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    Atp13a4 ATPase 13A4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 288026, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Atp13a4provided by RGD
    Official Full Name
    ATPase 13A4provided by RGD
    Primary source
    RGD:1306927
    See related
    EnsemblRapid:ENSRNOG00000001714 AllianceGenome:RGD:1306927
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1306927
    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. Orthologous to human ATP13A4 (ATPase 13A4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 34.8), Brain (RPKM 20.7) and 1 other tissue See more
    Orthologs
    human mouse all
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    Genomic context

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    See Atp13a4 in Genome Data Viewer
    Location:
    11q22
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (84727014..84864747)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (71222196..71359933)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (74833824..74968160)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481019 Neighboring gene OPA1, mitochondrial dynamin like GTPase Neighboring gene interleukin 13 receptor subunit alpha 1, pseudogene 1 Neighboring gene uncharacterized LOC102552083 Neighboring gene ATPase 13A5 Neighboring gene phospholipase A and acyltransferase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The E646D-ATP13A4 mutation associated with autism reveals a defect in calcium regulation. Vallipuram J, et al. Cell Mol Neurobiol, 2010 Mar. PMID 19731010
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 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 P-type transmembrane 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
    		  
    acts_upstream_of_or_within intracellular calcium ion homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in monoatomic cation transmembrane transport IEA
    Inferred from Electronic Annotation
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in recycling endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    probable cation-transporting ATPase 13A4
    Names
    ATPase type 13A4
    NP_001178587.2
    XP_008767018.1
    XP_038944033.1
    XP_038944034.1
    XP_038944035.1
    XP_063126444.1

    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_001191658.2 → NP_001178587.2  probable cation-transporting ATPase 13A4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      F1M9L4
      Related
      ENSRNOP00000002333.6, ENSRNOT00000002333.9
      Conserved Domains (2) summary
      cd07542
      Location:174 → 1000
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:17 → 142
      P5-ATPase; P5-type ATPase cation transporter

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086029.1 Reference GRCr8

      Range
      84727014..84864747
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039088105.2 → XP_038944033.1  probable cation-transporting ATPase 13A4 isoform X1

      UniProtKB/TrEMBL
      F1M9L4
      Conserved Domains (2) summary
      cd07542
      Location:174 → 1000
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:17 → 142
      P5-ATPase; P5-type ATPase cation transporter

    2. XM_008768796.4 → XP_008767018.1  probable cation-transporting ATPase 13A4 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AH69
      Related
      ENSRNOP00000091978.1, ENSRNOT00000107765.2
      Conserved Domains (4) summary
      pfam00122
      Location:228 → 472
      E1-E2_ATPase; E1-E2 ATPase
      pfam00690
      Location:170 → 218
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam12409
      Location:18 → 137
      P5-ATPase; P5-type ATPase cation transporter
      pfam13246
      Location:596 → 635
      Cation_ATPase; Cation transport ATPase (P-type)

    3. XM_063270374.1 → XP_063126444.1  probable cation-transporting ATPase 13A4 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AH69

    4. XM_039088106.2 → XP_038944034.1  probable cation-transporting ATPase 13A4 isoform X2

      Conserved Domains (1) summary
      cd07542
      Location:82 → 908
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

    5. XM_039088107.1 → XP_038944035.1  probable cation-transporting ATPase 13A4 isoform X3

      Conserved Domains (1) summary
      cd07542
      Location:1 → 768
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

    RNA

    1. XR_005490999.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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