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

    Gene ID: 492, updated on 9-Dec-2024

    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; AllianceGenome:HGNC:816
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See ATP2B3 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153517642..153582929)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (151791198..151856492)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (152783100..152848387)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene HAUS augmin like complex subunit 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152753877-152754691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152756808-152757380 Neighboring gene extracellular matrix protein X-linked, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30036 Neighboring gene biglycan Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152809330-152810182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152825847-152826631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152831014-152831626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21065 Neighboring gene uncharacterized LOC105373383 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21066 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

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in GABA-ergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in GABA-ergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in GABA-ergic synapse NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in extracellular vesicle HDA PubMed 
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in glutamatergic synapse NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in parallel fiber ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in parallel fiber to Purkinje cell synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in presynaptic membrane ISS
    Inferred from Sequence or Structural Similarity
    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_001375289.1
    NP_001375290.1
    NP_001375291.1
    NP_001397637.1
    NP_068768.2
    XP_005274746.1
    XP_005274748.1
    XP_011529479.1
    XP_016885042.1
    XP_024308154.1
    XP_047298097.1
    XP_047298098.1
    XP_054183106.1
    XP_054183107.1
    XP_054183108.1
    XP_054183109.1
    XP_054183110.1
    XP_054183111.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_015896.2 RefSeqGene

      Range
      5002..70289
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001001344.3NP_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. Variants 2 and 4 encode the same isoform.
      Source sequence(s)
      AF274858, U82695
      Consensus CDS
      CCDS35440.1
      UniProtKB/Swiss-Prot
      B7WNR8, B7WNY5, Q12995, Q16720, Q16858
      Related
      ENSP00000263519.4, ENST00000263519.5
      Conserved Domains (2) summary
      TIGR01517
      Location:271061
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:11001146
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    2. NM_001388360.1NP_001375289.1  plasma membrane calcium-transporting ATPase 3 isoform 3a

      Status: REVIEWED

      Description
      Transcript Variant: Variants 1 and 3 encode the same isoform (3a).
      Source sequence(s)
      AF274858, U82695
      Consensus CDS
      CCDS14722.1
      Conserved Domains (2) summary
      TIGR01517
      Location:271061
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:11001145
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    3. NM_001388361.1NP_001375290.1  plasma membrane calcium-transporting ATPase 3 isoform 3b

      Status: REVIEWED

      Description
      Transcript Variant: Variants 2 and 4 encode the same isoform (3b).
      Source sequence(s)
      AF274858, U82695
      Consensus CDS
      CCDS35440.1
      UniProtKB/Swiss-Prot
      B7WNR8, B7WNY5, Q12995, Q16720, Q16858
      Related
      ENSP00000343886.2, ENST00000349466.6
      Conserved Domains (2) summary
      TIGR01517
      Location:271061
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:11001146
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    4. NM_001388362.1NP_001375291.1  plasma membrane calcium-transporting ATPase 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AF274858, U82695
      Related
      ENST00000684004.1
      Conserved Domains (2) summary
      TIGR01517
      Location:271061
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:11001114
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    5. NM_001410708.1NP_001397637.1  plasma membrane calcium-transporting ATPase 3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AF274858, U82695
      Consensus CDS
      CCDS94697.1
    6. NM_021949.4NP_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 longest transcript, but encodes the shortest isoform (3a). Variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AF274858, U82695
      Consensus CDS
      CCDS14722.1
      UniProtKB/Swiss-Prot
      Q16720
      Related
      ENSP00000352062.3, ENST00000359149.9
      Conserved Domains (2) summary
      TIGR01517
      Location:271061
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:11001145
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      153517642..153582929
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005274689.4XP_005274746.1  plasma membrane calcium-transporting ATPase 3 isoform X2

      UniProtKB/TrEMBL
      A0A994J5M1
      Related
      ENSP00000516173.1, ENST00000496610.2
      Conserved Domains (2) summary
      TIGR01517
      Location:271061
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:11001175
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    2. XM_024452386.2XP_024308154.1  plasma membrane calcium-transporting ATPase 3 isoform X6

      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
    3. XM_005274691.4XP_005274748.1  plasma membrane calcium-transporting ATPase 3 isoform X4

      See identical proteins and their annotated locations for XP_005274748.1

      UniProtKB/Swiss-Prot
      Q16720
      Conserved Domains (2) summary
      TIGR01517
      Location:271047
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:10861132
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    4. XM_047442141.1XP_047298097.1  plasma membrane calcium-transporting ATPase 3 isoform X5

      Related
      ENSP00000516174.1, ENST00000705862.1
      Conserved Domains (2) summary
      TIGR01517
      Location:271061
      ATPase-IIB_Ca; plasma-membrane calcium-translocating P-type ATPase
      pfam12424
      Location:11001140
      ATP_Ca_trans_C; Plasma membrane calcium transporter ATPase C terminal
    5. XM_011531177.3XP_011529479.1  plasma membrane calcium-transporting ATPase 3 isoform X3

      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)
    6. XM_047442142.1XP_047298098.1  plasma membrane calcium-transporting ATPase 3 isoform X7

      Related
      ENSP00000377425.1, ENST00000393842.5
    7. XM_017029553.2XP_016885042.1  plasma membrane calcium-transporting ATPase 3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      151791198..151856492
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327132.1XP_054183107.1  plasma membrane calcium-transporting ATPase 3 isoform X2

      UniProtKB/TrEMBL
      A0A994J5M1
    2. XM_054327135.1XP_054183110.1  plasma membrane calcium-transporting ATPase 3 isoform X6

    3. XM_054327134.1XP_054183109.1  plasma membrane calcium-transporting ATPase 3 isoform X4

    4. XM_054327133.1XP_054183108.1  plasma membrane calcium-transporting ATPase 3 isoform X3

    5. XM_054327136.1XP_054183111.1  plasma membrane calcium-transporting ATPase 3 isoform X7

    6. XM_054327131.1XP_054183106.1  plasma membrane calcium-transporting ATPase 3 isoform X1