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ATP2B3 ATPase plasma membrane Ca2+ transporting 3 [ Homo sapiens (human) ]

Gene ID: 492, updated on 3-May-2020

Summary

Official Symbol
ATP2B3provided by HGNC
Official Full Name
ATPase plasma membrane Ca2+ transporting 3provided by HGNC
Primary source
HGNC:HGNC:816
See related
Ensembl:ENSG00000067842 MIM:300014
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLA2; OPCA; PMCA3; SCAX1; CFAP39; PMCA3a
Summary
The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. This gene encodes the plasma membrane calcium ATPase isoform 3. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 3.7) and adrenal (RPKM 2.1) See more
Orthologs

Genomic context

See ATP2B3 in Genome Data Viewer
Location:
Xq28
Exon count:
25
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (153517677..153582929)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (152783905..152848387)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene HAUS augmin like complex subunit 7 Neighboring gene extracellular matrix protein 2-like Neighboring gene biglycan Neighboring gene uncharacterized LOC105373383 Neighboring gene cyclin Q

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
PDZ domain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
calcium-transporting ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium-transporting ATPase activity involved in regulation of presynaptic cytosolic calcium ion concentration IDA
Inferred from Direct Assay
more info
PubMed 
calcium-transporting ATPase activity involved in regulation of presynaptic cytosolic calcium ion concentration IMP
Inferred from Mutant Phenotype
more info
PubMed 
calmodulin binding IEA
Inferred from Electronic Annotation
more info
 
cation-transporting ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
calcium ion export across plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
cellular calcium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
regulation of cardiac conduction TAS
Traceable Author Statement
more info
 
regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cytosolic calcium ion concentration IDA
Inferred from Direct Assay
more info
PubMed 
regulation of presynaptic cytosolic calcium ion concentration IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
GABA-ergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
GABA-ergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell IEA
Inferred from Electronic Annotation
more info
 
extracellular vesicle HDA PubMed 
glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
presynapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
plasma membrane calcium-transporting ATPase 3
Names
ATPase, Ca++ transporting, plasma membrane 3
cilia and flagella associated protein 39
plasma membrane calcium ATPase
plasma membrane calcium pump
NP_001001344.1
NP_068768.2
XP_005274746.1
XP_005274747.1
XP_005274748.1
XP_005274749.1
XP_011529476.1
XP_011529479.1
XP_016885042.1
XP_024308154.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_015896.1 RefSeqGene

    Range
    5001..51808
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001001344.2NP_001001344.1  plasma membrane calcium-transporting ATPase 3 isoform 3b

    See identical proteins and their annotated locations for NP_001001344.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, which leads to a frameshift, compared to variant 1. The resulting isoform (3b) contains a longer and distinct C-terminus compared to isoform 3a.
    Source sequence(s)
    AF274858, U82695
    Consensus CDS
    CCDS35440.1
    UniProtKB/Swiss-Prot
    Q16720
    Related
    ENSP00000263519.4, ENST00000263519.4
    Conserved Domains (2) summary
    pfam12424
    Location:11001146
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    cl27747
    Location:271061
    E1-E2_ATPase; E1-E2 ATPase
  2. NM_021949.3NP_068768.2  plasma membrane calcium-transporting ATPase 3 isoform 3a

    See identical proteins and their annotated locations for NP_068768.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript, but encodes the shorter isoform (3a).
    Source sequence(s)
    AF274858, U82695
    Consensus CDS
    CCDS14722.1
    UniProtKB/Swiss-Prot
    Q16720
    Related
    ENSP00000352062.3, ENST00000359149.7
    Conserved Domains (2) summary
    pfam12424
    Location:11001145
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    cl27747
    Location:271061
    E1-E2_ATPase; E1-E2 ATPase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    153517677..153582929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011531174.2XP_011529476.1  plasma membrane calcium-transporting ATPase 3 isoform X2

    See identical proteins and their annotated locations for XP_011529476.1

    Conserved Domains (7) summary
    TIGR01517
    Location:271061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam00122
    Location:164462
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:8771055
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam00690
    Location:51121
    Cation_ATPase_N; Cation transporter/ATPase, N-terminus
    pfam12424
    Location:11001114
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    pfam12710
    Location:684803
    HAD; haloacid dehalogenase-like hydrolase
    pfam13246
    Location:523612
    Cation_ATPase; Cation transport ATPase (P-type)
  2. XM_011531177.2XP_011529479.1  plasma membrane calcium-transporting ATPase 3 isoform X4

    Conserved Domains (7) summary
    TIGR01517
    Location:271047
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam00122
    Location:164448
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:8631041
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam00690
    Location:51121
    Cation_ATPase_N; Cation transporter/ATPase, N-terminus
    pfam12424
    Location:10861100
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    pfam12710
    Location:670789
    HAD; haloacid dehalogenase-like hydrolase
    pfam13246
    Location:509598
    Cation_ATPase; Cation transport ATPase (P-type)
  3. XM_005274689.3XP_005274746.1  plasma membrane calcium-transporting ATPase 3 isoform X3

    Conserved Domains (7) summary
    TIGR01517
    Location:271061
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam00122
    Location:164462
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:8771055
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam00690
    Location:51121
    Cation_ATPase_N; Cation transporter/ATPase, N-terminus
    pfam12424
    Location:11001176
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    pfam12710
    Location:684803
    HAD; haloacid dehalogenase-like hydrolase
    pfam13246
    Location:523612
    Cation_ATPase; Cation transport ATPase (P-type)
  4. XM_005274690.3XP_005274747.1  plasma membrane calcium-transporting ATPase 3 isoform X5

    See identical proteins and their annotated locations for XP_005274747.1

    UniProtKB/Swiss-Prot
    Q16720
    Conserved Domains (2) summary
    pfam12424
    Location:11001146
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    cl27747
    Location:271061
    E1-E2_ATPase; E1-E2 ATPase
  5. XM_024452386.1XP_024308154.1  plasma membrane calcium-transporting ATPase 3 isoform X8

    Related
    ENSP00000359205.1, ENST00000370186.5
    Conserved Domains (2) summary
    pfam12424
    Location:10861131
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    cl27747
    Location:271047
    E1-E2_ATPase; E1-E2 ATPase
  6. XM_005274691.3XP_005274748.1  plasma membrane calcium-transporting ATPase 3 isoform X6

    See identical proteins and their annotated locations for XP_005274748.1

    UniProtKB/Swiss-Prot
    Q16720
    Conserved Domains (7) summary
    TIGR01517
    Location:271047
    ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
    pfam00122
    Location:164448
    E1-E2_ATPase; E1-E2 ATPase
    pfam00689
    Location:8631041
    Cation_ATPase_C; Cation transporting ATPase, C-terminus
    pfam00690
    Location:51121
    Cation_ATPase_N; Cation transporter/ATPase, N-terminus
    pfam12424
    Location:10861133
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    pfam12710
    Location:670789
    HAD; haloacid dehalogenase-like hydrolase
    pfam13246
    Location:509598
    Cation_ATPase; Cation transport ATPase (P-type)
  7. XM_005274692.3XP_005274749.1  plasma membrane calcium-transporting ATPase 3 isoform X7

    See identical proteins and their annotated locations for XP_005274749.1

    UniProtKB/Swiss-Prot
    Q16720
    Conserved Domains (2) summary
    pfam12424
    Location:11001145
    ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    cl27747
    Location:271061
    E1-E2_ATPase; E1-E2 ATPase
  8. XM_017029553.1XP_016885042.1  plasma membrane calcium-transporting ATPase 3 isoform X1

RNA

  1. XR_001755693.2 RNA Sequence

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