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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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