Atp2c2 (ATPase secretory pathway Ca2+ transporting 2) - Rat Genome Database

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Gene: Atp2c2 (ATPase secretory pathway Ca2+ transporting 2) Rattus norvegicus
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Symbol: Atp2c2
Name: ATPase secretory pathway Ca2+ transporting 2
RGD ID: 620647
Description: Predicted to enable 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 several cellular components, including cytoplasmic side of plasma membrane; perinuclear region of cytoplasm; and trans-Golgi network membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum; and plasma membrane. Orthologous to human ATP2C2 (ATPase secretory pathway Ca2+ transporting 2); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; all-trans-retinoic acid; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ATPase 2C2; ATPase, Ca++ transporting, type 2C, member 2; Ca(2+)/Mn(2+)-ATPase 2C2; calcium-transporting ATPase 2C2; calcium-transporting ATPase type 2C member 2; putative secretory pathway Ca-ATPase SPCA2; secretory pathway Ca(2+)-ATPase 2; secretory pathway Ca(2+)-transporting ATPase type 2; Spca2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21947,754,120 - 47,811,369 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1947,754,120 - 47,811,368 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1954,548,443 - 54,605,713 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01955,229,178 - 55,286,443 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01957,442,334 - 57,499,435 (+)NCBIRnor_WKY
Rnor_6.01952,347,480 - 52,404,608 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,347,580 - 52,404,607 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01963,095,398 - 63,150,054 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1947,012,092 - 47,068,905 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Calcium pumps in health and disease. Brini M and Carafoli E, Physiol Rev. 2009 Oct;89(4):1341-78. doi: 10.1152/physrev.00032.2008.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
8. Information Derived from GenBank Report RGD, Sept. 2003
Additional References at PubMed
PMID:23840669  


Genomics

Comparative Map Data
Atp2c2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21947,754,120 - 47,811,369 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1947,754,120 - 47,811,368 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1954,548,443 - 54,605,713 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01955,229,178 - 55,286,443 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01957,442,334 - 57,499,435 (+)NCBIRnor_WKY
Rnor_6.01952,347,480 - 52,404,608 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,347,580 - 52,404,607 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01963,095,398 - 63,150,054 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1947,012,092 - 47,068,905 (+)NCBICelera
Cytogenetic Map19q12NCBI
ATP2C2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381684,368,538 - 84,464,187 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1684,368,527 - 84,464,187 (+)EnsemblGRCh38hg38GRCh38
GRCh371684,402,144 - 84,497,793 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361682,959,634 - 83,055,294 (+)NCBINCBI36Build 36hg18NCBI36
Celera1668,704,219 - 68,799,880 (+)NCBICelera
Cytogenetic Map16q24.1NCBI
HuRef1670,154,815 - 70,250,533 (+)NCBIHuRef
CHM1_11685,813,737 - 85,909,368 (+)NCBICHM1_1
T2T-CHM13v2.01690,434,936 - 90,530,568 (+)NCBIT2T-CHM13v2.0
Atp2c2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398120,426,748 - 120,484,457 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8120,426,748 - 120,484,456 (+)EnsemblGRCm39 Ensembl
GRCm388119,700,009 - 119,757,718 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8119,700,009 - 119,757,717 (+)EnsemblGRCm38mm10GRCm38
MGSCv378122,223,909 - 122,281,618 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368122,584,182 - 122,643,695 (+)NCBIMGSCv36mm8
Celera8123,917,258 - 123,973,935 (+)NCBICelera
Cytogenetic Map8E1NCBI
Atp2c2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495554147,768 - 94,878 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495554147,803 - 95,074 (+)NCBIChiLan1.0ChiLan1.0
ATP2C2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11684,383,377 - 84,469,126 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1684,375,658 - 84,468,671 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01665,033,470 - 65,127,403 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ATP2C2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1567,986,120 - 68,046,391 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl567,986,355 - 68,046,272 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha568,000,953 - 68,060,899 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0568,219,736 - 68,279,549 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl568,219,971 - 68,279,574 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1568,232,631 - 68,292,428 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0568,068,969 - 68,128,897 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0568,484,329 - 68,544,264 (-)NCBIUU_Cfam_GSD_1.0
Atp2c2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934927,751,111 - 27,798,901 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049366413,498,693 - 3,547,968 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATP2C2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl64,237,440 - 4,313,247 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.164,237,331 - 4,313,273 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.264,664,868 - 4,737,426 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATP2C2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1569,771,909 - 69,861,030 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl569,801,818 - 69,860,576 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660475,892,830 - 5,981,240 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Atp2c2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247461,413,813 - 1,445,646 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247461,399,368 - 1,445,999 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Atp2c2
160 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:44
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000074753
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat

