https://www.alphaknockout.com
Mouse Slc12a9 Knockout Project (CRISPR/Cas9)
Objective: To create a Slc12a9 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering.
Strategy summary: The Slc12a9 gene (NCBI Reference Sequence: NM_031406 ; Ensembl: ENSMUSG00000037344 ) is located on Mouse chromosome 5. 14 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 14 (Transcript: ENSMUST00000039991). Exon 2~7 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 2~7 covers 35.63% of the coding region. The size of effective KO region: ~5308 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 4 5 6 7 14
Legends Exon of mouse Slc12a9 Knockout region
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Overview of the Dot Plot (up) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 769 bp section upstream of Exon 2 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.
Overview of the Dot Plot (down) Window size: 15 bp
Forward Reverse Complement
Sequence 12
Note: The 1696 bp section downstream of Exon 7 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(769bp) | A(20.16% 155) | C(19.77% 152) | T(29.13% 224) | G(30.95% 238)
Note: The 769 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(1696bp) | A(23.0% 390) | C(22.64% 384) | T(29.72% 504) | G(24.65% 418)
Note: The 1696 bp section downstream of Exon 7 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 769 1 769 769 100.0% chr5 - 137332637 137333405 769 browser details YourSeq 43 581 623 769 100.0% chr2 - 21963596 21963638 43 browser details YourSeq 42 582 623 769 100.0% chr5 - 123827415 123827456 42 browser details YourSeq 42 582 623 769 100.0% chr4 - 52271725 52271766 42 browser details YourSeq 24 679 705 769 96.3% chr1 - 53448846 53448881 36 browser details YourSeq 24 61 89 769 76.0% chr1 + 122858550 122858574 25 browser details YourSeq 23 26 51 769 96.0% chr1 - 120531486 120531511 26 browser details YourSeq 22 19 40 769 100.0% chr5 + 108712055 108712076 22 browser details YourSeq 22 75 96 769 100.0% chr10 + 127712712 127712733 22 browser details YourSeq 20 77 96 769 100.0% chr11 - 51858489 51858508 20 browser details YourSeq 20 25 44 769 100.0% chr10 + 78364980 78364999 20
Note: The 769 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 1696 1 1696 1696 100.0% chr5 - 137325675 137327370 1696 browser details YourSeq 256 258 758 1696 94.2% chr15 + 98890222 98890986 765 browser details YourSeq 240 408 762 1696 92.9% chr11 + 77775008 77775543 536 browser details YourSeq 238 208 758 1696 95.5% chr12 + 59100303 59101078 776 browser details YourSeq 237 408 781 1696 93.5% chr11 + 46408993 46469240 60248 browser details YourSeq 236 196 628 1696 88.5% chr6 + 83926147 83926543 397 browser details YourSeq 231 408 947 1696 92.9% chr14 - 27358771 27359452 682 browser details YourSeq 229 408 770 1696 93.2% chr11 + 50819527 50819977 451 browser details YourSeq 226 196 627 1696 91.4% chrX - 101348198 101348627 430 browser details YourSeq 225 401 763 1696 96.0% chr6 + 72168030 72326797 158768 browser details YourSeq 224 206 627 1696 94.5% chr11 + 115599211 115599699 489 browser details YourSeq 221 170 628 1696 86.0% chr11 - 77669922 77670314 393 browser details YourSeq 221 408 764 1696 91.2% chr11 + 4914957 4915302 346 browser details YourSeq 220 222 626 1696 88.5% chr11 - 117594096 117594379 284 browser details YourSeq 218 408 762 1696 89.3% chr4 - 125233482 125233812 331 browser details YourSeq 218 408 762 1696 93.2% chr8 + 33698947 33699398 452 browser details YourSeq 213 406 775 1696 87.2% chr9 + 59507623 59507957 335 browser details YourSeq 211 196 629 1696 86.0% chr16 - 8745384 8745676 293 browser details YourSeq 210 408 742 1696 95.3% chr12 + 21356171 21356755 585 browser details YourSeq 209 408 756 1696 92.6% chr5 + 130255743 130256292 550
Note: The 1696 bp section downstream of Exon 7 is BLAT searched against the genome. No significant similarity is found.
