https://www.alphaknockout.com
Mouse Wipf1 Knockout Project (CRISPR/Cas9)
Objective: To create a Wipf1 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Wipf1 gene (NCBI Reference Sequence: NM_153138 ; Ensembl: ENSMUSG00000075284 ) is located on Mouse chromosome 2. 8 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 8 (Transcript: ENSMUST00000094681). Exon 3~6 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: Homozygous mutants have immunological abnormalities, although lymphocyte development appears normal. Mutants show abnormal B and T cell proliferative responses, high serum immunoglobulin levels and impaired immunological synapse formation.
Exon 3 starts from about 3.52% of the coding region. Exon 3~6 covers 85.26% of the coding region. The size of effective KO region: ~9629 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 3 4 5 6 8
Legends Exon of mouse Wipf1 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 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 802 bp section downstream of Exon 6 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(29.2% 584) | C(20.75% 415) | T(26.75% 535) | G(23.3% 466)
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(802bp) | A(26.43% 212) | C(24.69% 198) | T(30.42% 244) | G(18.45% 148)
Note: The 802 bp section downstream of Exon 6 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% chr2 - 73444575 73446574 2000 browser details YourSeq 25 1025 1057 2000 87.9% chr6 + 133223149 133223181 33 browser details YourSeq 25 1792 1830 2000 82.1% chr1 + 74824080 74824118 39 browser details YourSeq 23 850 873 2000 100.0% chr9 + 58506331 58506356 26 browser details YourSeq 22 857 878 2000 100.0% chr9 - 98157020 98157041 22 browser details YourSeq 22 262 283 2000 100.0% chr5 - 118320931 118320952 22
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 802 1 802 802 100.0% chr2 - 73434144 73434945 802 browser details YourSeq 108 300 422 802 95.2% chr13 - 52512843 52513020 178 browser details YourSeq 106 304 429 802 92.3% chr2 - 28697289 28697411 123 browser details YourSeq 106 300 427 802 90.6% chr14 + 99356327 99356450 124 browser details YourSeq 103 300 774 802 79.4% chr15 - 93727405 93727575 171 browser details YourSeq 102 300 427 802 87.2% chr19 - 46030559 46030676 118 browser details YourSeq 102 304 424 802 94.0% chr1 + 39804011 39804131 121 browser details YourSeq 101 305 427 802 92.0% chrX - 51751905 51752025 121 browser details YourSeq 101 54 419 802 89.9% chr12 - 10474974 10475527 554 browser details YourSeq 101 305 450 802 93.9% chr11 + 117785997 117786469 473 browser details YourSeq 100 300 420 802 92.2% chr11 - 50167736 50167855 120 browser details YourSeq 98 300 415 802 95.5% chr9 - 72754448 72754577 130 browser details YourSeq 98 300 426 802 85.4% chr14 + 122194552 122194667 116 browser details YourSeq 97 304 426 802 91.5% chr7 - 90877760 90877896 137 browser details YourSeq 97 305 414 802 92.6% chr19 - 56899878 56899985 108 browser details YourSeq 97 295 414 802 91.6% chr15 + 64973827 64973953 127 browser details YourSeq 96 304 427 802 87.8% chr2 - 123254262 123254381 120 browser details YourSeq 96 305 422 802 91.0% chr14 - 83596060 83596175 116 browser details YourSeq 96 305 415 802 94.6% chr15 + 81160573 81160702 130 browser details YourSeq 95 305 422 802 91.1% chr6 - 135534004 135534120 117
Note: The 802 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Wipf1 WAS/WASL interacting protein family, member 1 [ Mus musculus (house mouse) ] Gene ID: 215280, updated on 12-Aug-2019
Gene summary
Official Symbol Wipf1 provided by MGI Official Full Name WAS/WASL interacting protein family, member 1 provided by MGI Primary source MGI:MGI:2178801 See related Ensembl:ENSMUSG00000075284 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 WIP; Waspip; AI115543; D2Ertd120e Expression Broad expression in spleen adult (RPKM 10.8), thymus adult (RPKM 7.3) and 25 other tissues See more Orthologs human all
Genomic context
Location: 2 C3; 2 43.68 cM See Wipf1 in Genome Data Viewer Exon count: 13
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (73429610..73529487, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (73267674..73367467, complement)
Chromosome 2 - NC_000068.7
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Transcript information: This gene has 7 transcripts
Gene: Wipf1 ENSMUSG00000075284
Description WAS/WASL interacting protein family, member 1 [Source:MGI Symbol;Acc:MGI:2178801] Gene Synonyms D2Ertd120e, WIP, Waspip Location Chromosome 2: 73,429,610-73,529,734 reverse strand. GRCm38:CM000995.2 About this gene This gene has 7 transcripts (splice variants), 175 orthologues, 2 paralogues, is a member of 1 Ensembl protein family and is associated with 39 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Wipf1-201 ENSMUST00000094681.10 4728 493aa ENSMUSP00000092268.4 Protein coding CCDS16131 Q8K1I7 TSL:1 GENCODE basic APPRIS P1
Wipf1-203 ENSMUST00000102680.7 4032 493aa ENSMUSP00000099741.1 Protein coding CCDS16131 Q8K1I7 TSL:1 GENCODE basic APPRIS P1
Wipf1-202 ENSMUST00000102679.7 2039 493aa ENSMUSP00000099740.1 Protein coding CCDS16131 Q8K1I7 TSL:1 GENCODE basic APPRIS P1
Wipf1-205 ENSMUST00000141264.7 717 196aa ENSMUSP00000119190.1 Protein coding - F6QWW7 CDS 3' incomplete TSL:2
Wipf1-207 ENSMUST00000151939.1 532 58aa ENSMUSP00000121335.1 Protein coding - F6RQI2 CDS 3' incomplete TSL:3
Wipf1-206 ENSMUST00000143061.1 374 No protein - lncRNA - - TSL:5
Wipf1-204 ENSMUST00000129594.1 354 No protein - lncRNA - - TSL:5
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120.12 kb Forward strand 73.42Mb 73.44Mb 73.46Mb 73.48Mb 73.50Mb 73.52Mb Genes D230022J07Rik-201 >lncRNA Gm13708-201 >lncRNA (Comprehensive set...
Gm13707-201 >lncRNA
Contigs AL928813.10 > Genes < Wipf1-201protein coding (Comprehensive set...
< Wipf1-203protein coding
< Wipf1-202protein coding
< Wipf1-205protein coding
< Wipf1-207protein coding
< Wipf1-206lncRNA
< Wipf1-204lncRNA
Regulatory Build
73.42Mb 73.44Mb 73.46Mb 73.48Mb 73.50Mb 73.52Mb Reverse strand 120.12 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
RNA gene
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Transcript: ENSMUST00000094681
< Wipf1-201protein coding
Reverse strand 100.12 kb
ENSMUSP00000092... MobiDB lite Low complexity (Seg) SMART WH2 domain
Pfam WH2 domain PROSITE profiles WH2 domain PANTHER PTHR23202
PTHR23202:SF32 Gene3D PH-like domain superfamily
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend inframe deletion missense variant synonymous variant
Scale bar 0 60 120 180 240 300 360 420 493
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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