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    ATP6V0B ATPase H+ transporting V0 subunit b [ Homo sapiens (human) ]

    Gene ID: 533, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ATP6V0Bprovided by HGNC
    Official Full Name
    ATPase H+ transporting V0 subunit bprovided by HGNC
    Primary source
    HGNC:HGNC:861
    See related
    Ensembl:ENSG00000117410 MIM:603717; AllianceGenome:HGNC:861
    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
    ATP6F; HATPL; VMA16
    Summary
    This gene encodes a portion of the V0 domain of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Activity of this enzyme is necessary for such varied processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
    Expression
    Ubiquitous expression in bone marrow (RPKM 52.4), kidney (RPKM 31.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATP6V0B in Genome Data Viewer
    Location:
    1p34.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (43974960..43978295)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (43846040..43849375)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44440632..44443967)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 796 Neighboring gene importin 13 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:44426574-44427773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44436478-44437024 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:44437355-44438554 Neighboring gene uncharacterized LOC124904167 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44439785-44440618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44440619-44441451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44443584-44444175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44444176-44444766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44444767-44445358 Neighboring gene diphthamide biosynthesis 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44447723-44448312 Neighboring gene beta-1,4-galactosyltransferase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 801 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 802 Neighboring gene Sharpr-MPRA regulatory region 11322 Neighboring gene coiled-coil domain containing 24 Neighboring gene solute carrier family 6 member 9

    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 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. Identification and characterization of the gene encoding a second proteolipid subunit of human vacuolar H(+)-ATPase (ATP6F). Nishigori H, et al. Genomics, 1998 Jun 1. PMID 9653649
    2. Plasmalemmal V-H(+)-ATPases regulate intracellular pH in human lung microvascular endothelial cells. Rojas JD, et al. Biochem Biophys Res Commun, 2004 Aug 6. PMID 15249206
    3. Structural and functional characterization of two human V-ATPase subunit gene promoters. Izumi H, et al. Biochim Biophys Acta, 2003 Jul 28. PMID 12890556
    4. Physical interaction between aldolase and vacuolar H+-ATPase is essential for the assembly and activity of the proton pump. Lu M, et al. J Biol Chem, 2007 Aug 24. PMID 17576770
    5. Structure and Roles of V-type ATPases. Vasanthakumar T, et al. Trends Biochem Sci, 2020 Apr. PMID 32001091

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. there is an important role for physical association between aldolase and the A, B and E subunits of V-ATPase in the regulation of the proton pump
      Title: Physical interaction between aldolase and vacuolar H+-ATPase is essential for the assembly and activity of the proton pump.
    2. These studies show a Na(+)- and HCO(3)(-)-independent pH(cyt) regulatory mechanism in HLMVE cells that is mediated by pmV-ATPases.
      Title: Plasmalemmal V-H(+)-ATPases regulate intracellular pH in human lung microvascular endothelial cells.
    3. proximal promoter region contains cis-acting elements required for expression in cancer cells
      Title: Structural and functional characterization of two human V-ATPase subunit gene promoters.
    Submit: New GeneRIF Correction

    Phenotypes

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    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 ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b (ATP6V0B) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables proton-transporting ATPase activity, rotational mechanism IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi lumen acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endosomal lumen acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in intracellular pH reduction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in lysosomal lumen acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in proton transmembrane transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of macroautophagy NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vacuolar acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in clathrin-coated vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in phagocytic vesicle membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of proton-transporting V-type ATPase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of vacuolar proton-transporting V-type ATPase, V0 domain ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    V-type proton ATPase 21 kDa proteolipid subunit c''
    Names
    ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b
    ATPase, H+ transporting, lysosomal, 21-KD, V0 subunit C-prime, prime
    ATPase, H+ transporting, lysosomal, subunit F
    H(+)-transporting two-sector ATPase, subunit F
    V-ATPase 21 kDa proteolipid subunit
    V-ATPase 21 kDa proteolipid subunit c''
    V-ATPase subunit b
    V-ATPase subunit c''
    V-type proton ATPase 21 kDa proteolipid subunit
    vacuolar ATP synthase 21 kDa proteolipid subunit
    vacuolar proton pump 21 kDa proteolipid subunit
    vacuolar proton pump 21 kDa proteolipid subunit c''
    NP_001034546.1
    NP_001281262.1
    NP_004038.1
    XP_047278606.1
    XP_054193068.1

    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)

    1. NM_001039457.3 → NP_001034546.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform 2

      See identical proteins and their annotated locations for NP_001034546.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame in the 5' coding region and uses a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AI439545, BG475609, D89052
      Consensus CDS
      CCDS41315.1
      UniProtKB/Swiss-Prot
      Q99437
      Related
      ENSP00000236067.4, ENST00000236067.8
      Conserved Domains (2) summary
      cd18177
      Location:2 → 64
      ATP-synt_Vo_c_ATP6F_rpt1; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins
      cd18178
      Location:86 → 150
      ATP-synt_Vo_c_ATP6F_rpt2; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins

    2. NM_001294333.2 → NP_001281262.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform 3

      See identical proteins and their annotated locations for NP_001281262.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate segment in the 3' region, which results in a frameshift, compared to variant 1. The encoded isoform (3) has a longer and distinct C-terminus, compared to variant 1.
      Source sequence(s)
      AL357079
      Consensus CDS
      CCDS72772.1
      UniProtKB/TrEMBL
      E9PNL3
      Related
      ENSP00000434729.1, ENST00000532642.5
      Conserved Domains (2) summary
      PRK08344
      Location:48 → 199
      PRK08344; V-type ATP synthase subunit K; Validated
      pfam00137
      Location:136 → 196
      ATP-synt_C; ATP synthase subunit C

    3. NM_004047.5 → NP_004038.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform 1

      See identical proteins and their annotated locations for NP_004038.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AI439545, D89052
      Consensus CDS
      CCDS505.1
      UniProtKB/Swiss-Prot
      D3DPY5, Q6IB32, Q99437
      UniProtKB/TrEMBL
      E9PNU0
      Related
      ENSP00000431605.1, ENST00000472174.7
      Conserved Domains (2) summary
      cd18177
      Location:49 → 111
      ATP-synt_Vo_c_ATP6F_rpt1; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins
      cd18178
      Location:133 → 197
      ATP-synt_Vo_c_ATP6F_rpt2; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      43974960..43978295
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422650.1 → XP_047278606.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform X1

      Related
      ENSP00000434094.1, ENST00000498664.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      43846040..43849375
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337093.1 → XP_054193068.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99437.1 GenPept UniProtKB/Swiss-Prot:Q99437

    Gene LinkOut

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

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