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    Atp13a4 ATPase type 13A4 [ Mus musculus (house mouse) ]

    Gene ID: 224079, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Atp13a4provided by MGI
    Official Full Name
    ATPase type 13A4provided by MGI
    Primary source
    MGI:MGI:1924456
    See related
    Ensembl:ENSMUSG00000038094 AllianceGenome:MGI:1924456
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    4832416L12; 4631413J11Rik; 9330174J19Rik
    Summary
    Predicted to enable P-type calcium transporter activity. Acts upstream of or within cellular calcium ion homeostasis. Located in endoplasmic reticulum membrane and endosome membrane. Is expressed in brain and embryo. Orthologous to human ATP13A4 (ATPase 13A4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in genital fat pad adult (RPKM 4.5), cerebellum adult (RPKM 2.4) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    16 B2; 16 20.24 cM
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (29208685..29363682, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (29389103..29544864, complement)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene predicted gene 8253 Neighboring gene STARR-seq mESC enhancer starr_40521 Neighboring gene phospholipase A and acyltransferase 1 Neighboring gene ATPase type 13A5 Neighboring gene STARR-seq mESC enhancer starr_40522 Neighboring gene STARR-seq mESC enhancer starr_40523 Neighboring gene zinc finger protein 788 pseudogene Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:29579308-29579525 Neighboring gene STARR-seq mESC enhancer starr_40527 Neighboring gene OPA1, mitochondrial dynamin like GTPase Neighboring gene STARR-seq mESC enhancer starr_40530 Neighboring gene STARR-seq mESC enhancer starr_40532 Neighboring gene STARR-seq mESC enhancer starr_40534 Neighboring gene predicted gene, 32740 Neighboring gene predicted gene, 46567

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    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. Parkinson disease related ATP13A2 evolved early in animal evolution. Sørensen DM, et al. PLoS One, 2018. PMID 29505581, Free PMC Article
    3. Characterization of the P5 subfamily of P-type transport ATPases in mice. Schultheis PJ, et al. Biochem Biophys Res Commun, 2004 Oct 22. PMID 15381061
    4. A mutation in the Srrm4 gene causes alternative splicing defects and deafness in the Bronx waltzer mouse. Nakano Y, et al. PLoS Genet, 2012. PMID 23055939, Free PMC Article
    5. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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 ATPase-coupled monoatomic cation transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables P-type calcium transporter activity IC
    Inferred by Curator
    more info
    		 PubMed 
    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables polyamine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within calcium ion transmembrane transport IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in intracellular calcium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within intracellular calcium ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in polyamine transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    probable cation-transporting ATPase 13A4
    Names
    P5-ATPase
    type V P-type ATPase
    NP_001158084.1
    NP_001158085.1
    NP_766201.3
    XP_006522114.1
    XP_006522116.1
    XP_006522117.1
    XP_006522118.1
    XP_017172444.1
    XP_017172445.1
    XP_030104933.1
    XP_036015780.1
    XP_036015781.1
    XP_036015782.1
    XP_036015783.1
    XP_036015784.1

    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_001164612.1 → NP_001158084.1  probable cation-transporting ATPase 13A4 isoform 1

      See identical proteins and their annotated locations for NP_001158084.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC175464
      Consensus CDS
      CCDS49816.1
      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      UniProtKB/TrEMBL
      S4R234
      Related
      ENSMUSP00000138479.2, ENSMUST00000182627.8
      Conserved Domains (6) summary
      COG4087
      Location:821 → 870
      COG4087; Soluble P-type ATPase [General function prediction only]
      TIGR01657
      Location:18 → 1115
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      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)

    2. NM_001164613.1 → NP_001158085.1  probable cation-transporting ATPase 13A4 isoform 3

      See identical proteins and their annotated locations for NP_001158085.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR, and 3' coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK028776, BE955453
      Consensus CDS
      CCDS49817.1
      UniProtKB/TrEMBL
      A0A0R4J0M2
      Related
      ENSMUSP00000048753.8, ENSMUST00000039090.9
      Conserved Domains (2) summary
      cd07542
      Location:174 → 762
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:18 → 137
      P5-ATPase; P5-type ATPase cation transporter

