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ATP13A4 ATPase 13A4 [ Homo sapiens (human) ]

Gene ID: 84239, updated on 27-Nov-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, Nov 2024]
Expression
Biased expression in thyroid (RPKM 10.9), lung (RPKM 10.1) and 6 other tissues See more
Orthologs
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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: 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. 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

  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

  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

Gene LinkOut

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

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