SLC4A8 solute carrier family 4 member 8 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC4A8provided by HGNC
Official Full Name: solute carrier family 4 member 8provided by HGNC
Primary source: HGNC:HGNC:11034
See related: Ensembl:ENSG00000050438 MIM:605024; AllianceGenome:HGNC:11034
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: NBC3; NDCBE
Summary: The protein encoded by this gene is a membrane protein that functions to transport sodium and bicarbonate ions across the cell membrane. The encoded protein is important for pH regulation in neurons. The activity of this protein can be inhibited by 4,4'-Di-isothiocyanatostilbene-2,2'-disulfonic acid (DIDS). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
Expression: Biased expression in testis (RPKM 5.0), brain (RPKM 4.6) and 9 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.13

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (51391446..51515763)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (51354255..51479285)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (51785230..51909547)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE.
Title: Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE.
The crystal structure at 2.8 A resolution of the regulatory N-terminal domain of human NDCBE represents the first crystal structure of an electroneutral sodium-bicarbonate cotransporter. The crystal structure forms an equivalent dimeric interface as observed for the cytoplasmic domain of Band 3, and thus establishes that the consensus motif VTVLP is the key minimal dimerization motif.
Title: The crystal structure of the regulatory domain of the human sodium-driven chloride/bicarbonate exchanger.
This study confirmed the presence in human cDNA of mouse NDCBE-like transcripts (human NDCBE-A) and three novel transcripts NDCBE-C, NDCBE-D, and NDCBE-D'.
Title: Cloning and characterization of novel human SLC4A8 gene products encoding Na+-driven Cl-/HCO3(-) exchanger variants NDCBE-A, -C, and -D.

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

EBI GWAS Catalog

Description
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

fk57e05.x1 (e-PCR)
- UniSTS:201226

D12S1633 (e-PCR), detects polymorphism
- UniSTS:25131

D8S2279 (e-PCR)
- UniSTS:473907

sY3084 (e-PCR)
- UniSTS:515126

WI-11123 (e-PCR)
- UniSTS:44875

L18426 (e-PCR)
- UniSTS:34648

D1S1423 (e-PCR)
- UniSTS:149619

D11S3114 (e-PCR)
- UniSTS:152207

G60556 (e-PCR)
- UniSTS:137662

L18023 (e-PCR)
- UniSTS:79818

NoName (e-PCR)
- UniSTS:486613

GDB:631802 (e-PCR)
- UniSTS:158429

D5S1597E (e-PCR)
- UniSTS:151019

G64245 (e-PCR)
- UniSTS:166648

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables bicarbonate transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables chloride transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables sodium ion transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables sodium,bicarbonate:chloride antiporter activity	IDA Inferred from Direct Assay more info	PubMed
enables sodium,bicarbonate:chloride antiporter activity	IEA Inferred from Electronic Annotation more info
enables sodium:bicarbonate symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium:bicarbonate symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables solute:inorganic anion antiporter activity	TAS Traceable Author Statement more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in basolateral protein secretion	IEA Inferred from Electronic Annotation more info
involved_in bicarbonate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in bicarbonate transport	IDA Inferred from Direct Assay more info	PubMed
involved_in bicarbonate transport	TAS Traceable Author Statement more info
involved_in chloride transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within modulation of chemical synaptic transmission	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of synaptic vesicle exocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of intracellular pH	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of intracellular pH	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of intracellular pH	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of membrane potential	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation 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 apical plasma membrane	IEA Inferred from Electronic Annotation more info
located_in asymmetric synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in axon terminus	ISS Inferred from Sequence or Structural Similarity more info
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in glial cell projection	ISS Inferred from Sequence or Structural Similarity more info
located_in glutamatergic synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in hippocampal mossy fiber	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in neuronal cell body membrane	ISS Inferred from Sequence or Structural Similarity more info
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	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in presynapse	ISS Inferred from Sequence or Structural Similarity more info
located_in presynaptic membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in symmetric synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in terminal bouton	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: electroneutral sodium bicarbonate exchanger 1

Names: electroneutral Na(+)-driven Cl-HCO3 exchanger; k-NBC3; solute carrier family 4, sodium bicarbonate cotransporter, member 8

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

NG_032675.2 RefSeqGene

Range

38385..129317

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001039960.3 → NP_001035049.1 electroneutral sodium bicarbonate exchanger 1 isoform a

See identical proteins and their annotated locations for NP_001035049.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC025097, AW118662, DQ063579

Consensus CDS

CCDS44890.1

UniProtKB/Swiss-Prot

A0MMZ1, B4DHY0, E7EML0, F5GZ31, F5H7F5, O94843, O95233, Q004B4, Q2Y0W8, Q8N3U2, Q8TC60, Q9UKX8

Related

ENSP00000405812.2, ENST00000453097.7

Conserved Domains (3) summary

TIGR00834
Location:117 → 1005

ae; anion exchange protein

pfam00955
Location:445 → 958

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:145 → 404

Band_3_cyto; Band 3 cytoplasmic domain
NM_001258401.3 → NP_001245330.1 electroneutral sodium bicarbonate exchanger 1 isoform c

See identical proteins and their annotated locations for NP_001245330.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.

