https://www.alphaknockout.com
Mouse Zdhhc14 Knockout Project (CRISPR/Cas9)
Objective: To create a Zdhhc14 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Zdhhc14 gene (NCBI Reference Sequence: NM_146073 ; Ensembl: ENSMUSG00000034265 ) is located on Mouse chromosome 17. 9 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 9 (Transcript: ENSMUST00000089185). Exon 2 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 about 16.77% of the coding region. Exon 2 covers 10.97% of the coding region. The size of effective KO region: ~161 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 9
Legends Exon of mouse Zdhhc14 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 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.
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Overview of the GC Content Distribution (up) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(23.0% 460) | C(25.95% 519) | T(27.85% 557) | G(23.2% 464)
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(31.25% 625) | C(20.3% 406) | T(22.95% 459) | G(25.5% 510)
Note: The 2000 bp section downstream 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.
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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% chr17 + 5645904 5647903 2000 browser details YourSeq 44 1736 1795 2000 86.7% chr15 + 83817973 83818032 60 browser details YourSeq 41 1729 1794 2000 90.4% chr14 - 122782759 122782829 71 browser details YourSeq 37 1741 1798 2000 95.2% chr8 + 112158094 112158252 159 browser details YourSeq 36 1741 1786 2000 89.2% chr16 + 5866680 5866725 46 browser details YourSeq 33 1750 1795 2000 87.2% chr15 - 50839442 50839486 45 browser details YourSeq 33 1737 1783 2000 90.3% chr14 - 98654623 98654672 50 browser details YourSeq 33 1750 1800 2000 82.4% chr2 + 94079925 94079975 51 browser details YourSeq 32 1680 1749 2000 88.3% chr5 + 31460569 31460636 68 browser details YourSeq 26 1657 1696 2000 71.5% chr9 - 110286171 110286199 29 browser details YourSeq 26 1753 1796 2000 67.9% chr1 - 16312601 16312632 32 browser details YourSeq 24 1736 1762 2000 96.2% chr5 - 137545209 137545236 28 browser details YourSeq 24 122 145 2000 100.0% chr11 - 65371915 65371938 24 browser details YourSeq 22 1777 1798 2000 100.0% chr1 - 31569719 31569740 22 browser details YourSeq 21 125 145 2000 100.0% chr2 - 46752896 46752916 21 browser details YourSeq 21 1742 1762 2000 100.0% chr1 - 153035136 153035156 21 browser details YourSeq 21 1733 1753 2000 100.0% chr9 + 92126121 92126141 21
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% chr17 + 5648065 5650064 2000 browser details YourSeq 596 175 859 2000 93.5% chr13 + 52245315 52245988 674 browser details YourSeq 594 175 1014 2000 92.3% chr5 + 85635007 85635679 673 browser details YourSeq 593 175 855 2000 93.9% chr9 + 79851049 79851722 674 browser details YourSeq 587 175 842 2000 95.1% chr17 + 3543820 3544491 672 browser details YourSeq 585 175 844 2000 93.5% chr9 + 54042184 54042836 653 browser details YourSeq 585 175 823 2000 94.9% chr14 + 58135304 58135951 648 browser details YourSeq 584 175 827 2000 95.1% chrX - 152585057 152585714 658 browser details YourSeq 584 175 829 2000 95.1% chr4 - 15778967 16178033 399067 browser details YourSeq 584 175 828 2000 95.0% chr12 - 5468406 5469066 661 browser details YourSeq 584 175 938 2000 94.6% chr8 + 118822819 118823862 1044 browser details YourSeq 583 175 853 2000 93.4% chr3 - 75008248 75008918 671 browser details YourSeq 583 175 844 2000 93.6% chr10 - 94070120 94070773 654 browser details YourSeq 582 175 828 2000 94.7% chr16 + 6546185 6546840 656 browser details YourSeq 581 175 828 2000 94.0% chr2 - 17816599 17817248 650 browser details YourSeq 581 175 826 2000 94.8% chr10 + 70672914 70673565 652 browser details YourSeq 580 175 822 2000 94.8% chr4 - 116385682 116386328 647 browser details YourSeq 580 175 823 2000 94.3% chr12 + 83358380 83359026 647 browser details YourSeq 580 175 826 2000 94.8% chr11 + 22511432 22512085 654 browser details YourSeq 579 175 842 2000 93.3% chr7 - 6462709 6463361 653
Note: The 2000 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: Zdhhc14 zinc finger, DHHC domain containing 14 [ Mus musculus (house mouse) ] Gene ID: 224454, updated on 21-Aug-2019
Gene summary
Official Symbol Zdhhc14 provided by MGI Official Full Name zinc finger, DHHC domain containing 14 provided by MGI Primary source MGI:MGI:2653229 See related Ensembl:ENSMUSG00000034265 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 New1cp; B530001K09Rik Expression Ubiquitous expression in cerebellum adult (RPKM 3.4), thymus adult (RPKM 3.0) and 28 other tissues See more Orthologs human all
Genomic context
Location: 17; 17 A1 See Zdhhc14 in Genome Data Viewer Exon count: 12
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (5492562..5753891)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (5492600..5753891)
Chromosome 17 - NC_000083.6
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Transcript information: This gene has 1 transcript
Gene: Zdhhc14 ENSMUSG00000034265
Description zinc finger, DHHC domain containing 14 [Source:MGI Symbol;Acc:MGI:2653229] Gene Synonyms B530001K09Rik, New1cp Location Chromosome 17: 5,492,557-5,753,811 forward strand. GRCm38:CM001010.2 About this gene This gene has 1 transcript (splice variant), 244 orthologues, 17 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Zdhhc14-201 ENSMUST00000089185.5 3078 489aa ENSMUSP00000086589.4 Protein coding CCDS37422 Q8BQQ1 TSL:1 GENCODE basic APPRIS P1
281.25 kb Forward strand 5.5Mb 5.6Mb 5.7Mb Genes (Comprehensive set... Zdhhc14-201 >protein coding
Contigs AC163715.5 > AC133198.3 > Genes < Gm8363-201processed pseudogene (Comprehensive set...
Regulatory Build
5.5Mb 5.6Mb 5.7Mb Reverse strand 281.25 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site
Gene Legend Protein Coding
merged Ensembl/Havana
Non-Protein Coding
pseudogene
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Transcript: ENSMUST00000089185
261.25 kb Forward strand
Zdhhc14-201 >protein coding
ENSMUSP00000086... Transmembrane heli... Low complexity (Seg) Pfam Palmitoyltransferase, DHHC domain PROSITE profiles PS50216 PANTHER PTHR22883
PTHR22883:SF28
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend missense variant synonymous variant
Scale bar 0 60 120 180 240 300 360 420 489
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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