Atp2c1 ATPase secretory pathway Ca2+ transporting 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Atp2c1provided by RGD
Full Name: ATPase secretory pathway Ca2+ transporting 1provided by RGD
Primary source: RGD:621311
See related: EnsemblRapid:ENSRNOG00000013305 AllianceGenome:RGD:621311
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Spca1
Summary: Enables P-type calcium transporter activity. Involved in calcium ion transport and intracellular calcium ion homeostasis. Located in secretory granule. 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, Nov 2024]
Expression: Biased expression in Brain (RPKM 384.0), Kidney (RPKM 263.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q32

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (114913551..115034706, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (106034777..106155854, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (113953959..114039965, complement)

Chromosome 8 - NC_086026.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ultrashort wave alleviates oxygen-glucose deprivation/reoxygenation injury via up-regulation of SPCA1 expression in N2a cells.
Title: Ultrashort wave alleviates oxygen-glucose deprivation/reoxygenation injury via up-regulation of SPCA1 expression in N2a cells.
Short wave therapy protected against focal cerebral I/R injury by increasing SPCA1 expression to modulate Golgi apparatus stress.
Title: A New Approach of Short Wave Protection against Middle Cerebral Artery Occlusion/Reperfusion Injury via Attenuation of Golgi Apparatus Stress by Inhibition of Downregulation of Secretory Pathway Ca(2+)-ATPase Isoform 1 in Rats.
The secretory pathway Ca(2+)-ATPase isoform 1 (SPCA1) was expressed in liver and WIF-B cells.
Title: Vesicular distribution of Secretory Pathway Ca²+-ATPase isoform 1 and a role in manganese detoxification in liver-derived polarized cells.
SPCA1 expression significantly increasaed in A7r5 vascular smooth muscle cells cultured in high glucose (25.0 mM)-supplemented medium compared with normal glucose (5.55 mM)-supplemented medium.
Title: Changes in expression and activity of the secretory pathway Ca2+ ATPase 1 (SPCA1) in A7r5 vascular smooth muscle cells cultured at different glucose concentrations.
Ca(2+)-ATPases play a role in the control of beta-cell Ca(2+) homeostasis and insulin secretion.
Title: Role for plasma membrane-related Ca2+-ATPase-1 (ATP2C1) in pancreatic beta-cell Ca2+ homeostasis revealed by RNA silencing.
Expression of SPCA1 in astroglial, ependymal, and oligodendroglial cells.
Title: Distribution of secretory pathway Ca2+ ATPase (SPCA1) in neuronal and glial cell cultures.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH131266 (e-PCR)
- UniSTS:214549

BF390084 (e-PCR)
- UniSTS:249379

D8Got171 (e-PCR)
- UniSTS:113703

BE114010 (e-PCR)
- UniSTS:247373

RH133189 (e-PCR)
- UniSTS:216472

RH130674 (e-PCR)
- UniSTS:213958

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
enables P-type calcium transporter activity	IEA Inferred from Electronic Annotation more info
NOT enables P-type calcium transporter activity	ISO Inferred from Sequence Orthology 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 ion transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables P-type manganese transporter activity	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
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	IC Inferred by Curator more info	PubMed
involved_in Golgi calcium ion transport	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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 import	IC Inferred by Curator more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium ion transport	IMP Inferred from Mutant Phenotype more info	PubMed
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	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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	IMP Inferred from Mutant Phenotype more info	PubMed
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	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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	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	IEA Inferred from Electronic Annotation more info
located_in Golgi cisterna membrane	ISO Inferred from Sequence Orthology more info
located_in Golgi cisterna membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in Golgi membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
located_in cis-Golgi network membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endomembrane system	IEA Inferred from Electronic Annotation more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in secretory granule	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network	IEA Inferred from Electronic Annotation 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; ATPase, Ca++-sequestering; Ca(2+)/Mn(2+)-ATPase 2C1; calcium-transporting ATPase 2C1; secretory pathway Ca(2+)-ATPase 1; secretory pathway Ca(2+)-transporting ATPase type 1

NP_571982.2

EC 7.2.2.10

XP_038936657.1

EC 7.2.2.10

XP_063120874.1

EC 7.2.2.10

XP_063120875.1

EC 7.2.2.10

XP_063120876.1

EC 7.2.2.10

XP_063120877.1

EC 7.2.2.10

XP_063120878.1

EC 7.2.2.10

XP_063120879.1

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_131907.2 → NP_571982.2 calcium-transporting ATPase type 2C member 1

See identical proteins and their annotated locations for NP_571982.2

Status: PROVISIONAL

Source sequence(s)

BC086994

UniProtKB/Swiss-Prot

Q64566, Q64567

UniProtKB/TrEMBL

A0A8I6GM06, A6I2N4, Q5PQW5

Related

ENSRNOP00000096296.1, ENSRNOT00000095638.2

Conserved Domains (6) summary

TIGR01522
Location:23 → 903

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

COG4087
Location:611 → 679

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

pfam00122
Location:106 → 339

E1-E2_ATPase; E1-E2 ATPase

pfam00689
Location:726 → 898

Cation_ATPase_C; Cation transporting ATPase, C-terminus

pfam00690
Location:26 → 94

Cation_ATPase_N; Cation transporter/ATPase, N-terminus

pfam13246
Location:410 → 493

Cation_ATPase; Cation transport ATPase (P-type)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086026.1 Reference GRCr8

Range

114913551..115034706 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039080729.2 → XP_038936657.1 calcium-transporting ATPase type 2C member 1 isoform X1

UniProtKB/TrEMBL

A0A8I6G9F5, A6I2N3

Related

ENSRNOP00000085864.1, ENSRNOT00000103991.2

Conserved Domains (1) summary

cd02085
Location:88 → 930

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_063264808.1 → XP_063120878.1 calcium-transporting ATPase type 2C member 1 isoform X3
XM_063264805.1 → XP_063120875.1 calcium-transporting ATPase type 2C member 1 isoform X2
XM_063264807.1 → XP_063120877.1 calcium-transporting ATPase type 2C member 1 isoform X3
XM_063264809.1 → XP_063120879.1 calcium-transporting ATPase type 2C member 1 isoform X4
XM_063264806.1 → XP_063120876.1 calcium-transporting ATPase type 2C member 1 isoform X3

Related

ENSRNOP00000088420.1, ENSRNOT00000097914.2
XM_063264804.1 → XP_063120874.1 calcium-transporting ATPase type 2C member 1 isoform X2