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    ATP2C2 ATPase secretory pathway Ca2+ transporting 2 [ Homo sapiens (human) ]

    Gene ID: 9914, updated on 10-Dec-2024

    Summary

    Official Symbol
    ATP2C2provided by HGNC
    Official Full Name
    ATPase secretory pathway Ca2+ transporting 2provided by HGNC
    Primary source
    HGNC:HGNC:29103
    See related
    Ensembl:ENSG00000064270 MIM:613082; AllianceGenome:HGNC:29103
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPCA2
    Summary
    Enables P-type calcium transporter activity and P-type manganese transporter activity. Predicted to be involved in calcium ion transmembrane transport; intracellular calcium ion homeostasis; and manganese ion transport. Predicted to act upstream of or within mammary gland epithelium development; positive regulation of calcium ion import; and protein localization to plasma membrane. Predicted to be located in trans-Golgi network membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in colon (RPKM 16.5), skin (RPKM 9.9) and 12 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See ATP2C2 in Genome Data Viewer
    Location:
    16q24.1
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84368538..84464187)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90434936..90530568)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84402144..84497793)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903734 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:84340158-84341357 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84348057-84348215 Neighboring gene WAP four-disulfide core domain 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84353071-84353592 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:84393612-84394811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84492707-84493206 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84494562-84495761 Neighboring gene ATP2C2 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:84512589-84513788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84516869-84517370 Neighboring gene MTOR associated protein, eak-7 homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84537675-84538175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84538296-84539243 Neighboring gene uncharacterized LOC124903736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7783 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84540344-84540580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84540853-84541353

    Genomic regions, transcripts, and products

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2018-09-17)

    ClinGen Genome Curation Page
    Haploinsufficency

    No evidence available (Last evaluated 2018-09-17)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide association analysis of blood biomarkers in chronic obstructive pulmonary disease.
    EBI GWAS Catalog
    Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0703, DKFZp686H22230

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables P-type calcium transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables P-type calcium transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables P-type manganese transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intracellular calcium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mammary gland epithelium development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in manganese ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in manganese ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of calcium ion import IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization to plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
     
    located_in basolateral plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasmic side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in trans-Golgi network membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    calcium-transporting ATPase type 2C member 2
    Names
    ATPase 2C2
    ATPase, Ca++ transporting, type 2C, member 2
    Ca(2+)/Mn(2+)-ATPase 2C2
    secretory pathway Ca(2+)-ATPase 2
    secretory pathway Ca(2+)-transporting ATPase type 2
    secretory pathway calcium ATPase 2
    NP_001273456.2
    NP_001278383.1
    NP_055676.3
    XP_011521788.1
    XP_011521789.1
    XP_047290950.1
    XP_054170532.1
    XP_054170533.1
    XP_054170534.1

    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.

    mRNA and Protein(s)

    1. NM_001286527.3NP_001273456.2  calcium-transporting ATPase type 2C member 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC022165, AY791884, BX648333
      Consensus CDS
      CCDS67088.1
      UniProtKB/TrEMBL
      B7ZA13
      Related
      ENSP00000397925.2, ENST00000416219.6
      Conserved Domains (6) summary
      TIGR01522
      Location:55960
      ATPase-IIA2_Ca; golgi membrane calcium-translocating P-type ATPase
      COG4087
      Location:625709
      COG4087; Soluble P-type ATPase [General function prediction only]
      pfam00122
      Location:149368
      E1-E2_ATPase; E1-E2 ATPase
      pfam00689
      Location:756957
      Cation_ATPase_C; Cation transporting ATPase, C-terminus
      pfam00690
      Location:63125
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam13246
      Location:441523
      Cation_ATPase; Cation transport ATPase (P-type)
    2. NM_001291454.2NP_001278383.1  calcium-transporting ATPase type 2C member 2 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, contains multiple differences in the coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The resulting isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK091051, AY791884, BX648333
      UniProtKB/TrEMBL
      B3KR57
      Related
      ENST00000420010.6
      Conserved Domains (5) summary
      COG4087
      Location:474558
      COG4087; Soluble P-type ATPase [General function prediction only]
      TIGR01116
      Location:23777
      ATPase-IIA1_Ca; sarco/endoplasmic reticulum calcium-translocating P-type ATPase
      pfam00122
      Location:23217
      E1-E2_ATPase; E1-E2 ATPase
      pfam00689
      Location:605777
      Cation_ATPase_C; Cation transporting ATPase, C-terminus
      pfam13246
      Location:290372
      Cation_ATPase; Cation transport ATPase (P-type)
    3. NM_014861.4NP_055676.3  calcium-transporting ATPase type 2C member 2 isoform 2

      See identical proteins and their annotated locations for NP_055676.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AY791884, BX648333
      Consensus CDS
      CCDS42207.1
      UniProtKB/Swiss-Prot
      B4DU76, E7ES94, O75185, Q5HYC3, Q5S053, Q68CQ2
      UniProtKB/TrEMBL
      B7ZA13
      Related
      ENSP00000262429.4, ENST00000262429.9
      Conserved Domains (1) summary
      cd02085
      Location:85927
      P-type_ATPase_SPCA; golgi-associated secretory pathway Ca(2+) transport ATPases, similar to human ATPase secretory pathway Ca(2+) transporting 1/hSPCA1 and Saccharomyces cerevisiae Ca(2+)/Mn(2+)-transporting P-type ATPase, Pmr1p

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      84368538..84464187
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011523486.3XP_011521788.1  calcium-transporting ATPase type 2C member 2 isoform X1

      UniProtKB/TrEMBL
      B7ZA13
      Conserved Domains (6) summary
      TIGR01522
      Location:32937
      ATPase-IIA2_Ca; golgi membrane calcium-translocating P-type ATPase
      COG4087
      Location:602686
      COG4087; Soluble P-type ATPase [General function prediction only]
      pfam00122
      Location:126345
      E1-E2_ATPase; E1-E2 ATPase
      pfam00689
      Location:733934
      Cation_ATPase_C; Cation transporting ATPase, C-terminus
      pfam00690
      Location:40102
      Cation_ATPase_N; Cation transporter/ATPase, N-terminus
      pfam13246
      Location:418500
      Cation_ATPase; Cation transport ATPase (P-type)
    2. XM_047434994.1XP_047290950.1  calcium-transporting ATPase type 2C member 2 isoform X2

      UniProtKB/TrEMBL
      B7ZA13
    3. XM_011523487.3XP_011521789.1  calcium-transporting ATPase type 2C member 2 isoform X3

      Conserved Domains (3) summary
      COG4087
      Location:282366
      COG4087; Soluble P-type ATPase [General function prediction only]
      pfam00689
      Location:413614
      Cation_ATPase_C; Cation transporting ATPase, C-terminus
      pfam13246
      Location:98180
      Cation_ATPase; Cation transport ATPase (P-type)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      90434936..90530568
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314557.1XP_054170532.1  calcium-transporting ATPase type 2C member 2 isoform X1

      UniProtKB/TrEMBL
      B7ZA13
    2. XM_054314558.1XP_054170533.1  calcium-transporting ATPase type 2C member 2 isoform X2

      UniProtKB/TrEMBL
      B7ZA13
    3. XM_054314559.1XP_054170534.1  calcium-transporting ATPase type 2C member 2 isoform X3