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

Gene ID: 9914, updated on 17-Jun-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; cellular 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. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in colon (RPKM 16.5), skin (RPKM 9.9) and 12 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84368538..84464187)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90434936..90530568)
105.20220307 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: 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?

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)

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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_2023_10

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