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SLC12A6 solute carrier family 12 member 6 [ Homo sapiens (human) ]

Gene ID: 9990, updated on 12-Oct-2019

Summary

Official Symbol
SLC12A6provided by HGNC
Official Full Name
solute carrier family 12 member 6provided by HGNC
Primary source
HGNC:HGNC:10914
See related
Ensembl:ENSG00000140199 MIM:604878
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KCC3; ACCPN; KCC3A; KCC3B
Summary
This gene is a member of the K-Cl cotransporter (KCC) family. K-Cl cotransporters are integral membrane proteins that lower intracellular chloride concentrations below the electrochemical equilibrium potential. The proteins encoded by this gene are activated by cell swelling induced by hypotonic conditions. Alternate splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are associated with agenesis of the corpus callosum with peripheral neuropathy. [provided by RefSeq, Jul 2008]
Expression
Broad expression in testis (RPKM 15.1), bone marrow (RPKM 10.0) and 24 other tissues See more
Orthologs

Genomic context

See SLC12A6 in Genome Data Viewer
Location:
15q14
Exon count:
27
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (34229784..34338057, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (34522197..34630265, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene piggyBac transposable element derived 4 Neighboring gene katanin regulatory subunit B1 like 1 Neighboring gene ER membrane protein complex subunit 4 Neighboring gene NOP10 ribonucleoprotein Neighboring gene NUT midline carcinoma family member 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp434D2135

Gene Ontology Provided by GOA

Function Evidence Code Pubs
potassium:chloride symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
potassium:chloride symporter activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
angiogenesis NAS
Non-traceable Author Statement
more info
PubMed 
cell volume homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular hypotonic salinity response IDA
Inferred from Direct Assay
more info
PubMed 
chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chloride ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chloride transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ion transport IDA
Inferred from Direct Assay
more info
PubMed 
ion transport TAS
Traceable Author Statement
more info
 
potassium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
potassium ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
basolateral plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
cell IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
solute carrier family 12 member 6
Names
K-Cl cotransporter 3
electroneutral potassium-chloride cotransporter 3
potassium chloride cotransporter 3
potassium chloride cotransporter KCC3a-S3
potassium-chloride transporter-3a
potassium-chloride transporter-3b
solute carrier family 12 (potassium/chloride transporter), member 6
solute carrier family 12 (potassium/chloride transporters), member 6

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007951.1 RefSeqGene

    Range
    5001..113069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_270

mRNA and Protein(s)

  1. NM_001042494.2NP_001035959.1  solute carrier family 12 member 6 isoform c

    See identical proteins and their annotated locations for NP_001035959.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an additional exon in its 5' UTR and uses an alternate in-frame splice site in the first protein coding exon, compared to variant 1. The encoded protein (isoform c) uses a downstream start codon, compared to isoform a.
    Source sequence(s)
    AC021822, AC079203, AF531259
    Consensus CDS
    CCDS42012.1
    UniProtKB/Swiss-Prot
    Q9UHW9
    UniProtKB/TrEMBL
    A0A024R9K8
    Related
    ENSP00000387725.2, ENST00000458406.6
    Conserved Domains (3) summary
    TIGR00930
    Location:501091
    2a30; K-Cl cotransporter
    pfam03522
    Location:7151091
    SLC12; Solute carrier family 12
    cl00456
    Location:150301
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. NM_001042495.2NP_001035960.1  solute carrier family 12 member 6 isoform c

    See identical proteins and their annotated locations for NP_001035960.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an additional exon in its 5' UTR and uses an alternate in-frame splice site in the first protein coding exon, compared to variant 1. The encoded protein (isoform c) uses a downstream start codon, compared to isoform a.
    Source sequence(s)
    AC079203, BC070107
    Consensus CDS
    CCDS42012.1
    UniProtKB/Swiss-Prot
    Q9UHW9
    UniProtKB/TrEMBL
    A0A024R9K8, Q6NSI7
    Related
    ENSP00000380814.2, ENST00000397702.6
    Conserved Domains (3) summary
    TIGR00930
    Location:501091
    2a30; K-Cl cotransporter
    pfam03522
    Location:7151091
    SLC12; Solute carrier family 12
    cl00456
    Location:150301
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. NM_001042496.2NP_001035961.1  solute carrier family 12 member 6 isoform d

