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SLC4A3 solute carrier family 4 member 3 [ Homo sapiens (human) ]

Gene ID: 6508, updated on 3-Apr-2024

Summary

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Official Symbol
SLC4A3provided by HGNC
Official Full Name
solute carrier family 4 member 3provided by HGNC
Primary source
HGNC:HGNC:11029
See related
Ensembl:ENSG00000114923 MIM:106195; AllianceGenome:HGNC:11029
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
AE3; SQT7; SLC2C; CAE3/BAE3
Summary
The protein encoded by this gene is a plasma membrane anion exchange protein. The encoded protein has been found in brain, heart, kidney, small intestine, and lung. [provided by RefSeq, May 2016]
Expression
Biased expression in heart (RPKM 53.3), ovary (RPKM 25.3) and 5 other tissues See more
Orthologs
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Genomic context

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Location:
2q35
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (219627630..219641971)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (220112359..220126699)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (220492352..220506693)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17156 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:220469784-220470983 Neighboring gene serine/threonine kinase 11 interacting protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220472989-220473488 Neighboring gene uncharacterized LOC124908064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220492855-220493557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220493558-220494259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220508228-220508999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220509771-220510541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220510542-220511311 Neighboring gene CRISPRi-validated cis-regulatory element chr2.6714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220528008-220528541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220537307-220537807 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:220548733-220549932 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:220552697-220553896 Neighboring gene DNAJB6 pseudogene 3 Neighboring gene ribosomal protein L23 pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Investigation of SLA4A3 as a candidate gene for human retinal disease. Downs LM, et al. J Negat Results Biomed, 2016 May 23. PMID 27211793, Free PMC Article
  2. Boric acid increases the expression levels of human anion exchanger genes SLC4A2 and SLC4A3. Akbas F, et al. Genet Mol Res, 2012 Apr 3. PMID 22576912
  3. The AE gene family of Cl/HCO3- exchangers. Alper SL, et al. J Nephrol, 2002 Mar-Apr. PMID 12027221
  4. Detection of Cl--HCO3- and Na+-H+ exchangers in human airways epithelium. Al-Bazzaz FJ, et al. JOP, 2001 Jul. PMID 11875273
  5. Regulation of Na+-independent Cl-/HCO3- exchangers by pH. Alper SL, et al. JOP, 2001 Jul. PMID 11875255

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic analysis identifies the SLC4A3 anion exchanger as a major gene for short QT syndrome.
    Title: Genetic analysis identifies the SLC4A3 anion exchanger as a major gene for short QT syndrome.
  2. Identify a missense mutation in the anion exchanger (AE3)-encoding SLC4A3 gene in two unrelated families with short QT syndrome. The mutation causes reduced surface expression of AE3 and reduced membrane bicarbonate transport.
    Title: Loss-of-activity-mutation in the cardiac chloride-bicarbonate exchanger AE3 causes short QT syndrome.
  3. SLC4A3 remains an excellent candidate gene for human retinal degeneration, and with the advent of whole exome and whole genome sequencing of cohorts of molecularly unsolved patients with syndromic and non-syndromic forms of retinal degeneration
    Title: Investigation of SLA4A3 as a candidate gene for human retinal disease.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic susceptibility to febrile seizures: case-control association studies.
  5. It was concluded that the A867D allele is a functional mutant of AE3 and that the decreased activity of this mutation may cause changes in cell volume and abnormal intracellular pH.
    Title: Characterization of an epilepsy-associated variant of the human Cl-/HCO3(-) exchanger AE3.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Short QT syndrome 7
MedGen: C5774304 OMIM: 620231 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide SNP associations with rubella-specific cytokine responses in measles-mumps-rubella vaccine recipients.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables bicarbonate transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables chloride:bicarbonate antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables solute:inorganic anion antiporter activity TAS
Traceable Author Statement
more info
  
enables transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in bicarbonate transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in bicarbonate transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in bicarbonate transport TAS
Traceable Author Statement
more info
  
acts_upstream_of_or_within cardiac conduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cardiac muscle cell action potential ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in pH reduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of cardiac muscle cell action potential IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of intracellular pH IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in external side of plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
anion exchange protein 3
Names
Anion exchanger 3, neuronal
cardiac/brain band 3-like protein
neuronal band 3-like protein
solute carrier family 4 (anion exchanger), member 3

