097 2000 96.0% chr5 - 11673990 11674379 390 browser details YourSeq 55 983 1086 2000 73.7% chr17 - 40325101 40325187 87 browser details YourSeq 53 1042 1111 2000 84.8% chr11 - 91075543 91075606 64 browser details YourSeq 52 1041 1111 2000 95.0% chr1 - 142339382 142339452 71 browser details YourSeq 50 983 1185 2000 89.3% chr5 - 146573794 146574091 298 browser details YourSeq 48 1003 1104 2000 98.0% chr10 - 90295098 90295452 355 browser details YourSeq 45 1012 1087 2000 79.7% chr15 - 85664868 85664934 67 browser details YourSeq 44 1019 1093 2000 75.0% chr17 + 74142510 74142558 49 browser details YourSeq 43 1004 1069 2000 77.1% chr18 + 80835717 80835770 54 browser details YourSeq 42 1010 1078 2000 95.7% chr10 + 7235518 7235587 70 browser details YourSeq 40 959 1030 2000 93.7% chr17 + 94533970 94534041 72 browser details YourSeq 40 1007 1069 2000 73.4% chr1 + 76165735 76165779 45 browser details YourSeq 39 1005 1071 2000 72.8% chr5 - 21893674 21893722 49 browser details YourSeq 37 977 1081 2000 73.2% chr7 + 81160198 81160283 86 browser details YourSeq 35 1020 1080 2000 76.8% chr2 - 41137136 41137190 55 browser details YourSeq 32 1010 1043 2000 100.0% chr3 + 145011999 145012058 60 browser details YourSeq 31 1004 1043 2000 83.8% chr11 - 29699655 29699692 38 browser details YourSeq 31 1012 1051 2000 91.7% chr15 + 37649376 37649422 47 browser details YourSeq 25 1532 1560 2000 96.3% chr4 - 63194326 63194356 31
Note: The 2000 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Exoc2 exocyst complex component 2 [ Mus musculus (house mouse) ] Gene ID: 66482, updated on 24-Oct-2019
Gene summary
Official Symbol Exoc2 provided by MGI Official Full Name exocyst complex component 2 provided by MGI Primary source MGI:MGI:1913732 See related Ensembl:ENSMUSG00000021357 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 Sec5; Sec5l1; AI648199; 2410030I24Rik Expression Ubiquitous expression in CNS E18 (RPKM 9.5), CNS E14 (RPKM 7.9) and 28 other tissues See more Orthologs human all
Genomic context
Location: 13; 13 A3.2 See Exoc2 in Genome Data Viewer Exon count: 34
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (30789516..30974096, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 13 NC_000079.5 (30905787..31065916, complement)
Chromosome 13 - NC_000079.6
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Transcript information: This gene has 7 transcripts
Gene: Exoc2 ENSMUSG00000021357
Description exocyst complex component 2 [Source:MGI Symbol;Acc:MGI:1913732] Gene Synonyms 2410030I24Rik, Sec5, Sec5l1 Location Chromosome 13: 30,813,919-30,974,093 reverse strand. GRCm38:CM001006.2 About this gene This gene has 7 transcripts (splice variants), 201 orthologues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Exoc2-202 ENSMUST00000102946.7 4375 924aa ENSMUSP00000100010.1 Protein coding CCDS26420 Q9D4H1 TSL:1 GENCODE basic APPRIS P1
Exoc2-201 ENSMUST00000021785.7 4256 924aa ENSMUSP00000021785.6 Protein coding CCDS26420 Q9D4H1 TSL:1 GENCODE basic APPRIS P1
Exoc2-206 ENSMUST00000222133.1 1787 No protein - Retained intron - - TSL:1
Exoc2-204 ENSMUST00000220532.1 1441 No protein - Retained intron - - TSL:1
Exoc2-205 ENSMUST00000221678.1 688 No protein - Retained intron - - TSL:3
Exoc2-207 ENSMUST00000223216.1 639 No protein - Retained intron - - TSL:3
Exoc2-203 ENSMUST00000220490.1 543 No protein - lncRNA - - TSL:3
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180.18 kb Forward strand 30.82Mb 30.84Mb 30.86Mb 30.88Mb 30.90Mb 30.92Mb 30.94Mb 30.96Mb 30.98Mb Genes Gm5447-202 >TEC (Comprehensive set...
Gm5447-201 >TEC
Contigs AL645745.7 > AL606764.19 > Genes (Comprehensive set... < Exoc2-201protein coding
< Exoc2-202protein coding
< Exoc2-205retained intron < Exoc2-207retained intron
< Exoc2-203lncRNA < Hus1b-201protein coding
< Exoc2-206retained intron
< Exoc2-204retained intron
Regulatory Build
30.82Mb 30.84Mb 30.86Mb 30.88Mb 30.90Mb 30.92Mb 30.94Mb 30.96Mb 30.98Mb Reverse strand 180.18 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000021785
< Exoc2-201protein coding
Reverse strand 160.14 kb
ENSMUSP00000021... PDB-ENSP mappings Low complexity (Seg) Superfamily Immunoglobulin E-set Pfam IPT domain Exocyst complex component EXOC2/Sec5, N-terminal domain
PANTHER Exocyst complex component EXOC2/Sec5
PTHR13043:SF1 Gene3D Immunoglobulin-like fold
CDD cd00603
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend stop gained missense variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 800 924
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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