Slc4a7 solute carrier family 4 member 7 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slc4a7provided by RGD
Official Full Name: solute carrier family 4 member 7provided by RGD
Primary source: RGD:621208
See related: Ensembl:ENSRNOG00000005957 AllianceGenome:RGD:621208
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: NBC3; NBCn1
Summary: Predicted to enable sodium:bicarbonate symporter activity. Predicted to be involved in several processes, including auditory receptor cell development; bicarbonate transport; and regulation of intracellular pH. Predicted to act upstream of or within cochlear nucleus development; eye development; and visual perception. Located in several cellular components, including apical plasma membrane; basolateral plasma membrane; and stereocilium. Orthologous to human SLC4A7 (solute carrier family 4 member 7). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 165.8), Thymus (RPKM 78.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p16

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (13015854..13095485, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (10585307..10664780, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (11832611..11912923, complement)

Chromosome 15 - NC_086033.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dynamic localization of the Na+-HCO3- co-transporter NBCn1 to the plasma membrane, centrosomes, spindle and primary cilia.
Title: Dynamic localization of the Na+-HCO3- co-transporter NBCn1 to the plasma membrane, centrosomes, spindle and primary cilia.
Trafficking, localization and degradation of the Na(+),HCO3(-) co-transporter NBCn1 in kidney and breast epithelial cells
Title: Trafficking, localization and degradation of the Na(+),HCO(3)(-) co-transporter NBCn1 in kidney and breast epithelial cells.
The finding of a genotypic influence on SLC4A7 expression and pHi regulation in vascular smooth muscle cells provides an insight into the molecular mechanism underlying the association of variation at the SLC4A7 locus with blood pressure
Title: Increased NBCn1 expression, Na+/HCO3- co-transport and intracellular pH in human vascular smooth muscle cells with a risk allele for hypertension.
PSD-95 interacts with NBCn1 and increases its channel-like activity while negligibly affecting Na/HCO(3) cotransport.
Title: PSD-95 interacts with NBCn1 and enhances channel-like activity without affecting Na/HCO(3) cotransport.
A binding site for calcineurin A beta was found to reside within splice cassette II of NBCn1.
Title: Splice cassette II of Na+,HCO3(-) cotransporter NBCn1 (slc4a7) interacts with calcineurin A: implications for transporter activity and intracellular pH control during rat artery contractions.
Current-voltage relationships showed a positive and nearly linear relationship between NH(4)Cl-mediated current and voltage, which was markedly reduced by NBCn1.
Title: Sodium-bicarbonate cotransporter NBCn1/Slc4a7 inhibits NH4Cl-mediated inward current in Xenopus oocytes.
The electroneutral sodium bicarbonate co-transporter SLC4A7 localizes in mitochondria and suppresses the ischaemia-induced activation of the mitochondrial pathway of apoptosis in coronary endothelial cells.
Title: SLC4A7 sodium bicarbonate co-transporter controls mitochondrial apoptosis in ischaemic coronary endothelial cells.
In acidic conditions, kidney medullary thick ascending DIDS-sensitive bicarbonate extrusion is inactivated, while NBCn1 is upregulated to stimulate ammonium transport.
Title: Sodium-bicarbonate cotransporter NBCn1 in the kidney medullary thick ascending limb cell line is upregulated under acidic conditions and enhances ammonium transport.
It was concluded that NBCn1 in neurons is upregulated by chronic acid loads, and this upregulation is associated with glutamate excitotoxicity.
Title: Neuronal expression of sodium/bicarbonate cotransporter NBCn1 (SLC4A7) and its response to chronic metabolic acidosis.
We conclude that the primary function of cassette II is to reduce NBCn1 protein expression
Title: Inhibition of rat Na+(-)HCO3(-) cotransporter (NBCn1) function and expression by the alternative splice domain.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables monoatomic anion transmembrane transporter activity	IEA Inferred from Electronic Annotation more info
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
enables sodium:bicarbonate symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables sodium:bicarbonate symporter activity	ISO Inferred from Sequence Orthology more info
enables solute:inorganic anion antiporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in auditory receptor cell development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within auditory receptor cell development	ISO Inferred from Sequence Orthology more info
involved_in bicarbonate transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in bicarbonate transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within camera-type eye photoreceptor cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to growth factor stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cochlear nucleus development	ISO Inferred from Sequence Orthology more info
involved_in inorganic anion transport	IEA Inferred from Electronic Annotation more info
involved_in locomotory exploration behavior	ISO Inferred from Sequence Orthology more info
involved_in monoatomic anion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in phagosome acidification	ISO Inferred from Sequence Orthology more info
involved_in purine nucleotide biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in pyrimidine nucleotide biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of intracellular pH	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of intracellular pH	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retina vasculature morphogenesis in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retinal cell programmed cell death	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within visual perception	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in apical plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in basolateral plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in lateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
located_in stereocilium	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sodium bicarbonate cotransporter 3

