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

    Gene ID: 150159, updated on 26-Nov-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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    See SLC9B1 in Genome Data Viewer
    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_000004.12Genomic 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. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Lim SH, et al. Mol Syst Biol, 2022 Feb. PMID 35156780, Free PMC Article

    See all (7) 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 Variation Viewer (GRCh37.p13)

    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

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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