Human Gene ATP2B3 (ENST00000263519.5_5) from GENCODE V47lift37
  Description: ATPase plasma membrane Ca2+ transporting 3, transcript variant 5 (from RefSeq NM_001388362.1)
Gencode Transcript: ENST00000263519.5_5
Gencode Gene: ENSG00000067842.19_10
Transcript (Including UTRs)
   Position: hg19 chrX:152,783,100-152,848,387 Size: 65,288 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chrX:152,801,706-152,845,756 Size: 44,051 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:152,783,100-152,848,387)mRNA (may differ from genome)Protein (1220 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: AT2B3_HUMAN
DESCRIPTION: RecName: Full=Plasma membrane calcium-transporting ATPase 3; Short=PMCA3; EC=3.6.3.8; AltName: Full=Plasma membrane calcium ATPase isoform 3; AltName: Full=Plasma membrane calcium pump isoform 3;
FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium out of the cell.
CATALYTIC ACTIVITY: ATP + H(2)O + Ca(2+)(Side 1) = ADP + phosphate + Ca(2+)(Side 2).
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Isoform XE and isoform XB are the most abundant isoforms and are detected at low levels in brain and fetal skeletal muscle. The other isoforms are only found at lower levels and not in fetal tissues.
SIMILARITY: Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIB subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ATP2B3
Diseases sorted by gene-association score: spinocerebellar ataxia, x-linked 1* (890), spinocerebellar ataxia, x-linked 5* (350), microcephaly* (151), alacrima, achalasia, and mental retardation syndrome* (82), intellectual disability* (71), cerebellar ataxia (14), sialolithiasis (11), striatonigral degeneration (9), detrusor sphincter dyssynergia (8), cerebellar disease (7), olivopontocerebellar atrophy (7), kluver-bucy syndrome (7), adrenal adenoma (7), multiple cranial nerve palsy (7), ideomotor apraxia (6), ataxia (5), glossopharyngeal nerve disease (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 15.28 RPKM in Brain - Cerebellum
Total median expression: 93.09 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
5' UTR -226.10480-0.471 Picture PostScript Text
3' UTR -870.102631-0.331 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
IPR022141 - ATP_Ca_trans_C
IPR023306 - ATPase_cation_domN
IPR008250 - ATPase_P-typ_ATPase-assoc-dom
IPR006408 - ATPase_P-typ_Ca-transp_PMCA
IPR006068 - ATPase_P-typ_cation-transptr_C
IPR004014 - ATPase_P-typ_cation-transptr_N
IPR023300 - ATPase_P-typ_cyto_domA
IPR023299 - ATPase_P-typ_cyto_domN
IPR001757 - ATPase_P-typ_ion-transptr
IPR018303 - ATPase_P-typ_P_site
IPR023298 - ATPase_P-typ_TM_dom
IPR005834 - Dehalogen-like_hydro
IPR023214 - HAD-like_dom

Pfam Domains:
PF00122 - E1-E2 ATPase
PF00689 - Cation transporting ATPase, C-terminus
PF00690 - Cation transporter/ATPase, N-terminus
PF00702 - haloacid dehalogenase-like hydrolase
PF08282 - haloacid dehalogenase-like hydrolase
PF12424 - Plasma membrane calcium transporter ATPase C terminal
PF13246 - Cation transport ATPase (P-type)

SCOP Domains:
81653 - Calcium ATPase, transduction domain A
56784 - HAD-like
81660 - Metal cation-transporting ATPase, ATP-binding domain N
81665 - Calcium ATPase, transmembrane domain M

ModBase Predicted Comparative 3D Structure on Q16720
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005388 calcium-transporting ATPase activity
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005524 ATP binding
GO:0015085 calcium ion transmembrane transporter activity
GO:0016787 hydrolase activity
GO:0030165 PDZ domain binding
GO:0046872 metal ion binding

Biological Process:
GO:0006811 ion transport
GO:0006816 calcium ion transport
GO:0034220 ion transmembrane transport
GO:0051480 regulation of cytosolic calcium ion concentration
GO:0070588 calcium ion transmembrane transport
GO:0099132 ATP hydrolysis coupled cation transmembrane transport
GO:1903779 regulation of cardiac conduction
GO:1990034 calcium ion export from cell

Cellular Component:
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043231 intracellular membrane-bounded organelle
GO:1903561 extracellular vesicle