Source sequence(s)

AC025097, AK295315, AW118662, DQ975204

Consensus CDS

CCDS73470.1

UniProtKB/Swiss-Prot

Q2Y0W8

Related

ENSP00000351483.4, ENST00000358657.7

Conserved Domains (3) summary

TIGR00834
Location:64 → 952

ae; anion exchange protein

pfam00955
Location:392 → 905

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:92 → 351

Band_3_cyto; Band 3 cytoplasmic domain
NM_001258402.2 → NP_001245331.1 electroneutral sodium bicarbonate exchanger 1 isoform d

See identical proteins and their annotated locations for NP_001245331.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

BC025994, DB220099

UniProtKB/Swiss-Prot

Q2Y0W8

Conserved Domains (1) summary

cl26877
Location:117 → 623

Band_3_cyto; Band 3 cytoplasmic domain
NM_001258403.2 → NP_001245332.1 electroneutral sodium bicarbonate exchanger 1 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' and 3' UTRs and coding sequences compared to variant 1. The resulting isoform (e) is shorter at the N-terminus and has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AC107031, AL831915

Consensus CDS

CCDS58232.1

UniProtKB/TrEMBL

B4DS29

Related

ENSP00000442561.2, ENST00000514353.7

Conserved Domains (3) summary

pfam07565
Location:92 → 351

Band_3_cyto; Band 3 cytoplasmic domain

pfam13900
Location:695 → 714

GVQW; Putative domain of unknown function

cl23746
Location:392 → 671

HCO3_cotransp; HCO3- transporter family
NM_001267615.2 → NP_001254544.1 electroneutral sodium bicarbonate exchanger 1 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (7) has an alternate first exon and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (f) is shorter at the N-terminus and has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AK295315, BC025994

Consensus CDS

CCDS58233.1

UniProtKB/Swiss-Prot

Q2Y0W8

Related

ENSP00000441520.1, ENST00000535225.6

Conserved Domains (2) summary

pfam07565
Location:92 → 351

Band_3_cyto; Band 3 cytoplasmic domain

cl23746
Location:392 → 593

HCO3_cotransp; HCO3- transporter family
NM_001405266.1 → NP_001392195.1 electroneutral sodium bicarbonate exchanger 1 isoform e

Status: REVIEWED

Source sequence(s)

AC046135, AC107031

Consensus CDS

CCDS58232.1
NM_001405268.1 → NP_001392197.1 electroneutral sodium bicarbonate exchanger 1 isoform 7

Status: REVIEWED

Source sequence(s)

AC025097, AC107031
NM_001405270.1 → NP_001392199.1 electroneutral sodium bicarbonate exchanger 1 isoform 8

Status: REVIEWED

Source sequence(s)

AC025097, AC046135, AC107031

RNA

NR_047672.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks most of the 3' end and contains an alternate 3' exon compared to variant 1. This variant is not thought to be protein-coding.

Source sequence(s)

AI377345, DB220099

Related

ENST00000548811.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

51391446..51515763

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011539011.2 → XP_011537313.1 electroneutral sodium bicarbonate exchanger 1 isoform X2

Conserved Domains (1) summary

cl26877
Location:64 → 970

Band_3_cyto; Band 3 cytoplasmic domain
XM_011539010.2 → XP_011537312.1 electroneutral sodium bicarbonate exchanger 1 isoform X1

Conserved Domains (1) summary

cl26877
Location:117 → 1023

Band_3_cyto; Band 3 cytoplasmic domain
XM_047429911.1 → XP_047285867.1 electroneutral sodium bicarbonate exchanger 1 isoform X3

Related

ENST00000319957.10
XM_006719700.2 → XP_006719763.1 electroneutral sodium bicarbonate exchanger 1 isoform X4

UniProtKB/TrEMBL

B4DS29

Conserved Domains (3) summary

pfam07565
Location:145 → 404

Band_3_cyto; Band 3 cytoplasmic domain

pfam13900
Location:748 → 767

GVQW; Putative domain of unknown function

cl23746
Location:445 → 724

HCO3_cotransp; HCO3- transporter family
XM_011539014.4 → XP_011537316.1 electroneutral sodium bicarbonate exchanger 1 isoform X5

Conserved Domains (1) summary

pfam00955
Location:1 → 487

HCO3_cotransp; HCO3- transporter family

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

51354255..51479285

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054373876.1 → XP_054229851.1 electroneutral sodium bicarbonate exchanger 1 isoform X2
XM_054373875.1 → XP_054229850.1 electroneutral sodium bicarbonate exchanger 1 isoform X1
XM_054373877.1 → XP_054229852.1 electroneutral sodium bicarbonate exchanger 1 isoform X4
XM_054373878.1 → XP_054229853.1 electroneutral sodium bicarbonate exchanger 1 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_004858.2: Suppressed sequence

Description

NM_004858.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.