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    ATP13A4 ATPase 13A4 [ Homo sapiens (human) ]

    Gene ID: 84239, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ATP13A4provided by HGNC
    Official Full Name
    ATPase 13A4provided by HGNC
    Primary source
    HGNC:HGNC:25422
    See related
    Ensembl:ENSG00000127249 MIM:609556; AllianceGenome:HGNC:25422
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable ATPase-coupled monoatomic cation transmembrane transporter activity and polyamine transmembrane transporter activity. Predicted to be involved in intracellular calcium ion homeostasis and polyamine transmembrane transport. Predicted to be located in early endosome membrane and recycling endosome membrane. Predicted to be active in endoplasmic reticulum membrane and late endosome membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in thyroid (RPKM 10.9), lung (RPKM 10.1) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATP13A4 in Genome Data Viewer
    Location:
    3q29
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (193398967..193593119, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (196094346..196288725, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (193116756..193272684, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized protein MGC2889 Neighboring gene phospholipase A and acyltransferase 1 Neighboring gene ATPase 13A5 Neighboring gene ATP13A5 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:193065706-193066384 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:193107044-193107612 Neighboring gene ATP13A4 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:193310659-193311310 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:193311311-193311962 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 23 Neighboring gene OPA1 mitochondrial dynamin like GTPase Neighboring gene OPA1 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:193364377-193365576 Neighboring gene uncharacterized LOC102724808 Neighboring gene MPRA-validated peak4976 silencer

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. ATP13A4 Upregulation Drives the Elevated Polyamine Transport System in the Breast Cancer Cell Line MCF7. van Veen S, et al. Biomolecules, 2023 May 31. PMID 37371498, Free PMC Article
    2. mRNA expression of the P5 ATPase ATP13A4 is increased in Broca's area from subjects with schizophrenia. Gibbons AS, et al. World J Biol Psychiatry, 2020 Jun. PMID 30501451
    3. Characterization of a novel cation transporter ATPase gene (ATP13A4) interrupted by 3q25-q29 inversion in an individual with language delay. Kwasnicka-Crawford DA, et al. Genomics, 2005 Aug. PMID 15925480
    4. TNF-α inhibits glucocorticoid receptor-induced gene expression by reshaping the GR nuclear cofactor profile. Dendoncker K, et al. Proc Natl Acad Sci U S A, 2019 Jun 25. PMID 31182584, Free PMC Article
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ATP13A4 Upregulation Drives the Elevated Polyamine Transport System in the Breast Cancer Cell Line MCF7.
      Title: ATP13A4 Upregulation Drives the Elevated Polyamine Transport System in the Breast Cancer Cell Line MCF7.
    2. mRNA expression of the P5 ATPase ATP13A4 is increased in Broca's area from subjects with schizophrenia.
      Title: mRNA expression of the P5 ATPase ATP13A4 is increased in Broca's area from subjects with schizophrenia.
    3. ATP13A4 is a novel gene coding for a cation-transporting P-type ATPase and is interrupted by 3q25-q29 inversion in an individual with language delay
      Title: Characterization of a novel cation transporter ATPase gene (ATP13A4) interrupted by 3q25-q29 inversion in an individual with language delay.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • MGC126545, DKFZp761I1011

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATPase-coupled monoatomic cation transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATPase-coupled monoatomic cation transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables P-type ion transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables polyamine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular calcium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in monoatomic cation transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoatomic ion transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in polyamine transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in recycling endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    probable cation-transporting ATPase 13A4
    Names
    ATPase type 13A4
    P5-ATPase
    cation-transporting P5-ATPase
    NP_115655.2
    XP_016862808.2
    XP_047305019.1
    XP_054204062.1
    XP_054204063.1

    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_032279.4 → NP_115655.2  probable cation-transporting ATPase 13A4

      See identical proteins and their annotated locations for NP_115655.2

      Status: VALIDATED

      Source sequence(s)
      AC105057, AK096510, AY358110, AY823162, BC101496, DA117883
      Consensus CDS
      CCDS3304.2
      UniProtKB/Swiss-Prot
      B7WPC7, Q4VNC1, Q6UY23, Q8N1Q9, Q9H043
      UniProtKB/TrEMBL
      B7WPN9
      Related
      ENSP00000339182.4, ENST00000342695.9
      Conserved Domains (6) summary
      COG4087
      Location:820 → 869
      COG4087; Soluble P-type ATPase [General function prediction only]
      TIGR01657
      Location:17 → 1114
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      pfam00122
      Location:268 → 471
      E1-E2_ATPase; E1-E2 ATPase
      pfam00690
      Location:157 → 217
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam12409
      Location:16 → 136
      P5-ATPase; P5-type ATPase cation transporter
      pfam13246
      Location:595 → 634
      Cation_ATPase; Cation transport ATPase (P-type)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      193398967..193593119 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449063.1 → XP_047305019.1  probable cation-transporting ATPase 13A4 isoform X1

      UniProtKB/TrEMBL
      B7WPN9

    2. XM_017007319.2 → XP_016862808.2  probable cation-transporting ATPase 13A4 isoform X2

    RNA

    1. XR_007095757.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      196094346..196288725 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348087.1 → XP_054204062.1  probable cation-transporting ATPase 13A4 isoform X1

      UniProtKB/TrEMBL
      B7WPN9

    2. XM_054348088.1 → XP_054204063.1  probable cation-transporting ATPase 13A4 isoform X2

    RNA

    1. XR_008486842.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4VNC1.3 GenPept UniProtKB/Swiss-Prot:Q4VNC1

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