Slc9a6 solute carrier family 9 member A6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slc9a6provided by RGD
Official Full Name: solute carrier family 9 member A6provided by RGD
Primary source: RGD:1563582
See related: EnsemblRapid:ENSRNOG00000000879 AllianceGenome:RGD:1563582
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: NHE-6; RGD1563582
Summary: Predicted to enable identical protein binding activity; potassium:proton antiporter activity; and sodium:proton antiporter activity. Involved in glial cell activation and regulation of synaptic vesicle lumen acidification. Is active in presynapse. Human ortholog(s) of this gene implicated in Christianson syndrome. Orthologous to human SLC9A6 (solute carrier family 9 member A6). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Brain (RPKM 158.8), Lung (RPKM 95.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq36

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (139468045..139524111)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (134430677..134486747)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (158979081..159045019)

Chromosome X - NC_086039.1 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 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?

Slc9a6 mutation causes Purkinje cell loss and ataxia in the shaker rat.
Title: Slc9a6 mutation causes Purkinje cell loss and ataxia in the shaker rat.
SCAMP5 mediates activity-dependent enhancement of NHE6 recruitment to synaptic vesicles during synaptic plasticity.
Title: SCAMP5 mediates activity-dependent enhancement of NHE6 recruitment to synaptic vesicles during synaptic plasticity.

Submit: New GeneRIF Correction

General gene information

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Markers

DXRat55 (e-PCR), detects polymorphism
- UniSTS:228434

Slc9a6 (e-PCR), detects polymorphism
- UniSTS:496017

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables potassium:proton antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables potassium:proton antiporter activity	ISO Inferred from Sequence Orthology more info
enables sodium:proton antiporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium:proton antiporter activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within axon extension	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain-derived neurotrophic factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendrite extension	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendritic spine development	ISO Inferred from Sequence Orthology more info
involved_in establishment of cell polarity	ISO Inferred from Sequence Orthology more info
involved_in establishment of cell polarity	ISS Inferred from Sequence or Structural Similarity more info
involved_in glial cell activation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in potassium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within proton transmembrane transport	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 regulation of neurotrophin TRK receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic vesicle lumen acidification	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synaptic vesicle lumen acidification	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation of synaptic vesicle lumen acidification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within synapse organization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in Schaffer collateral - CA1 synapse	ISO Inferred from Sequence Orthology more info
located_in axon terminus	ISO Inferred from Sequence Orthology more info
located_in axonal spine	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in early endosome membrane	ISO Inferred from Sequence Orthology more info
located_in early endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endosome	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
NOT located_in mitochondrion	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	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in presynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in recycling endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in recycling endosome	ISO Inferred from Sequence Orthology more info
located_in recycling endosome membrane	ISO Inferred from Sequence Orthology more info
located_in recycling endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sodium/hydrogen exchanger 6

Names: Na(+)/H(+) exchanger 6; solute carrier family 9 (sodium/hydrogen exchanger), member 6; solute carrier family 9 member 6; solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6

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_001419592.1 → NP_001406521.1 sodium/hydrogen exchanger 6

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

Related

ENSRNOP00000104438.1, ENSRNOT00000122635.1

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_086039.1 Reference GRCr8

Range

139468045..139524111

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039100496.2 → XP_038956424.1 sodium/hydrogen exchanger 6 isoform X2

UniProtKB/TrEMBL

A6KSN8

Conserved Domains (1) summary

TIGR00840
Location:94 → 540

b_cpa1; sodium/hydrogen exchanger 3
XM_217630.11 → XP_217630.3 sodium/hydrogen exchanger 6 isoform X1

See identical proteins and their annotated locations for XP_217630.3

UniProtKB/TrEMBL

A6KSN8

Related

ENSRNOP00000060014.4, ENSRNOT00000066809.5

Conserved Domains (1) summary

pfam00999
Location:177 → 534

Na_H_Exchanger; Sodium/hydrogen exchanger family