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

Gene ID: 150159, updated on 11-Apr-2024

Summary

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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

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Location:
4q24
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (102885049..103019705, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (106199371..106331591, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (103806206..103940862, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 D3 Neighboring gene UBE2D3 antisense RNA 1 Neighboring gene RNA, U7 small nuclear 151 pseudogene Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21762 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15603 Neighboring gene CDGSH iron sulfur domain 2 Neighboring gene poly(A) binding protein cytoplasmic 1 pseudogene 7 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:103859100-103859749 Neighboring gene ACTR3B pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:103940703-103941203 Neighboring gene solute carrier family 9 member B2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21763 Neighboring gene 3-hydroxybutyrate dehydrogenase 2 Neighboring gene centromere protein E Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:104119362-104119916

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. SLC9B1 methylation predicts fetal intolerance of labor. Knight AK, et al. Epigenetics, 2018. PMID 29235940, Free PMC Article
  2. Identification and characterization of methylation-dependent/independent DNA regulatory elements in the human SLC9B1 gene. Kumar PL, et al. Gene, 2015 May 1. PMID 25701605, Free PMC Article
  3. Cloning of a novel human NHEDC1 (Na+/H+ exchanger like domain containing 1) gene expressed specifically in testis. Ye G, et al. Mol Biol Rep, 2006 Sep. PMID 16850186
  4. A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication. Yeung ML, et al. J Biol Chem, 2009 Jul 17. PMID 19460752, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
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

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

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

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC131641

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

  1. NG_008662.3 RefSeqGene

    Range
    5000..123777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  1. 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

  2. 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

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    102885049..103019705 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    106199371..106331591 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q4ZJI4.2 GenPept UniProtKB/Swiss-Prot:Q4ZJI4

Gene LinkOut

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