SLC9B1 solute carrier family 9 member B1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC9B1provided by HGNC
Official Full Name: solute carrier family 9 member B1provided by HGNC
Primary source: HGNC:HGNC:24244
See related: Ensembl:ENSG00000164037 MIM:611527; AllianceGenome:HGNC:24244
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: NHA1; NHEDC1
Summary: The protein encoded by this gene is a sodium/hydrogen exchanger and transmembrane protein. Highly conserved orthologs of this gene have been found in other mammalian species. The expression of this gene may be limited to testis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
Expression: Broad expression in testis (RPKM 16.0), kidney (RPKM 1.8) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q24

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (102885049..103019705, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (106199371..106331591, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (103806206..103940862, complement)

Chromosome 4 - NC_000004.12 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 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?

DNA methylation patterns in maternal blood at four CpG sites in SLC9B1 are predictive of fetal intolerance of labor during the late second and early third trimester.
Title: SLC9B1 methylation predicts fetal intolerance of labor.
Results identified multiple cis-acting DNA regulatory elements in the 5 end of the SLC9B1 gene and shown that DNA methylation at these elements could provide mechanisms by which SLC9B1 expression is restricted to male germ cells.
Title: Identification and characterization of methylation-dependent/independent DNA regulatory elements in the human SLC9B1 gene.
cloning and characterization of a novel NHEDC1 (Na+/H+ exchanger like domain containing 1) gene; it was mapped to chromosome 4p24; molecular weight of NHEDC1 is about 56 KDa; it is exclusively expressed in the testis
Title: Cloning of a novel human NHEDC1 (Na+/H+ exchanger like domain containing 1) gene expressed specifically in testis.

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of solute carrier family 9, subfamily B (cation proton antiporter 2), member 1 (SLC9B1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D4S246 (e-PCR)
- UniSTS:147049

GDB:335751 (e-PCR)
- UniSTS:156601

WI-22115 (e-PCR)
- UniSTS:16853

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables sodium:proton antiporter activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in flagellated sperm motility	ISS Inferred from Sequence or Structural Similarity more info
involved_in inorganic cation transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic ion transmembrane transport	TAS Traceable Author Statement more info
involved_in proton transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of intracellular pH	ISS Inferred from Sequence or Structural Similarity more info
involved_in single fertilization	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in plasma membrane	TAS Traceable Author Statement more info
located_in sperm principal piece	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: sodium/hydrogen exchanger 9B1

Names: NHE domain-containing protein 1; Na(+)/H(+) exchanger-like domain-containing protein 1; sodium/hydrogen exchanger-like domain-containing protein 1; solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1; solute carrier family 9, subfamily B (cation proton antiporter 2), member 1; testicular tissue protein Li 127

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_008662.3 RefSeqGene

Range

5000..123777

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001100874.3 → NP_001094344.2 sodium/hydrogen exchanger 9B1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC018797, AC083826, AC097485

Consensus CDS

CCDS47119.1

UniProtKB/TrEMBL

A0A140VJQ1

Related

ENSP00000378269.3, ENST00000394789.7

Conserved Domains (1) summary

cl01133
Location:140 → 445

Na_H_Exchanger; Sodium/hydrogen exchanger family
NM_139173.4 → NP_631912.3 sodium/hydrogen exchanger 9B1 isoform 1

Status: REVIEWED

Description

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

Source sequence(s)

AC083826, AC097485

Consensus CDS

CCDS34041.1

UniProtKB/Swiss-Prot

A1KXV1, B9EH04, C9JBP7, Q49A30, Q4ZJI4, Q8NCV2, Q8WVZ0

UniProtKB/TrEMBL

A0A140VJQ1

Related

ENSP00000296422.7, ENST00000296422.12

Conserved Domains (1) summary

cl01133
Location:140 → 480

Na_H_Exchanger; Sodium/hydrogen exchanger family

RNA

NR_047513.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences, 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)

AC018797, AC083826, AC097485

Related

ENST00000514972.5
NR_047515.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) has multiple differences, 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)

AC018797, AC083826, AC097485

Related

ENST00000503584.5