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

Gene ID: 8671, updated on 8-Dec-2022

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; AllianceGenome:HGNC:11030
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; NBCe1; 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
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Genomic context

See SLC4A4 in Genome Data Viewer
Location:
4q13.3
Exon count:
37
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (71062660..71572083)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (74529023..74914352)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (72052482..72437800)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2882 Neighboring gene MOB kinase activator 1B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:71869952-71870648 Neighboring gene deoxycytidine kinase Neighboring gene uncharacterized LOC124900712 Neighboring gene probable UDP-sugar transporter protein SLC35A4 Neighboring gene SLC35A4 upstream open reading frame protein-like 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
Autosomal recessive proximal renal tubular acidosis
MedGen: C1970309 OMIM: 604278 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
EBI GWAS Catalog
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
EBI GWAS Catalog
Impact of ancestry and common genetic variants on QT interval in African Americans.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract.
EBI GWAS 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
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sodium:bicarbonate symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables sodium:bicarbonate symporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables sodium:bicarbonate symporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables sodium:bicarbonate symporter activity TAS
Traceable Author Statement
more info
PubMed 
enables solute:inorganic anion antiporter activity IEA
Inferred from Electronic Annotation
more info
 
enables symporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
involved_in bicarbonate transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in bicarbonate transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in bicarbonate transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in bicarbonate transport TAS
Traceable Author Statement
more info
 
involved_in inorganic anion transport IEA
Inferred from Electronic Annotation
more info
 
involved_in monoatomic anion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of positive regulation of glycolytic process IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of positive regulation of glycolytic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of regulation of intracellular pH IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of regulation of intracellular pH IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in regulation of intracellular pH IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of regulation of intracellular pH ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
acts_upstream_of regulation of membrane potential IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of regulation of membrane potential ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in sodium ion export across plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sodium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sodium ion transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in transmembrane transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
is_active_in basolateral plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in basolateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in basolateral plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular exosome HDA PubMed 
is_active_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in plasma membrane RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
electrogenic sodium bicarbonate cotransporter 1
Names
Na(+)/HCO3(-) cotransporter
kidney type Na+/HCO3- cotransporter
pancreatic sodium bicarbonate 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)

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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_012653.2 RefSeqGene

    Range
    129107..514425
    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
    Q9UP50, 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, ENST00000340595.4
    Conserved Domains (1) summary
    TIGR00834
    Location:65959
    ae; anion exchange protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    71062660..71572083
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024454268.2XP_024310036.1  electrogenic sodium bicarbonate cotransporter 1 isoform X2

    Related
    ENSP00000513771.1, ENST00000698522.1
    Conserved Domains (1) summary
    TIGR00834
    Location:1141008
    ae; anion exchange protein
  2. XM_024454269.2XP_024310037.1  electrogenic sodium bicarbonate cotransporter 1 isoform X2

    Conserved Domains (1) summary
    TIGR00834
    Location:1141008
    ae; anion exchange protein
  3. XM_024454270.2XP_024310038.1  electrogenic sodium bicarbonate cotransporter 1 isoform X3

    UniProtKB/Swiss-Prot
    Q9UP50
    Related
    ENSP00000497468.1, ENST00000649996.1
    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  4. XM_024454272.2XP_024310040.1  electrogenic sodium bicarbonate cotransporter 1 isoform X3

    UniProtKB/Swiss-Prot
    Q9UP50
    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  5. XM_024454271.2XP_024310039.1  electrogenic sodium bicarbonate cotransporter 1 isoform X3

    UniProtKB/Swiss-Prot
    Q9UP50
    Conserved Domains (1) summary
    TIGR00834
    Location:1091003
    ae; anion exchange protein
  6. XM_024454267.2XP_024310035.1  electrogenic sodium bicarbonate cotransporter 1 isoform X1

    Conserved Domains (1) summary
    TIGR00834
    Location:1401034
    ae; anion exchange protein
  7. XM_017008792.2XP_016864281.1  electrogenic sodium bicarbonate cotransporter 1 isoform X4

  8. XM_047416348.1XP_047272304.1  electrogenic sodium bicarbonate cotransporter 1 isoform X7

  9. XM_017008793.2XP_016864282.1  electrogenic sodium bicarbonate cotransporter 1 isoform X5

  10. XM_011532390.3XP_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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    74529023..74914352
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)