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

    Gene ID: 8671, updated on 12-Oct-2019

    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
    109.20190905 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (71062646..71572087)
    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 BioSystems

    • Bicarbonate transporters, organism-specific biosystem (from REACTOME)
      Bicarbonate transporters, organism-specific biosystemRespiratory oxidation in the mitochondria produces carbon dioxide (CO2) as a waste product. CO2 is in equilibrium with bicarbonate (HCO3-) and is the body's central pH buffering system. HCO3- is char...
    • Bile secretion, organism-specific biosystem (from KEGG)
      Bile secretion, organism-specific biosystemBile is a vital secretion, essential for digestion and absorption of fats and fat-soluble vitamins in the small intestine. Moreover, bile is an important route of elimination for excess cholesterol a...
    • Bile secretion, conserved biosystem (from KEGG)
      Bile secretion, conserved biosystemBile is a vital secretion, essential for digestion and absorption of fats and fat-soluble vitamins in the small intestine. Moreover, bile is an important route of elimination for excess cholesterol a...
    • Pancreatic secretion, organism-specific biosystem (from KEGG)
      Pancreatic secretion, organism-specific biosystemThe pancreas performs both exocrine and endocrine functions. The exocrine pancreas consists of two parts, the acinar and duct cells. The primary functions of pancreatic acinar cells are to synthesiz...
    • Pancreatic secretion, conserved biosystem (from KEGG)
      Pancreatic secretion, conserved biosystemThe pancreas performs both exocrine and endocrine functions. The exocrine pancreas consists of two parts, the acinar and duct cells. The primary functions of pancreatic acinar cells are to synthesiz...
    • Proximal tubule bicarbonate reclamation, organism-specific biosystem (from KEGG)
      Proximal tubule bicarbonate reclamation, organism-specific biosystemOne of the major tasks of the renal proximal tubule (PT) is to secrete acid into the tubule lumen, thereby reabsorbing approximately 80% of the filtered bicarbonate (HCO3(-)), as well as generating "...
    • Proximal tubule bicarbonate reclamation, conserved biosystem (from KEGG)
      Proximal tubule bicarbonate reclamation, conserved biosystemOne of the major tasks of the renal proximal tubule (PT) is to secrete acid into the tubule lumen, thereby reabsorbing approximately 80% of the filtered bicarbonate (HCO3(-)), as well as generating "...
    • SLC-mediated transmembrane transport, organism-specific biosystem (from REACTOME)
      SLC-mediated transmembrane transport, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the m...
    • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
      Transmembrane transport of small molecules, organism-specific biosystem
      Transmembrane transport of small molecules
    • Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystem (from REACTOME)
      Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystemTeleologically, one might argue that inorganic cation and anion transport would be evolutionarily among the oldest transport functions. Eight families comprise the group that transports exclusively i...

    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
    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
     
    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 TAS
    Traceable Author Statement
    more info
     
    inorganic anion transport IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of intracellular pH IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sodium ion transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular exosome HDA PubMed 
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    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_001134742.1NP_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)
      AA349118, AC019089, AC079230, AC096713, AV724814, BE855478, EF531618
      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_003759.3NP_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, AF007216
      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 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_000004.12 Reference GRCh38.p13 Primary Assembly

      Range
      71062646..71572087
      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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