Atp2c1 ATPase, Ca++-sequestering [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Atp2c1provided by MGI
Official Full Name: ATPase, Ca++-sequesteringprovided by MGI
Primary source: MGI:MGI:1889008
See related: Ensembl:ENSMUSG00000032570 AllianceGenome:MGI:1889008
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: HHD; BCPM; SPCA; pmr1; SPCA1; ATP2C1A; 1700121J11Rik; D930003G21Rik
Summary: Predicted to enable ATP binding activity; P-type ion transporter activity; and metal ion binding activity. Involved in Golgi calcium ion homeostasis and positive regulation of Golgi to plasma membrane protein transport. Located in Golgi cisterna membrane and cis-Golgi network membrane. Is expressed in several structures, including gut; heart; liver; lung; and mammary gland. Human ortholog(s) of this gene implicated in Hailey-Hailey disease. Orthologous to human ATP2C1 (ATPase secretory pathway Ca2+ transporting 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in CNS E18 (RPKM 19.7), frontal lobe adult (RPKM 16.1) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 F1; 9 56.61 cM

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (105288561..105398456, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (105411362..105521257, complement)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SPCA1 promotes neurulation by regulating the cytoskeletal dynamics
Title: Secretory pathway calcium ATPase 1 (SPCA1) controls mouse neural tube closure by regulating cytoskeletal dynamics.
The timing, magnitude of TMEM165 expression and its Golgi location supports a role for this Golgi Ca2+/H+ antiporter as a contributor to mammary Golgi calcium transport needs, in addition to the better-characterized roles of SPCA 1 and 2.
Title: The Ca(2+)/H(+) antiporter TMEM165 expression, localization in the developing, lactating and involuting mammary gland parallels the secretory pathway Ca(2+) ATPase (SPCA1).
The synthesized siPMR1 can significantly silence the expression of PMR1 and promote the secretion of insulin in the islet cells in vitro.
Title: [Plasma membrane-related Ca(2+)-ATPase-1 gene silencing promotes insulin secretion in islet beta cells NIT].
Impaired cellular divalent calcium ion Ca2+ homeostasis and/or the altered targeting of organellar proteins under conditions of SPCA1 knockdown highlight the importance of SPCA1 function for normal neural differentiation.
Title: Silencing the SPCA1 (secretory pathway Ca2+-ATPase isoform 1) impairs Ca2+ homeostasis in the Golgi and disturbs neural polarity.
Has a potential role in intracellular signaling and in Golgi secretory processes involved in dendritic growth and in functional maturation of the mouse nervous system.
Title: Activity and localization of the secretory pathway Ca2+-ATPase isoform 1 (SPCA1) in different areas of the mouse brain during postnatal development.
loss of the Golgi Ca(2+) pump causes Golgi stress, expansion of the Golgi, increased apoptosis, and embryonic lethality and demonstrates that SPCA1 haploinsufficiency causes a genetic predisposition to cancer.
Title: Loss of the Atp2c1 secretory pathway Ca(2+)-ATPase (SPCA1) in mice causes Golgi stress, apoptosis, and midgestational death in homozygous embryos and squamous cell tumors in adult heterozygotes.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (3)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9Dcr74 (e-PCR), detects polymorphism
- UniSTS:498997

D9Dcr75 (e-PCR), detects polymorphism
- UniSTS:498998

NoName (e-PCR)
- UniSTS:236240

AW061228 (e-PCR)
- UniSTS:179966

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP binding	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
enables P-type calcium transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables P-type calcium transporter activity	TAS Traceable Author Statement more info	PubMed
enables P-type manganese transporter activity	ISO Inferred from Sequence Orthology more info
enables P-type manganese transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables manganese ion binding	ISO Inferred from Sequence Orthology more info
enables manganese ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in Golgi calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in Golgi calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in Golgi calcium ion homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in Golgi calcium ion transport	ISO Inferred from Sequence Orthology more info
involved_in Golgi calcium ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in actin cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in calcium ion transport	ISO Inferred from Sequence Orthology more info
involved_in calcium ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	ISO Inferred from Sequence Orthology more info
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in epidermis development	ISO Inferred from Sequence Orthology more info
involved_in epidermis development	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in intracellular calcium ion homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular manganese ion homeostasis	ISO Inferred from Sequence Orthology more info
involved_in intracellular manganese ion homeostasis	ISS Inferred from Sequence or Structural Similarity 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 manganese ion transport	ISO Inferred from Sequence Orthology more info
involved_in manganese ion transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of Golgi to plasma membrane protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of Golgi to plasma membrane protein transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of Golgi to plasma membrane protein transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in trans-Golgi network membrane organization	ISO Inferred from Sequence Orthology more info
involved_in trans-Golgi network membrane organization	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi cisterna membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in Golgi membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi membrane	ISO Inferred from Sequence Orthology more info
located_in Golgi membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cis-Golgi network membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in secretory granule	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: calcium-transporting ATPase type 2C member 1

Names: ATP-dependent Ca(2+) pump PMR1; ATPase 2C1; ATPase, Ca++ transporting, type 2C, member 1; Ca(2+)/Mn(2+)-ATPase 2C1; secretory pathway Ca(2+)-transporting ATPase type 1

NP_001240760.1

EC 7.2.2.10

NP_001240763.1

EC 7.2.2.10

NP_001240765.1

EC 7.2.2.10

NP_001346751.1

EC 7.2.2.10

NP_001346752.1

EC 7.2.2.10

NP_778190.3

EC 7.2.2.10

XP_006511774.1

EC 7.2.2.10

XP_006511775.1

EC 7.2.2.10

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)

NM_001253831.1 → NP_001240760.1 calcium-transporting ATPase type 2C member 1 isoform 1

See identical proteins and their annotated locations for NP_001240760.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest protein (isoform 1).

