https://www.alphaknockout.com
Mouse Kctd12 Knockout Project (CRISPR/Cas9)
Objective: To create a Kctd12 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Kctd12 gene (NCBI Reference Sequence: NM_177715 ; Ensembl: ENSMUSG00000098557 ) is located on Mouse chromosome 14. 1 exon is identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 1 (Transcript: ENSMUST00000184744). Exon 1 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: Mice homozygous for a knock-out allele exhibit increased fear learning of a discrete auditory-conditioned stimulus, increased activity during the inactive (light) phase and increased intrinsic excitability of pyramidal neurons.
Exon 1 starts from about 0.1% of the coding region. Exon 1 covers 100.0% of the coding region. The size of effective KO region: ~979 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
Legends Exon of mouse Kctd12 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 start codon 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 stop codon 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(23.95% 479) | C(26.7% 534) | T(23.0% 460) | G(26.35% 527)
Note: The 2000 bp section upstream of start codon is analyzed to determine the GC content. Significant high GC-content regions are found. The gRNA site is selected outside of these high GC-content regions.
Overview of the GC Content Distribution (down) Window size: 300 bp
Sequence 12
Summary: Full Length(2000bp) | A(25.15% 503) | C(21.05% 421) | T(30.45% 609) | G(23.35% 467)
Note: The 2000 bp section downstream of stop codon 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% chr14 - 102982441 102984440 2000 browser details YourSeq 37 1664 1703 2000 97.5% chr17 - 44079045 44079188 144 browser details YourSeq 28 1668 1695 2000 100.0% chr11 + 115806675 115806702 28 browser details YourSeq 27 1673 1702 2000 96.7% chr10 - 60574016 60574050 35 browser details YourSeq 27 1664 1692 2000 100.0% chr2 + 13385264 13385294 31 browser details YourSeq 27 1659 1689 2000 86.7% chr1 + 133908472 133908501 30 browser details YourSeq 24 406 431 2000 96.2% chr1 + 71547239 71547264 26 browser details YourSeq 23 1665 1687 2000 100.0% chr10 - 111887844 111887866 23 browser details YourSeq 23 782 806 2000 87.5% chr1 - 183425568 183425591 24 browser details YourSeq 22 1667 1688 2000 100.0% chr1 + 15649730 15649751 22 browser details YourSeq 21 1446 1466 2000 100.0% chr7 - 118094186 118094206 21 browser details YourSeq 21 1666 1686 2000 100.0% chr18 - 68402211 68402231 21 browser details YourSeq 21 1664 1684 2000 100.0% chr16 - 13730721 13730741 21 browser details YourSeq 21 1665 1686 2000 100.0% chr6 + 73304215 73304237 23 browser details YourSeq 21 375 395 2000 100.0% chr12 + 94663586 94663606 21 browser details YourSeq 21 288 308 2000 100.0% chr10 + 45044178 45044198 21 browser details YourSeq 21 613 637 2000 92.0% chr1 + 48374667 48374691 25
Note: The 2000 bp section upstream of start codon 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% chr14 - 102979460 102981459 2000 browser details YourSeq 38 888 939 2000 91.5% chr4 + 151541669 151541746 78 browser details YourSeq 32 898 941 2000 77.0% chr7 + 145320469 145320507 39 browser details YourSeq 30 898 936 2000 78.8% chr4 + 124191682 124191715 34 browser details YourSeq 26 1261 1286 2000 100.0% chr10 - 97229966 97229991 26 browser details YourSeq 26 573 600 2000 88.9% chr10 + 69632377 69632403 27 browser details YourSeq 25 913 942 2000 82.2% chr2 - 134445979 134446006 28 browser details YourSeq 24 915 939 2000 100.0% chr3 - 23149301 23149326 26 browser details YourSeq 23 1264 1286 2000 100.0% chr19 - 24642730 24642752 23 browser details YourSeq 22 901 922 2000 100.0% chr12 - 103806655 103806676 22 browser details YourSeq 22 578 599 2000 100.0% chr2 + 119854226 119854247 22 browser details YourSeq 21 1720 1740 2000 100.0% chr3 - 88224916 88224936 21 browser details YourSeq 21 80 100 2000 100.0% chr17 + 31672311 31672331 21 browser details YourSeq 21 1171 1191 2000 100.0% chr1 + 28137794 28137814 21
Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Kctd12 potassium channel tetramerisation domain containing 12 [ Mus musculus (house mouse) ] Gene ID: 239217, updated on 11-Sep-2019
Gene summary
Official Symbol Kctd12 provided by MGI Official Full Name potassium channel tetramerisation domain containing 12 provided by MGI Primary source MGI:MGI:2145823 See related Ensembl:ENSMUSG00000098557 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 Pfet1; Pfetin; AU046135; AW538430 Orthologs human all
Genomic context
Location: 14; 14 E2.3 See Kctd12 in Genome Data Viewer
Exon count: 1
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (102976581..102982637, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 14 NC_000080.5 (103375798..103381854, complement)
Chromosome 14 - NC_000080.6
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Transcript information: This gene has 2 transcripts
Gene: Kctd12 ENSMUSG00000098557
Description potassium channel tetramerisation domain containing 12 [Source:MGI Symbol;Acc:MGI:2145823] Gene Synonyms Pfet1, Pfetin Location Chromosome 14: 102,976,581-102,982,637 reverse strand. GRCm38:CM001007.2 About this gene This gene has 2 transcripts (splice variants), 175 orthologues, 14 paralogues, is a member of 1 Ensembl protein family and is associated with 4 phenotypes. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Kctd12-202 ENSMUST00000184744.1 6057 327aa ENSMUSP00000139261.1 Protein coding CCDS70611 A0A0R4J2B2 TSL:NA GENCODE basic APPRIS P1
Kctd12-201 ENSMUST00000183756.1 539 No protein - lncRNA - - TSL:3
26.06 kb Forward strand
102.97Mb 102.98Mb 102.99Mb Contigs AC102815.31 >
Genes (Comprehensive set... < Kctd12-202protein coding < 4933432I03Rik-201lncRNA
< Kctd12-201lncRNA < Mir5130-201miRNA
Regulatory Build
102.97Mb 102.98Mb 102.99Mb Reverse strand 26.06 kb
Regulation Legend
CTCF Promoter Promoter Flank
Gene Legend Protein Coding
Ensembl protein coding
Non-Protein Coding
RNA gene
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Transcript: ENSMUST00000184744
< Kctd12-202protein coding
Reverse strand 6.06 kb
ENSMUSP00000139... MobiDB lite Low complexity (Seg) Superfamily SKP1/BTB/POZ domain superfamily
SMART BTB/POZ domain
Pfam Potassium channel tetramerisation-type BTB domain PANTHER PTHR14499
PTHR14499:SF29 Gene3D 3.30.710.10 CDD cd18397
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 40 80 120 160 200 240 280 327
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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