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Mouse Yipf4 Conditional Knockout Project (CRISPR/Cas9)
Objective: To create a Yipf4 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Yipf4 gene (NCBI Reference Sequence: NM_026417 ; Ensembl: ENSMUSG00000024072 ) is located on Mouse chromosome 17. 6 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 6 (Transcript: ENSMUST00000024873). 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 Yipf4 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-14N10 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:
Exon 2 starts from about 10.84% 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: 2551 bp, and the size of intron 2 for 3'-loxP site insertion: 1422 bp. The size of effective cKO region: ~660 bp. The cKO region does not have any other known gene.
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Overview of the Targeting Strategy
Wildtype allele gRNA region 5' gRNA region 3'
1 2 3 6 Targeting vector
Targeted allele
Constitutive KO allele (After Cre recombination)
Legends Exon of mouse Yipf4 Homology arm cKO region loxP site
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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(7160bp) | A(26.48% 1896) | C(20.14% 1442) | T(31.06% 2224) | G(22.32% 1598)
Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. Significant high GC-content regions are found. It may be difficult to construct this targeting vector.
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BLAT Search Results (up)
QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ------browser details YourSeq 3000 1 3000 3000 100.0% chr17 + 74489097 74492096 3000 browser details YourSeq 171 1651 1916 3000 92.5% chr1 + 74314104 74314491 388 browser details YourSeq 164 1468 1809 3000 87.0% chr7 - 42754839 42755273 435 browser details YourSeq 163 1651 2078 3000 87.8% chr7 - 27318253 27318588 336 browser details YourSeq 163 1651 2081 3000 86.4% chr11 + 68542045 68542317 273 browser details YourSeq 160 1626 1862 3000 94.0% chr11 + 57947079 57947371 293 browser details YourSeq 160 1269 1808 3000 87.6% chr1 + 93631943 93632372 430 browser details YourSeq 159 1266 1808 3000 85.8% chr10 - 21097226 21097486 261 browser details YourSeq 157 1639 1808 3000 94.0% chr4 + 155392126 155392291 166 browser details YourSeq 155 1639 1808 3000 96.5% chr16 - 17218936 17219600 665 browser details YourSeq 154 1647 1821 3000 97.0% chr6 - 140694705 140694884 180 browser details YourSeq 154 1651 1812 3000 97.6% chr13 - 64394051 64394212 162 browser details YourSeq 153 1640 1807 3000 95.9% chr6 - 96901430 96901602 173 browser details YourSeq 153 1639 1808 3000 94.1% chr16 - 48262150 48262317 168 browser details YourSeq 153 1649 1808 3000 98.2% chr2 + 103195317 103195487 171 browser details YourSeq 151 1642 1808 3000 95.9% chr7 + 123051779 123051956 178 browser details YourSeq 151 1639 1808 3000 95.3% chr6 + 148870711 148870892 182 browser details YourSeq 150 1471 1808 3000 92.7% chr9 - 114940090 114940429 340 browser details YourSeq 150 1651 1812 3000 96.3% chr9 + 64857929 64858090 162 browser details YourSeq 150 1651 1817 3000 93.0% chr14 + 7761637 7761792 156