-  Descriptions from all associated GenBank mRNAs
  U57971 - Human calcium ATPase isoform 3x/a mRNA, complete cds.
U60414 - Human plasma membrane calcium ATPase isoform 3x/b mRNA, complete cds.
BC130009 - Homo sapiens ATPase, Ca++ transporting, plasma membrane 3, mRNA (cDNA clone MGC:158926 IMAGE:40067815), complete cds.
AK307765 - Homo sapiens cDNA, FLJ97713.
AK308705 - Homo sapiens cDNA, FLJ98746.
DQ201779 - Homo sapiens PMCA3a (ATP2B3) mRNA, partial cds.
JD519271 - Sequence 500295 from Patent EP1572962.
JD241351 - Sequence 222375 from Patent EP1572962.
JD380635 - Sequence 361659 from Patent EP1572962.
KJ904423 - Synthetic construct Homo sapiens clone ccsbBroadEn_13817 ATP2B3 gene, encodes complete protein.
U15689 - Human clone hPMCA3g alternatively spliced plasma membrane calcium pump (ATP2B3) mRNA, partial cds.
U15690 - Human clone hPMCA3a alternatively spliced plasma membrane calcium pump (ATP2B3) mRNA, partial cds.
JD170396 - Sequence 151420 from Patent EP1572962.
JD157851 - Sequence 138875 from Patent EP1572962.
JD133377 - Sequence 114401 from Patent EP1572962.
JD363798 - Sequence 344822 from Patent EP1572962.
JD141474 - Sequence 122498 from Patent EP1572962.
JD404581 - Sequence 385605 from Patent EP1572962.
JD046523 - Sequence 27547 from Patent EP1572962.
JD051300 - Sequence 32324 from Patent EP1572962.
JD100321 - Sequence 81345 from Patent EP1572962.
JD056965 - Sequence 37989 from Patent EP1572962.
JD097346 - Sequence 78370 from Patent EP1572962.
JD363764 - Sequence 344788 from Patent EP1572962.
JD377848 - Sequence 358872 from Patent EP1572962.
JD342748 - Sequence 323772 from Patent EP1572962.
JD120642 - Sequence 101666 from Patent EP1572962.
JD532816 - Sequence 513840 from Patent EP1572962.
JD339046 - Sequence 320070 from Patent EP1572962.
JD343229 - Sequence 324253 from Patent EP1572962.
JD471378 - Sequence 452402 from Patent EP1572962.
JD339985 - Sequence 321009 from Patent EP1572962.
JD471159 - Sequence 452183 from Patent EP1572962.
JD065599 - Sequence 46623 from Patent EP1572962.
JD250824 - Sequence 231848 from Patent EP1572962.
BC047580 - Homo sapiens ATPase, Ca++ transporting, plasma membrane 3, mRNA (cDNA clone IMAGE:4820468).
JD081415 - Sequence 62439 from Patent EP1572962.
JD537851 - Sequence 518875 from Patent EP1572962.
JD363609 - Sequence 344633 from Patent EP1572962.
JD350559 - Sequence 331583 from Patent EP1572962.
JD323673 - Sequence 304697 from Patent EP1572962.
JD378823 - Sequence 359847 from Patent EP1572962.
JD382437 - Sequence 363461 from Patent EP1572962.
AK094500 - Homo sapiens cDNA FLJ37181 fis, clone BRALZ2001279.
JD148813 - Sequence 129837 from Patent EP1572962.
JD096182 - Sequence 77206 from Patent EP1572962.
JD157148 - Sequence 138172 from Patent EP1572962.
JD270395 - Sequence 251419 from Patent EP1572962.
JD499581 - Sequence 480605 from Patent EP1572962.
JD360081 - Sequence 341105 from Patent EP1572962.
JD436790 - Sequence 417814 from Patent EP1572962.
JD334267 - Sequence 315291 from Patent EP1572962.
JD540945 - Sequence 521969 from Patent EP1572962.
JD339959 - Sequence 320983 from Patent EP1572962.
JD471045 - Sequence 452069 from Patent EP1572962.
JD173380 - Sequence 154404 from Patent EP1572962.
JD226521 - Sequence 207545 from Patent EP1572962.
JD111062 - Sequence 92086 from Patent EP1572962.
JD221954 - Sequence 202978 from Patent EP1572962.
JD282992 - Sequence 264016 from Patent EP1572962.
JD516088 - Sequence 497112 from Patent EP1572962.
JD051700 - Sequence 32724 from Patent EP1572962.
JD439905 - Sequence 420929 from Patent EP1572962.
JD477760 - Sequence 458784 from Patent EP1572962.
JD348641 - Sequence 329665 from Patent EP1572962.
JD228208 - Sequence 209232 from Patent EP1572962.
JD056341 - Sequence 37365 from Patent EP1572962.
JD117726 - Sequence 98750 from Patent EP1572962.
JD338823 - Sequence 319847 from Patent EP1572962.
JD206420 - Sequence 187444 from Patent EP1572962.
JD173085 - Sequence 154109 from Patent EP1572962.

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

Protein Q16720 (Reactome details) participates in the following event(s):

R-HSA-418309 ATP2B1-4 transport cytosolic Ca2+ to extracellular region
R-HSA-418359 Reduction of cytosolic Ca++ levels
R-HSA-936837 Ion transport by P-type ATPases
R-HSA-5578775 Ion homeostasis
R-HSA-418360 Platelet calcium homeostasis
R-HSA-983712 Ion channel transport
R-HSA-5576891 Cardiac conduction
R-HSA-418346 Platelet homeostasis
R-HSA-382551 Transport of small molecules
R-HSA-397014 Muscle contraction
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: AT2B3_HUMAN, ATP2B3 , B7WNR8, B7WNY5, ENST00000263519.1, ENST00000263519.2, ENST00000263519.3, ENST00000263519.4, NM_001388362, Q12995, Q16720, Q16858, uc317hkf.1, uc317hkf.2
UCSC ID: ENST00000263519.5_5
RefSeq Accession: NM_001001344.3
Protein: Q16720 (aka AT2B3_HUMAN or ATB3_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ATP2B3:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
  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.