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Gene and protein information: Slc12a9 solute carrier family 12 (potassium/chloride transporters), member 9 [ Mus musculus (house mouse) ] Gene ID: 83704, updated on 24-Oct-2019
Gene summary
Official Symbol Slc12a9 provided by MGI Official Full Name solute carrier family 12 (potassium/chloride transporters), member 9 provided by MGI Primary source MGI:MGI:1933532 See related Ensembl:ENSMUSG00000037344 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 CIP1 Expression Ubiquitous expression in ovary adult (RPKM 11.1), adrenal adult (RPKM 11.0) and 28 other tissues See more Orthologs human all
Genomic context
Location: 5; 5 G2 See Slc12a9 in Genome Data Viewer Exon count: 18
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (137314558..137340070, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 5 NC_000071.5 (137755786..137774810, complement)
Chromosome 5 - NC_000071.6
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Transcript information: This gene has 4 transcripts
Gene: Slc12a9 ENSMUSG00000037344
Description solute carrier family 12 (potassium/chloride transporters), member 9 [Source:MGI Symbol;Acc:MGI:1933532] Gene Synonyms CIP1 Location Chromosome 5: 137,314,558-137,333,597 reverse strand. GRCm38:CM000998.2 About this gene This gene has 4 transcripts (splice variants), 173 orthologues, 9 paralogues and is a member of 1 Ensembl protein family. Transcripts
Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags
Slc12a9-201 ENSMUST00000039991.13 3330 914aa ENSMUSP00000038106.7 Protein coding CCDS19766 Q99MR3 TSL:1 GENCODE basic APPRIS P1
Slc12a9-204 ENSMUST00000156646.2 365 60aa ENSMUSP00000117757.2 Protein coding - D3Z362 CDS 3' incomplete TSL:5
Slc12a9-203 ENSMUST00000149847.1 1815 No protein - Retained intron - - TSL:1
Slc12a9-202 ENSMUST00000141517.1 637 No protein - Retained intron - - TSL:3
39.04 kb Forward strand 137.31Mb 137.32Mb 137.33Mb 137.34Mb Genes Gm43013-201 >processed pseudogene Gm43012-201 >TEC (Comprehensive set...
Contigs AC150682.2 > Genes (Comprehensive set... < Srrt-201protein coding< Trip6-201protein coding < Slc12a9-202retained intron < Slc12a9-203retained intron
< Srrt-212protein coding < Trip6-203protein coding < Slc12a9-204protein coding
< Srrt-209protein coding < Trip6-202retained intron
< Srrt-211nonsense mediated decay < Trip6-204lncRNA
< Srrt-214retained intron < Slc12a9-201protein coding
< Srrt-210nonsense mediated decay
Regulatory Build
137.31Mb 137.32Mb 137.33Mb 137.34Mb Reverse strand 39.04 kb
Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank
Gene Legend Protein Coding
merged Ensembl/Havana Ensembl protein coding
Non-Protein Coding
processed transcript RNA gene pseudogene
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Transcript: ENSMUST00000039991
< Slc12a9-201protein coding
Reverse strand 19.04 kb
ENSMUSP00000038... Transmembrane heli... Low complexity (Seg) Pfam Amino acid permease/ SLC12A domain SLC12A transporter, C-terminal
PANTHER Solute carrier family 12 member 9
PTHR11827 Gene3D 1.20.1740.10
All sequence SNPs/i... Sequence variants (dbSNP and all other sources)
Variant Legend
missense variant synonymous variant
Scale bar 0 80 160 240 320 400 480 560 640 720 800 914
We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC.
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