Human Gene ATP9A (uc002xwg.1) Description and Page Index
  Description: Homo sapiens ATPase, class II, type 9A (ATP9A), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr20:50,213,314-50,384,908 Size: 171,595 Total Exon Count: 28 Strand: -
Coding Region
   Position: hg19 chr20:50,217,750-50,384,908 Size: 167,159 Coding Exon Count: 28 

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 (chr20:50,213,314-50,384,908)mRNA (may differ from genome)Protein (1047 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: ATP9A_HUMAN
DESCRIPTION: RecName: Full=Probable phospholipid-transporting ATPase IIA; EC=3.6.3.1; AltName: Full=ATPase class II type 9A;
CATALYTIC ACTIVITY: ATP + H(2)O + phospholipid(In) = ADP + phosphate + phospholipid(Out).
SUBCELLULAR LOCATION: Early endosome membrane; Multi-pass membrane protein. Recycling endosome. Golgi apparatus, trans-Golgi network membrane. Note=Efficient exit from the endoplasmic reticulum does not require TMEM30A, nor TMEM30B.
SIMILARITY: Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IV subfamily.
SEQUENCE CAUTION: Sequence=BAD18775.1; Type=Erroneous initiation; Sequence=CAI18889.1; Type=Erroneous gene model prediction; Sequence=CAI19203.1; Type=Erroneous gene model prediction; Sequence=CAI22924.1; Type=Erroneous gene model prediction;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ATP9A
CDC HuGE Published Literature: ATP9A

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001564 Benzo(a)pyrene
  • C006253 pirinixic acid
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • D015632 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • D016604 Aflatoxin B1
  • D000393 Air Pollutants
  • D000643 Ammonium Chloride
  • D001554 Benzene
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 44.84 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 754.89 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -1416.364436-0.319 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
IPR006539 - ATPase_P-typ_Plipid-transl
IPR005834 - Dehalogen-like_hydro
IPR023214 - HAD-like_dom

Pfam Domains:
PF00122 - E1-E2 ATPase
PF00702 - haloacid dehalogenase-like hydrolase
PF13246 - Cation transport ATPase (P-type)
PF16209 - Phospholipid-translocating ATPase N-terminal
PF16212 - Phospholipid-translocating P-type ATPase C-terminal

SCOP Domains:
47266 - 4-helical cytokines
81653 - Calcium ATPase, transduction domain A
56784 - HAD-like
81660 - Metal cation-transporting ATPase, ATP-binding domain N

ModBase Predicted Comparative 3D Structure on O75110
FrontTopSide
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 BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004012 phospholipid-translocating ATPase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0006897 endocytosis
GO:0015914 phospholipid transport
GO:0045332 phospholipid translocation

Cellular Component:
GO:0005768 endosome
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031901 early endosome membrane
GO:0048471 perinuclear region of cytoplasm
GO:0055037 recycling endosome


-  Descriptions from all associated GenBank mRNAs
  AB014511 - Homo sapiens mRNA for KIAA0611 protein, partial cds.
AK172802 - Homo sapiens cDNA FLJ23963 fis, clone HEP15535, highly similar to Potential phospholipid-transporting ATPase IIA (EC 3.6.1.-).
AK299064 - Homo sapiens cDNA FLJ60816 complete cds, highly similar to Probable phospholipid-transporting ATPase IIA (EC 3.6.3.1).
BC167819 - Synthetic construct Homo sapiens clone IMAGE:100068209, MGC:195826 ATPase, class II, type 9A (ATP9A) mRNA, encodes complete protein.
AB385363 - Synthetic construct DNA, clone: pF1KA0611, Homo sapiens ATP9A gene for phospholipid-transporting ATPase IIA, complete cds, without stop codon, in Flexi system.
AF086357 - Homo sapiens full length insert cDNA clone ZD64H11.
BC016044 - Homo sapiens ATPase, class II, type 9A, mRNA (cDNA clone IMAGE:4549698), partial cds.
AK025559 - Homo sapiens cDNA: FLJ21906 fis, clone HEP03772.
BC036759 - Homo sapiens, clone IMAGE:5577438, mRNA.
BC043392 - Homo sapiens ATPase, Class II, type 9A, mRNA (cDNA clone IMAGE:5309798), with apparent retained intron.
JD156260 - Sequence 137284 from Patent EP1572962.
AK026513 - Homo sapiens cDNA: FLJ22860 fis, clone KAT01753.
JD324930 - Sequence 305954 from Patent EP1572962.
BC110591 - Homo sapiens ATPase, class II, type 9A, mRNA (cDNA clone IMAGE:40027528), partial cds.
BC110592 - Homo sapiens ATPase, class II, type 9A, mRNA (cDNA clone IMAGE:40027531), partial cds.
JD456352 - Sequence 437376 from Patent EP1572962.
JD241730 - Sequence 222754 from Patent EP1572962.
BC063701 - Homo sapiens cDNA clone IMAGE:4539878, containing frame-shift errors.

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

Protein O75110 (Reactome details) participates in the following event(s):

R-HSA-939763 P-type ATPases type IV transport external-facing APLs to internal side of the plasma membrane
R-HSA-947591 P-type ATPases type IV transport internal-facing APLs to external side of the plasma membrane
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: ATP9A_HUMAN, ATPIIA, E1P5Y3, E1P5Y4, KIAA0611, NM_006045, NP_006036, O75110, Q5TFW5, Q5TFW6, Q5TFW9, Q6ZMF3, Q9NQK6, Q9NQK7
UCSC ID: uc002xwg.1
RefSeq Accession: NM_006045
Protein: O75110 (aka ATP9A_HUMAN or AT9A_HUMAN)
CCDS: CCDS33489.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006045.1
exon count: 28CDS single in 3' UTR: no RNA size: 7580
ORF size: 3144CDS single in intron: no Alignment % ID: 99.99
txCdsPredict score: 6352.50frame shift in genome: no % Coverage: 100.00
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
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.