Human Gene ATP13A1 (uc002nnh.4) Description and Page Index
  Description: Homo sapiens ATPase type 13A1 (ATP13A1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr19:19,756,010-19,774,503 Size: 18,494 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg19 chr19:19,756,231-19,774,475 Size: 18,245 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr19:19,756,010-19,774,503)mRNA (may differ from genome)Protein (1204 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Probable cation-transporting ATPase 13A1; EC=3.6.3.-;
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (By similarity).
SIMILARITY: Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type V subfamily.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ATP13A1
CDC HuGE Published Literature: ATP13A1

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 43.58 RPKM in Spleen
Total median expression: 968.86 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -3.8028-0.136 Picture PostScript Text
3' UTR -88.39221-0.400 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR023306 - ATPase_cation_domN
IPR008250 - ATPase_P-typ_ATPase-assoc-dom
IPR023300 - ATPase_P-typ_cyto_domA
IPR023299 - ATPase_P-typ_cyto_domN
IPR001757 - ATPase_P-typ_ion-transptr
IPR018303 - ATPase_P-typ_P_site
IPR006544 - ATPase_P-typ_unknown-pump-sp
IPR023214 - HAD-like_dom

Pfam Domains:
PF00122 - E1-E2 ATPase
PF00702 - haloacid dehalogenase-like hydrolase

SCOP Domains:
81653 - Calcium ATPase, transduction domain A
56784 - HAD-like
81660 - Metal cation-transporting ATPase, ATP-binding domain N

ModBase Predicted Comparative 3D Structure on Q9HD20
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003674 molecular_function
GO:0005388 calcium-transporting ATPase activity
GO:0005524 ATP binding
GO:0015410 manganese-transporting ATPase activity
GO:0016787 hydrolase activity
GO:0016887 ATPase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006812 cation transport
GO:0006874 cellular calcium ion homeostasis
GO:0008150 biological_process
GO:0034220 ion transmembrane transport
GO:0070588 calcium ion transmembrane transport
GO:0071421 manganese ion transmembrane transport
GO:0099132 ATP hydrolysis coupled cation transmembrane transport

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043231 intracellular membrane-bounded organelle

-  Descriptions from all associated GenBank mRNAs
  AL834180 - Homo sapiens mRNA; cDNA DKFZp761L1623 (from clone DKFZp761L1623).
BC069211 - Homo sapiens ATPase type 13A1, mRNA (cDNA clone IMAGE:4585878), partial cds.
BC009302 - Homo sapiens ATPase type 13A1, mRNA (cDNA clone IMAGE:4128479), partial cds.
AK172778 - Homo sapiens cDNA FLJ23939 fis, clone HEP01940, highly similar to Cation-transporting ATPase 2 (EC 3.6.3.-).
AF288687 - Homo sapiens CGI-152 protein mRNA, complete cds.
AK026044 - Homo sapiens cDNA: FLJ22391 fis, clone HRC07832.
AK123780 - Homo sapiens cDNA FLJ41786 fis, clone KIDNE2001361, highly similar to Mus musculus catp mRNA for cation-transporting atpase.
AK095287 - Homo sapiens cDNA FLJ37968 fis, clone CTONG2009891, highly similar to Probable cation-transporting ATPase 13A1 (EC 3.6.3.-).
AK125861 - Homo sapiens cDNA FLJ43873 fis, clone TESTI4008429, highly similar to Probable cation-transporting ATPase 2 (EC 3.6.3.-).
AK074798 - Homo sapiens cDNA FLJ90317 fis, clone NT2RP2001514, weakly similar to PROBABLE CALCIUM-TRANSPORTING ATPASE 6 (EC
AK074920 - Homo sapiens cDNA FLJ90439 fis, clone NT2RP3000907, weakly similar to PROBABLE CALCIUM-TRANSPORTING ATPASE 6 (EC
AK130125 - Homo sapiens cDNA FLJ26615 fis, clone MPB06423, highly similar to Probable cation-transporting ATPase 2 (EC 3.6.3.-).
AK074159 - Homo sapiens mRNA for FLJ00232 protein.
AB058728 - Homo sapiens mRNA for KIAA1825 protein, partial cds.
AK056420 - Homo sapiens cDNA FLJ31858 fis, clone NT2RP7001166, highly similar to Probable cation-transporting ATPase 13A1 (EC 3.6.3.-).
JD120935 - Sequence 101959 from Patent EP1572962.
JD276566 - Sequence 257590 from Patent EP1572962.
JD455970 - Sequence 436994 from Patent EP1572962.
JD330188 - Sequence 311212 from Patent EP1572962.
JD239706 - Sequence 220730 from Patent EP1572962.
KJ902938 - Synthetic construct Homo sapiens clone ccsbBroadEn_12332 ATP13A1 gene, encodes complete protein.
BC156250 - Synthetic construct Homo sapiens clone IMAGE:100061633, MGC:190058 ATPase type 13A1 (ATP13A1) mRNA, encodes complete protein.
AB385506 - Synthetic construct DNA, clone: pF1KA1825, Homo sapiens ATP13A1 gene for cation-transporting ATPase 13A1, complete cds, without stop codon, in Flexi system.
CU679291 - Synthetic construct Homo sapiens gateway clone IMAGE:100018156 5' read ATP13A1 mRNA.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9HD20 (Reactome details) participates in the following event(s):

R-HSA-5692462 ATP13A1 transports Mn2+ from cytosol to ER lumen
R-HSA-936837 Ion transport by P-type ATPases
R-HSA-983712 Ion channel transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: AT131_HUMAN, ATP13A, B3KPJ2, B3KTA7, CGI-152, KIAA1825, NM_020410, NP_065143, Q9H6C6, Q9HD20
UCSC ID: uc002nnh.4
RefSeq Accession: NM_020410
Protein: Q9HD20 (aka AT131_HUMAN or ATY2_HUMAN)
CCDS: CCDS32970.2

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_020410.2
exon count: 26CDS single in 3' UTR: no RNA size: 3887
ORF size: 3615CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7277.00frame shift in genome: no % Coverage: 99.41
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.