Names: NBC-like protein; electroneutral sodium bicarbonate cotransporter 1; solute carrier family 4 sodium bicarbonate cotransporter member 7 variant NBCn1-G; solute carrier family 4 sodium bicarbonate cotransporter member 7 variant NBCn1-I; solute carrier family 4 sodium bicarbonate cotransporter member 7 variant NBCn1-J; solute carrier family 4, sodium bicarbonate cotransporter, member 7

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.

mRNA and Protein(s)

NM_001270860.2 → NP_001257789.1 sodium bicarbonate cotransporter 3 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) is shorter compared to isoform 1.

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A0A8L2Q3F3

Related

ENSRNOP00000008759.7, ENSRNOT00000008759.8

Conserved Domains (3) summary

TIGR00834
Location:118 → 1126

ae; anion exchange protein

pfam00955
Location:566 → 1079

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 523

Band_3_cyto; Band 3 cytoplasmic domain
NM_001270861.2 → NP_001257790.1 sodium bicarbonate cotransporter 3 isoform 3

See identical proteins and their annotated locations for NP_001257790.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) is shorter compared to isoform 1.

Source sequence(s)

JAXUCZ010000015

UniProtKB/Swiss-Prot

Q9QYD5, Q9R1L1, Q9R1N3

UniProtKB/TrEMBL

A0A8L2UM25

Related

ENSRNOP00000047758.5, ENSRNOT00000049771.5

Conserved Domains (3) summary

TIGR00834
Location:118 → 1139

ae; anion exchange protein

pfam00955
Location:579 → 1092

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 536

Band_3_cyto; Band 3 cytoplasmic domain
NM_001413732.1 → NP_001400661.1 sodium bicarbonate cotransporter 3 isoform 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

F1M0J3

Related

ENSRNOP00000063542.4, ENSRNOT00000068171.4
NM_001413733.1 → NP_001400662.1 sodium bicarbonate cotransporter 3 isoform 5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A0A0K0WYI6
NM_058211.3 → NP_478118.1 sodium bicarbonate cotransporter 3 isoform 1

See identical proteins and their annotated locations for NP_478118.1

Status: VALIDATED

Description

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

Source sequence(s)

JAXUCZ010000015

UniProtKB/TrEMBL

A0A8L2Q3F3

Related

ENSRNOP00000081091.1, ENSRNOT00000108026.1

Conserved Domains (3) summary

TIGR00834
Location:118 → 1139

ae; anion exchange protein

pfam00955
Location:579 → 1092

HCO3_cotransp; HCO3- transporter family

pfam07565
Location:146 → 536

Band_3_cyto; Band 3 cytoplasmic domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086033.1 Reference GRCr8

Range

13015854..13095485 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039092959.2 → XP_038948887.1 sodium bicarbonate cotransporter 3 isoform X1

UniProtKB/TrEMBL

A0A8L2QV99

Conserved Domains (1) summary

cl26877
Location:118 → 1016

Band_3_cyto; Band 3 cytoplasmic domain
XM_039092960.2 → XP_038948888.1 sodium bicarbonate cotransporter 3 isoform X2

Conserved Domains (1) summary

cl26877
Location:118 → 896

Band_3_cyto; Band 3 cytoplasmic domain
XM_063273919.1 → XP_063129989.1 sodium bicarbonate cotransporter 3 isoform X4
XM_039092961.2 → XP_038948889.1 sodium bicarbonate cotransporter 3 isoform X3

Conserved Domains (1) summary

cl26877
Location:118 → 585

Band_3_cyto; Band 3 cytoplasmic domain