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% chr17 + 74492757 74495756 3000 browser details YourSeq 443 452 1016 3000 93.8% chr6 + 44974256 44974966 711 browser details YourSeq 438 111 846 3000 90.9% chr2 + 5914967 5915596 630 browser details YourSeq 415 452 1016 3000 91.7% chr7 - 61705272 61705822 551 browser details YourSeq 398 250 846 3000 94.1% chr11 - 77256642 77257303 662 browser details YourSeq 384 451 970 3000 92.1% chr1 + 191308772 191309206 435 browser details YourSeq 383 452 958 3000 93.5% chr15 - 76775899 76776541 643 browser details YourSeq 376 394 860 3000 94.4% chr12 + 116730566 116731073 508 browser details YourSeq 370 451 970 3000 92.2% chr17 - 87033726 87034180 455 browser details YourSeq 369 452 970 3000 95.2% chr5 + 139219271 139219840 570 browser details YourSeq 366 445 851 3000 95.1% chr3 - 131008141 131008547 407 browser details YourSeq 366 451 856 3000 94.6% chr3 + 95548357 95548760 404 browser details YourSeq 363 454 846 3000 95.7% chr18 + 65912868 65913259 392 browser details YourSeq 362 444 846 3000 95.1% chr2 - 135248954 135249357 404 browser details YourSeq 362 452 859 3000 93.8% chr8 + 18534326 18534728 403 browser details YourSeq 361 394 846 3000 94.9% chr10 - 26951189 26951895 707 browser details YourSeq 361 449 852 3000 94.9% chrX + 67191505 67191909 405 browser details YourSeq 361 452 862 3000 95.0% chr9 + 94514197 94514606 410 browser details YourSeq 361 450 847 3000 95.5% chr2 + 44048304 44048702 399 browser details YourSeq 360 449 847 3000 95.3% chr3 - 149666249 149666648 400
Note: The 3000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Yipf4 Yip1 domain family, member 4 [ Mus musculus (house mouse) ] Gene ID: 67864, updated on 12-Aug-2019
Gene summary
Official Symbol Yipf4 provided by MGI Official Full Name Yip1 domain family, member 4 provided by MGI Primary source MGI:MGI:1915114 See related Ensembl:ENSMUSG00000024072 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 2310034L04Rik Expression Ubiquitous expression in adrenal adult (RPKM 43.1), duodenum adult (RPKM 26.4) and 28 other tissues See more Orthologs human all
Genomic context
Location: 17; 17 E2 See Yipf4 in Genome Data Viewer
Exon count: 6
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (74489493..74500277)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (74888854..74899617)
Chromosome 17 - NC_000083.6
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Transcript information: This gene has 6 transcripts
Gene: Yipf4 ENSMUSG00000024072
Description Yip1 domain family, member 4 [Source:MGI Symbol;Acc:MGI:1915114] Gene Synonyms 2310034L04Rik Location Chromosome 17: 74,489,493-74,500,277 forward strand. GRCm38:CM001010.2 About this gene This gene has 6 transcripts (splice variants), 192 orthologues, 3 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Yipf4- ENSMUST00000024873.6 2133 246aa ENSMUSP00000024873.6 Protein coding CCDS28971 Q8C407 TSL:1 201 GENCODE basic APPRIS P1
Yipf4- ENSMUST00000234432.1 1991 39aa ENSMUSP00000157350.1 Nonsense mediated - A0A3Q4L376 - 202 decay
Yipf4- ENSMUST00000234448.1 1082 No - lncRNA - - - 203 protein
Yipf4- ENSMUST00000234939.1 481 No - lncRNA - - - 205 protein
Yipf4- ENSMUST00000235064.1 343 No - lncRNA - - - 206 protein
Yipf4- ENSMUST00000234853.1 166 No - lncRNA - - - 204 protein
30.79 kb Forward strand 74.48Mb 74.49Mb 74.50Mb 74.51Mb Genes (Comprehensive set... Yipf4-201 >protein coding
Yipf4-205 >lncRNA Yipf4-204 >lncRNA
Yipf4-202 >nonsense mediated decay
Yipf4-203 >lncRNA
Yipf4-206 >lncRNA
Contigs < CT033749.8 Regulatory Build
74.48Mb 74.49Mb 74.50Mb 74.51Mb Reverse strand 30.79 kb
Regulation Legend CTCF Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
processed transcript RNA gene
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Transcript: ENSMUST00000024873
10.79 kb Forward strand
Yipf4-201 >protein coding
ENSMUSP00000024... Transmembrane heli... Low complexity (Seg) Pfam Yip1 domain PANTHER PTHR21236
PTHR21236:SF7
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 40 80 120 160 200 246
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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