Source sequence(s)

AK133703, AK163049, AK173154, BC043091

Consensus CDS

CCDS57698.1

UniProtKB/TrEMBL

Q3TVY6, Q3UZR5

Related

ENSMUSP00000082220.7, ENSMUST00000085133.13

Conserved Domains (6) summary

TIGR01522
Location:57 → 936

ATPase-IIA2_Ca; golgi membrane calcium-translocating P-type ATPase

COG4087
Location:589 → 712

COG4087; Soluble P-type ATPase [General function prediction only]

pfam00122
Location:152 → 372

E1-E2_ATPase; E1-E2 ATPase

pfam00689
Location:759 → 931

Cation_ATPase_C; Cation transporting ATPase, C-terminus

pfam00690
Location:60 → 128

Cation_ATPase_N; Cation transporter/ATPase, N-terminus

pfam13246
Location:443 → 526

Cation_ATPase; Cation transport ATPase (P-type)
NM_001253834.1 → NP_001240763.1 calcium-transporting ATPase type 2C member 1 isoform 2

See identical proteins and their annotated locations for NP_001240763.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has a different 5' end which results in the use of an alternate start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct N-terminus when it is compared to isoform 1. Variants 2 and 3 encode the same protein.

Source sequence(s)

AJ551270, AK163049, AK173154, BC043091, BU611728

Consensus CDS

CCDS40752.1

UniProtKB/Swiss-Prot

E9QMB9, Q80XR2, Q80YZ2

UniProtKB/TrEMBL

Q3TVY6

Related

ENSMUSP00000108177.3, ENSMUST00000112558.10

Conserved Domains (1) summary

cd02085
Location:54 → 895

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
NM_001253836.1 → NP_001240765.1 calcium-transporting ATPase type 2C member 1 isoform 3

See identical proteins and their annotated locations for NP_001240765.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) has a multiple differences, compared to variant 1. These differences result in distinct 5' and 3' UTRs and cause translation initiation at a downstream start codon, compared to variant 1. The encoded protein (isoform 3) is shorter than isoform 1.

Source sequence(s)

AK028393, BU611728, BU754887

Consensus CDS

CCDS57697.1

UniProtKB/TrEMBL

Q8BMS7

Related

ENSMUSP00000129617.3, ENSMUST00000163879.9

Conserved Domains (4) summary

COG4087
Location:594 → 662

COG4087; Soluble P-type ATPase [General function prediction only]

pfam00122
Location:102 → 322

E1-E2_ATPase; E1-E2 ATPase

pfam00690
Location:10 → 78

Cation_ATPase_N; Cation transporter/ATPase, N-terminus

pfam13246
Location:393 → 476

Cation_ATPase; Cation transport ATPase (P-type)
NM_001359822.1 → NP_001346751.1 calcium-transporting ATPase type 2C member 1 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (5) has a different 5' end which results in the use of an alternate start codon, compared to variant 1. The resulting protein (isoform 4) has a shorter and distinct N-terminus when it is compared to isoform 1.

Source sequence(s)

AC113016, AC117679, BC043091

UniProtKB/TrEMBL

Q3TVY6

Conserved Domains (1) summary

cd02085
Location:58 → 899

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
NM_001359823.1 → NP_001346752.1 calcium-transporting ATPase type 2C member 1 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (6) has a different 5' end which causes translation initiation at a downstream start codon, compared to variant 1. The resulting protein (isoform 5) has a shorter N-terminus when it is compared to isoform 1.

Source sequence(s)

AC113016, AC117679, BC043091

UniProtKB/TrEMBL

Q69ZL4

Related

ENSMUSP00000135802.2, ENSMUST00000177293.8

Conserved Domains (1) summary

cd02085
Location:38 → 879

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
NM_175025.4 → NP_778190.3 calcium-transporting ATPase type 2C member 1 isoform 2

See identical proteins and their annotated locations for NP_778190.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) has a different 5' end which results in the use of an alternate start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct N-terminus when it is compared to isoform 1. Variants 2 and 3 encode the same protein.

Source sequence(s)

AK173154, BC043091, BC043706, BU611728

Consensus CDS

CCDS40752.1

UniProtKB/Swiss-Prot

E9QMB9, Q80XR2, Q80YZ2

UniProtKB/TrEMBL

Q3TVY6

Related

ENSMUSP00000039103.8, ENSMUST00000038118.15

Conserved Domains (1) summary

cd02085
Location:54 → 895

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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

105288561..105398456 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006511712.5 → XP_006511775.1 calcium-transporting ATPase type 2C member 1 isoform X1

See identical proteins and their annotated locations for XP_006511775.1

UniProtKB/TrEMBL

Q3TVY6

Conserved Domains (1) summary

cd02085
Location:58 → 899

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
XM_006511711.5 → XP_006511774.1 calcium-transporting ATPase type 2C member 1 isoform X1

See identical proteins and their annotated locations for XP_006511774.1

UniProtKB/TrEMBL

Q3TVY6

Conserved Domains (1) summary

cd02085
Location:58 → 899

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