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_050748.2 RefSeqGene

    Range
    5002..19343
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001326559.2 → NP_001313488.2  anion exchange protein 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a longer protein (isoform 2), compared to isoform 1. Variants 2 and 4 both encode the same isoform (2).
    Source sequence(s)
    AC009955, KF459589
    Consensus CDS
    CCDS2446.1
    UniProtKB/TrEMBL
    B4DR53
    Conserved Domains (2) summary
    PHA03307
    Location:2 → 292
    PHA03307; transcriptional regulator ICP4; Provisional
    TIGR00834
    Location:349 → 1258
    ae; anion exchange protein

  2. NM_005070.4 → NP_005061.3  anion exchange protein 3 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC009955, KF459589
    Consensus CDS
    CCDS2445.1
    UniProtKB/Swiss-Prot
    A6H8L2, A8K1Q9, B7ZVX6, B9EGD1, P48751, Q6YIQ9
    UniProtKB/TrEMBL
    B4DR53
    Related
    ENSP00000350756.3, ENST00000358055.8
    Conserved Domains (1) summary
    TIGR00834
    Location:322 → 1231
    ae; anion exchange protein

  3. NM_201574.3 → NP_963868.3  anion exchange protein 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a longer protein (isoform 2), compared to isoform 1. Variants 2 and 4 both encode the same isoform (2).
    Source sequence(s)
    AC009955, KF459589
    Consensus CDS
    CCDS2446.1
    UniProtKB/TrEMBL
    B4DR53
    Related
    ENSP00000273063.6, ENST00000273063.10
    Conserved Domains (2) summary
    PHA03307
    Location:2 → 292
    PHA03307; transcriptional regulator ICP4; Provisional
    TIGR00834
    Location:349 → 1258
    ae; anion exchange protein

RNA

  1. NR_048551.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC009955, KF459589
    Related
    ENST00000425141.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    219627630..219641971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047445555.1 → XP_047301511.1  anion exchange protein 3 isoform X1

    UniProtKB/Swiss-Prot
    A6H8L2, A8K1Q9, B7ZVX6, B9EGD1, P48751, Q6YIQ9
    Related
    ENSP00000314006.3, ENST00000317151.7

  2. XM_011511665.3 → XP_011509967.1  anion exchange protein 3 isoform X2

    UniProtKB/TrEMBL
    B4DR53
    Conserved Domains (4) summary
    TIGR00834
    Location:296 → 1205
    ae; anion exchange protein
    pfam00955
    Location:649 → 1135
    HCO3_cotransp; HCO3- transporter family
    pfam07565
    Location:331 → 593
    Band_3_cyto; Band 3 cytoplasmic domain
    pfam15384
    Location:102 → 219
    PAXX; PAXX, PAralog of XRCC4 and XLF, also called C9orf142

  3. XM_047445557.1 → XP_047301513.1  anion exchange protein 3 isoform X4

  4. XM_047445556.1 → XP_047301512.1  anion exchange protein 3 isoform X4

  5. XM_005246790.5 → XP_005246847.1  anion exchange protein 3 isoform X3

    UniProtKB/TrEMBL
    B4DR53
    Conserved Domains (1) summary
    TIGR00834
    Location:124 → 1033
    ae; anion exchange protein

  6. XM_011511667.3 → XP_011509969.1  anion exchange protein 3 isoform X5

    UniProtKB/TrEMBL
    B4DS65
    Conserved Domains (2) summary
    pfam00955
    Location:184 → 670
    HCO3_cotransp; HCO3- transporter family
    pfam07565
    Location:4 → 128
    Band_3_cyto; Band 3 cytoplasmic domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    220112359..220126699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343463.1 → XP_054199438.1  anion exchange protein 3 isoform X1

  2. XM_054343466.1 → XP_054199441.1  anion exchange protein 3 isoform X4

  3. XM_054343464.1 → XP_054199439.1  anion exchange protein 3 isoform X2

  4. XM_054343467.1 → XP_054199442.1  anion exchange protein 3 isoform X4

  5. XM_054343465.1 → XP_054199440.1  anion exchange protein 3 isoform X3

  6. XM_054343468.1 → XP_054199443.1  anion exchange protein 3 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48751.2 GenPept UniProtKB/Swiss-Prot:P48751

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