    3. NM_172613.4 → NP_766201.3  probable cation-transporting ATPase 13A4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC175464
      Consensus CDS
      CCDS59623.1
      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      UniProtKB/TrEMBL
      E9QPP7
      Related
      ENSMUSP00000060987.9, ENSMUST00000057018.15
      Conserved Domains (6) summary
      COG4087
      Location:802 → 851
      COG4087; Soluble P-type ATPase [General function prediction only]
      TIGR01657
      Location:18 → 1096
      P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
      pfam00122
      Location:228 → 453
      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:577 → 616
      Cation_ATPase; Cation transport ATPase (P-type)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000082.7 Reference GRCm39 C57BL/6J

      Range
      29208685..29363682 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017316955.3 → XP_017172444.1  probable cation-transporting ATPase 13A4 isoform X3

      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      Conserved Domains (2) summary
      cd07542
      Location:174 → 1001
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:18 → 137
      P5-ATPase; P5-type ATPase cation transporter

    2. XM_006522051.5 → XP_006522114.1  probable cation-transporting ATPase 13A4 isoform X4

      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      Conserved Domains (2) summary
      cd07542
      Location:174 → 931
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:18 → 137
      P5-ATPase; P5-type ATPase cation transporter

    3. XM_036159889.1 → XP_036015782.1  probable cation-transporting ATPase 13A4 isoform X2

      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      Conserved Domains (2) summary
      cd07542
      Location:174 → 956
      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

    4. XM_036159887.1 → XP_036015780.1  probable cation-transporting ATPase 13A4 isoform X1

      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      Conserved Domains (2) summary
      cd07542
      Location:143 → 970
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:48 → 111
      P5-ATPase; P5-type ATPase cation transporter

    5. XM_036159890.1 → XP_036015783.1  probable cation-transporting ATPase 13A4 isoform X5

      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      Conserved Domains (1) summary
      cd07542
      Location:82 → 909
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

    6. XM_036159891.1 → XP_036015784.1  probable cation-transporting ATPase 13A4 isoform X6

      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      Conserved Domains (1) summary
      cd07542
      Location:1 → 769
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

    7. XM_036159888.1 → XP_036015781.1  probable cation-transporting ATPase 13A4 isoform X1

      UniProtKB/Swiss-Prot
      Q5XF90, Q80V28, Q8C105, Q8C184
      Conserved Domains (2) summary
      cd07542
      Location:143 → 970
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:48 → 111
      P5-ATPase; P5-type ATPase cation transporter

    8. XM_030249073.1 → XP_030104933.1  probable cation-transporting ATPase 13A4 isoform X9

      Conserved Domains (1) summary
      cd07542
      Location:1 → 471
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

    9. XM_006522055.4 → XP_006522118.1  probable cation-transporting ATPase 13A4 isoform X9

      Conserved Domains (1) summary
      cd07542
      Location:1 → 471
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p

    10. XM_006522053.5 → XP_006522116.1  probable cation-transporting ATPase 13A4 isoform X7

      Conserved Domains (2) summary
      cd07542
      Location:174 → 948
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:18 → 137
      P5-ATPase; P5-type ATPase cation transporter

    11. XM_006522054.4 → XP_006522117.1  probable cation-transporting ATPase 13A4 isoform X8

      Conserved Domains (2) summary
      cd07542
      Location:174 → 915
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:18 → 137
      P5-ATPase; P5-type ATPase cation transporter

    12. XM_017316956.3 → XP_017172445.1  probable cation-transporting ATPase 13A4 isoform X10

      UniProtKB/TrEMBL
      A0A0R4J0M2
      Conserved Domains (2) summary
      cd07542
      Location:174 → 762
      P-type_ATPase_cation; P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p
      pfam12409
      Location:18 → 137
      P5-ATPase; P5-type ATPase cation transporter

    RNA

    1. XR_004939185.1 RNA Sequence

    2. XR_001781812.3 RNA Sequence

    3. XR_003951779.2 RNA Sequence

      Related
      ENSMUST00000182013.8

    4. XR_384556.5 RNA Sequence

    5. XR_004939184.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5XF90.1 GenPept UniProtKB/Swiss-Prot:Q5XF90

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