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SLC4A4 solute carrier family 4 member 4 [ Homo sapiens (human) ]

Gene ID: 8671, updated on 9-Jun-2020

Summary

Official Symbol
SLC4A4provided by HGNC
Official Full Name
solute carrier family 4 member 4provided by HGNC
Primary source
HGNC:HGNC:11030
See related
Ensembl:ENSG00000080493 MIM:603345
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
KNBC; NBC1; NBC2; pNBC; HNBC1; hhNMC; kNBC1; SLC4A5; NBCe1-A
Summary
This gene encodes a sodium bicarbonate cotransporter (NBC) involved in the regulation of bicarbonate secretion and absorption and intracellular pH. Mutations in this gene are associated with proximal renal tubular acidosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
Expression
Biased expression in kidney (RPKM 56.0), pancreas (RPKM 31.5) and 12 other tissues See more
Orthologs

Genomic context

See SLC4A4 in Genome Data Viewer
Location:
4q13.3
Exon count:
36
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (71062646..71572083)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (72053003..72437804)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene MOB kinase activator 1B Neighboring gene deoxycytidine kinase Neighboring gene probable UDP-sugar transporter protein SLC35A4 Neighboring gene lactate dehydrogenase A like 6E, pseudogene Neighboring gene uncharacterized LOC107986285 Neighboring gene uncharacterized LOC105377271

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?

Phenotypes

Associated conditions

Description Tests
Renal tubular acidosis, proximal, with ocular abnormalities and mental retardation
MedGen: C1970309 OMIM: 604278 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
NHGRI GWA Catalog
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
NHGRI GWA Catalog
Impact of ancestry and common genetic variants on QT interval in African Americans.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp781H1314

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
inorganic anion exchanger activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sodium:bicarbonate symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium:bicarbonate symporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
sodium:bicarbonate symporter activity TAS
Traceable Author Statement
more info
PubMed 
symporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
anion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
bicarbonate transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bicarbonate transport IDA
Inferred from Direct Assay
more info
PubMed 
bicarbonate transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
bicarbonate transport TAS
Traceable Author Statement
more info
 
inorganic anion transport IEA
Inferred from Electronic Annotation
more info
 
positive regulation of glycolytic process IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of glycolytic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of intracellular pH IDA
Inferred from Direct Assay
more info
PubMed 
regulation of intracellular pH IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of intracellular pH IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of intracellular pH ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
regulation of membrane potential IDA
Inferred from Direct Assay
more info
PubMed 
regulation of membrane potential ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
sodium ion export across plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
sodium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
sodium ion transport IDA
Inferred from Direct Assay
more info
PubMed 
transmembrane transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
basolateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
spanning component of plasma membrane RCA
inferred from Reviewed Computational Analysis
more info
PubMed 

General protein information

Preferred Names
electrogenic sodium bicarbonate cotransporter 1
Names
Na(+)/HCO3(-) cotransporter
sodium bicarbonate cotransporter 1 (sodium bicarbonate cotransporter, kidney; sodium bicarbonate cotransporter, pancreas)
solute carrier family 4 (sodium bicarbonate cotransporter), member 4
solute carrier family 4, sodium bicarbonate cotransporter, member 4, brain type
solute carrier family 4, sodium bicarbonate cotransporter, member 5

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_012653.1 RefSeqGene

    Range
    5001..389802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001098484.3NP_001091954.1  electrogenic sodium bicarbonate cotransporter 1 isoform 1

    See identical proteins and their annotated locations for NP_001091954.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AC019089, AC079230, AC096713, AC110783
    Consensus CDS
    CCDS43236.1
    UniProtKB/Swiss-Prot
    Q9Y6R1
    UniProtKB/TrEMBL
    A0A024RD97
    Related
    ENSP00000264485.5, ENST00000264485.11
    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  2. NM_001134742.2NP_001128214.1  electrogenic sodium bicarbonate cotransporter 1 isoform 3

    See identical proteins and their annotated locations for NP_001128214.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 3' coding region that results in a frameshift, compared to variant 1. It encodes isoform 3 which has a longer and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC019089, AC079230, AC096713, AC110783
    Consensus CDS
    CCDS47071.1
    UniProtKB/TrEMBL
    A5JJ20
    Related
    ENSP00000393557.1, ENST00000425175.5
    Conserved Domains (3) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
    pfam00955
    Location:436955
    HCO3_cotransp; HCO3- transporter family
    pfam07565
    Location:137387
    Band_3_cyto; Band 3 cytoplasmic domain
  3. NM_003759.4NP_003750.1  electrogenic sodium bicarbonate cotransporter 1 isoform 2

    See identical proteins and their annotated locations for NP_003750.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and an isoform (2) with a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC019089, AC079230, AC110783
    Consensus CDS
    CCDS3549.1
    UniProtKB/Swiss-Prot
    Q9Y6R1
    Related
    ENSP00000344272.3, ENST00000340595.3
    Conserved Domains (1) summary
    TIGR00834
    Location:65959
    ae; anion exchange protein

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    71062646..71572083
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024454269.1XP_024310037.1  electrogenic sodium bicarbonate cotransporter 1 isoform X2

    Conserved Domains (1) summary
    TIGR00834
    Location:1141008
    ae; anion exchange protein
  2. XM_024454268.1XP_024310036.1  electrogenic sodium bicarbonate cotransporter 1 isoform X2

    Conserved Domains (1) summary
    TIGR00834
    Location:1141008
    ae; anion exchange protein
  3. XM_024454270.1XP_024310038.1  electrogenic sodium bicarbonate cotransporter 1 isoform X3

    Related
    ENSP00000497468.1, ENST00000649996.1
    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  4. XM_024454272.1XP_024310040.1  electrogenic sodium bicarbonate cotransporter 1 isoform X3

    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  5. XM_024454271.1XP_024310039.1  electrogenic sodium bicarbonate cotransporter 1 isoform X3

    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  6. XM_024454267.1XP_024310035.1  electrogenic sodium bicarbonate cotransporter 1 isoform X1

    Conserved Domains (1) summary
    TIGR00834
    Location:1401034
    ae; anion exchange protein
  7. XM_017008792.1XP_016864281.1  electrogenic sodium bicarbonate cotransporter 1 isoform X4

  8. XM_017008793.1XP_016864282.1  electrogenic sodium bicarbonate cotransporter 1 isoform X5

  9. XM_011532390.2XP_011530692.1  electrogenic sodium bicarbonate cotransporter 1 isoform X6

    Conserved Domains (2) summary
    pfam00955
    Location:250769
    HCO3_cotransp; HCO3- transporter family
    pfam07565
    Location:59201
    Band_3_cyto; Band 3 cytoplasmic domain
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