    See identical proteins and their annotated locations for NP_001035961.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has an additional exon in its 5' UTR and uses an alternate in-frame splice site in the first protein coding exon, compared to variant 1. The encoded protein (isoform d) uses a downstream start codon, compared to isoform a.
    Source sequence(s)
    AC021822, AC079203, DQ138323
    Consensus CDS
    CCDS42011.1
    UniProtKB/Swiss-Prot
    Q9UHW9
    Related
    ENSP00000452776.1, ENST00000558589.5
    Conserved Domains (3) summary
    TIGR00930
    Location:1001141
    2a30; K-Cl cotransporter
    pfam03522
    Location:7651141
    SLC12; Solute carrier family 12
    cl00456
    Location:200351
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. NM_001042497.2NP_001035962.1  solute carrier family 12 member 6 isoform e

    See identical proteins and their annotated locations for NP_001035962.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an alternate in-frame exon in the coding region, compared to variant 1. The encoded protein (isoform e) is shorter, compared to isoform a.
    Source sequence(s)
    AC021822, AC079203, AF531258
    Consensus CDS
    CCDS42010.1
    UniProtKB/Swiss-Prot
    Q9UHW9
    Related
    ENSP00000380819.2, ENST00000397707.6
    Conserved Domains (3) summary
    TIGR00930
    Location:941135
    2a30; K-Cl cotransporter
    pfam03522
    Location:7591135
    SLC12; Solute carrier family 12
    cl00456
    Location:194345
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. NM_001365088.1NP_001352017.1  solute carrier family 12 member 6 isoform a

    Status: REVIEWED

    Source sequence(s)
    AC079203, AF116242, AF477977, BC033894, BC051744, BX648195
    Related
    ENSP00000346112.3, ENST00000354181.8
    Conserved Domains (1) summary
    TIGR00930
    Location:1091150
    2a30; K-Cl cotransporter
  6. NM_005135.2NP_005126.1  solute carrier family 12 member 6 isoform b

    See identical proteins and their annotated locations for NP_005126.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate exon for the 5' UTR and 5' coding region, compared to variant 1. The encoded protein (isoform b) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC021822, AC079203, AF108831
    Consensus CDS
    CCDS10036.1
    UniProtKB/Swiss-Prot
    Q9UHW9
    Related
    ENSP00000290209.5, ENST00000290209.9
    Conserved Domains (3) summary
    TIGR00930
    Location:581099
    2a30; K-Cl cotransporter
    pfam03522
    Location:7231099
    SLC12; Solute carrier family 12
    cl00456
    Location:158309
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  7. NM_133647.1NP_598408.1  solute carrier family 12 member 6 isoform a

    See identical proteins and their annotated locations for NP_598408.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC079203, AF105366
    Consensus CDS
    CCDS58352.1
    UniProtKB/Swiss-Prot
    Q9UHW9
    UniProtKB/TrEMBL
    A0A024R9I5
    Related
    ENSP00000454168.1, ENST00000560611.5
    Conserved Domains (1) summary
    TIGR00930
    Location:1091150
    2a30; K-Cl cotransporter

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    34229784..34338057 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006720793.4XP_006720856.1  solute carrier family 12 member 6 isoform X1

    Related
    ENSP00000452705.1, ENST00000560164.5
    Conserved Domains (3) summary
    TIGR00930
    Location:1091101
    2a30; K-Cl cotransporter
    pfam03522
    Location:7251101
    SLC12; Solute carrier family 12
    cl00456
    Location:184311
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_011522269.3XP_011520571.1  solute carrier family 12 member 6 isoform X2

    Conserved Domains (2) summary
    TIGR00930
    Location:109680
    2a30; K-Cl cotransporter
    cl00456
    Location:209360
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RNA

  1. XR_931960.3 RNA Sequence

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