Markers in Region
D19Got62  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,766,031 - 47,766,291 (+)MAPPERmRatBN7.2
Rnor_6.01952,359,391 - 52,359,650NCBIRnor6.0
Rnor_5.01963,107,309 - 63,107,568UniSTSRnor5.0
Celera1947,024,003 - 47,024,262UniSTS
RH 3.4 Map19658.1RGD
RH 3.4 Map19658.1UniSTS
RH144624  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,811,135 - 47,811,301 (+)MAPPERmRatBN7.2
Rnor_6.01952,404,375 - 52,404,540NCBIRnor6.0
Rnor_5.01963,149,822 - 63,149,987UniSTSRnor5.0
Celera1947,068,673 - 47,068,838UniSTS
RH 3.4 Map19649.3UniSTS
Cytogenetic Map19q12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 7
Low 1 3 2 1 2 14 29 30 4
Below cutoff 33 19 6 16 6 3 4 44 6 11 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000074753   ⟹   ENSRNOP00000066506
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1947,754,120 - 47,811,368 (+)Ensembl
Rnor_6.0 Ensembl1952,347,580 - 52,404,426 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092131   ⟹   ENSRNOP00000070917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1952,374,298 - 52,404,607 (+)Ensembl
RefSeq Acc Id: NM_134462   ⟹   NP_604457
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21947,754,120 - 47,811,368 (+)NCBI
Rnor_6.01952,347,480 - 52,404,607 (+)NCBI
Rnor_5.01963,095,398 - 63,150,054 (+)NCBI
Celera1947,012,092 - 47,068,905 (+)RGD
Sequence:
RefSeq Acc Id: XM_008772596   ⟹   XP_008770818
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21947,788,434 - 47,811,369 (+)NCBI
Rnor_6.01952,380,906 - 52,404,608 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_604457   ⟸   NM_134462
- UniProtKB: Q8R4C1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008770818   ⟸   XM_008772596
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000070917   ⟸   ENSRNOT00000092131
RefSeq Acc Id: ENSRNOP00000066506   ⟸   ENSRNOT00000074753
Protein Domains
Cation_ATPase_N

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8R4C1-F1-model_v2 AlphaFold Q8R4C1 1-944 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620647 AgrOrtholog
BioCyc Gene G2FUF-5506 BioCyc
Ensembl Genes ENSRNOG00000049334 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066506 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074753 ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Gene3D-CATH 3.40.1110.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.1000 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ATP2C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_cation-transptr_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_cation-transptr_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_cyto_dom_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_P_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_TM_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-typ_transduc_dom_A_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HAD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HAD_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-type_ATPase_IIA_PMR1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_typ_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P_typ_ATPase_HD_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171496 UniProtKB/Swiss-Prot
NCBI Gene 171496 ENTREZGENE
PANTHER PTHR42861:SF23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cation_ATPase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cation_ATPase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Atp2c2 PhenoGen
PRINTS HATPASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ATPASE_E1_E2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Cation_ATPase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56784 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81653 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81660 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81665 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs ATPase-IIA2_Ca UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATPase_P-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt AT2C2_RAT UniProtKB/Swiss-Prot
  M0RAF9_RAT UniProtKB/TrEMBL
  Q8R4C1 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Atp2c2  ATPase secretory pathway Ca2+ transporting 2  Atp2c2  ATPase, Ca++ transporting, type 2C, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Atp2c2  ATPase, Ca++ transporting, type 2C, member 2  Spca2  putative secretory pathway Ca-ATPase SPCA2  Symbol and Name updated 1299863 APPROVED
2002-08-07 Spca2  putative secretory pathway Ca-ATPase SPCA2      Symbol and Name status set to provisional 70820 PROVISIONAL