Pmpca (peptidase, mitochondrial processing subunit alpha) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pmpca (peptidase, mitochondrial processing subunit alpha) Rattus norvegicus
Analyze
Symbol: Pmpca
Name: peptidase, mitochondrial processing subunit alpha
RGD ID: 727897
Description: Enables endopeptidase activity. Contributes to metallopeptidase activity. Involved in protein processing. Predicted to be located in mitochondrial inner membrane. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 2. Orthologous to human PMPCA (peptidase, mitochondrial processing subunit alpha); PARTICIPATES IN presequence pathway of mitochondrial protein import; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-methoxyethanol; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: alpha-MPP; inactive zinc metalloprotease alpha; MGC93916; mitochondrial processing peptidase alpha subunit, mitochondrial; mitochondrial processing peptidase alpha subunit, mitochondrial precursor; mitochondrial-processing peptidase subunit alpha; P-55; peptidase (mitochondrial processing) alpha; peptidase, mitochondrial processing alpha subunit
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
mRatBN7.239,207,731 - 9,216,846 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,207,717 - 9,216,844 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx312,261,246 - 12,269,510 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0320,844,476 - 20,852,740 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0319,099,813 - 19,108,077 (+)NCBIRnor_WKY
Rnor_6.033,834,262 - 3,842,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,834,078 - 3,842,078 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.039,195,490 - 9,203,287 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,560,961 - 4,568,758 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.134,560,966 - 4,568,716 (+)NCBI
Celera34,027,067 - 4,034,864 (+)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. A putative metal-binding site in the beta subunit of rat mitochondrial processing peptidase is essential for its catalytic activity. Kitada S, etal., J Biochem. 1995 Jun;117(6):1148-50.
4. The general mitochondrial matrix processing protease from rat liver: structural characterization of the catalytic subunit. Kleiber J, etal., Proc Natl Acad Sci U S A 1990 Oct;87(20):7978-82.
5. Processing of mitochondrial presequences. Mossmann D, etal., Biochim Biophys Acta. 2012 Sep-Oct;1819(9-10):1098-106. doi: 10.1016/j.bbagrm.2011.11.007. Epub 2011 Dec 7.
6. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:18614015   PMID:22354088   PMID:22664934   PMID:25808372   PMID:31505169  


Genomics

Comparative Map Data
Pmpca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.239,207,731 - 9,216,846 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,207,717 - 9,216,844 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx312,261,246 - 12,269,510 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0320,844,476 - 20,852,740 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0319,099,813 - 19,108,077 (+)NCBIRnor_WKY
Rnor_6.033,834,262 - 3,842,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,834,078 - 3,842,078 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.039,195,490 - 9,203,287 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.434,560,961 - 4,568,758 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.134,560,966 - 4,568,716 (+)NCBI
Celera34,027,067 - 4,034,864 (+)NCBICelera
Cytogenetic Map3p13NCBI
PMPCA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,410,658 - 136,423,761 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9136,410,630 - 136,427,992 (+)EnsemblGRCh38hg38GRCh38
GRCh379139,305,110 - 139,318,213 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,424,937 - 138,438,034 (+)NCBINCBI36Build 36hg18NCBI36
Build 349136,580,952 - 136,594,049NCBI
Celera9109,819,961 - 109,833,058 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9108,764,482 - 108,777,579 (+)NCBIHuRef
CHM1_19139,453,320 - 139,466,417 (+)NCBICHM1_1
T2T-CHM13v2.09148,639,988 - 148,653,102 (+)NCBIT2T-CHM13v2.0
Pmpca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,275,554 - 26,287,133 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl226,279,351 - 26,287,134 (+)EnsemblGRCm39 Ensembl
GRCm38226,389,348 - 26,397,121 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,389,339 - 26,397,122 (+)EnsemblGRCm38mm10GRCm38
MGSCv37226,244,868 - 26,252,641 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36226,211,357 - 26,219,130 (+)NCBIMGSCv36mm8
Celera226,107,024 - 26,114,797 (+)NCBICelera
Cytogenetic Map2A3NCBI
Pmpca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,315,159 - 4,322,609 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555134,315,159 - 4,322,609 (-)NCBIChiLan1.0ChiLan1.0
PMPCA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19136,464,070 - 136,477,569 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9136,464,070 - 136,477,569 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09107,483,608 - 107,499,176 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PMPCA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,073,124 - 49,083,302 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,073,108 - 49,224,961 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,323,798 - 48,334,000 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,949,879 - 49,960,083 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,947,786 - 49,960,010 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,730,499 - 48,740,634 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,024,590 - 49,034,785 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,072,094 - 49,082,307 (-)NCBIUU_Cfam_GSD_1.0
Pmpca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,979,349 - 201,994,196 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366691,386,817 - 1,395,597 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366691,385,010 - 1,395,715 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PMPCA
(Sus scrofa - pig)
No map positions available.
PMPCA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,778,376 - 1,791,878 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl121,776,983 - 1,791,787 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660583,424,477 - 3,437,983 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pmpca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247601,568,710 - 1,575,867 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247601,568,655 - 1,576,273 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pmpca
24 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:227
Count of miRNA genes:143
Interacting mature miRNAs:154
Transcripts:ENSRNOT00000031607, ENSRNOT00000031622
Prediction methods:Microtar, 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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat

Markers in Region
RH142014  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.239,214,999 - 9,215,192 (+)MAPPERmRatBN7.2
Rnor_6.033,841,531 - 3,841,723NCBIRnor6.0
Rnor_5.039,202,759 - 9,202,951UniSTSRnor5.0
RGSC_v3.434,568,230 - 4,568,422UniSTSRGSC3.4
Celera34,034,336 - 4,034,528UniSTS
Cytogenetic Map3p13UniSTS


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031607   ⟹   ENSRNOP00000037642
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,207,717 - 9,216,844 (+)Ensembl
Rnor_6.0 Ensembl33,834,078 - 3,842,078 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000031622   ⟹   ENSRNOP00000038295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,207,718 - 9,215,484 (+)Ensembl
Rnor_6.0 Ensembl33,834,268 - 3,841,877 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105584   ⟹   ENSRNOP00000090125
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,207,861 - 9,216,844 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108671   ⟹   ENSRNOP00000091234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,207,861 - 9,216,844 (+)Ensembl
RefSeq Acc Id: NM_001003673   ⟹   NP_001003673
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,207,731 - 9,215,528 (+)NCBI
Rnor_6.033,834,262 - 3,842,059 (+)NCBI
Rnor_5.039,195,490 - 9,203,287 (+)NCBI
RGSC_v3.434,560,961 - 4,568,758 (+)RGD
Celera34,027,067 - 4,034,864 (+)RGD
Sequence:
RefSeq Acc Id: XM_039104724   ⟹   XP_038960652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.239,207,867 - 9,216,846 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001003673   ⟸   NM_001003673
- UniProtKB: Q68FX8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000038295   ⟸   ENSRNOT00000031622
RefSeq Acc Id: ENSRNOP00000037642   ⟸   ENSRNOT00000031607
RefSeq Acc Id: XP_038960652   ⟸   XM_039104724
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AB79 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000091234   ⟸   ENSRNOT00000108671
RefSeq Acc Id: ENSRNOP00000090125   ⟸   ENSRNOT00000105584
Protein Domains
Peptidase_M16   Peptidase_M16_C

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P20069-F1-model_v2 AlphaFold P20069 1-524 view protein structure

Transcriptome

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

Promoters
RGD ID:13691903
Promoter ID:EPDNEW_R2428
Type:multiple initiation site
Name:Pmpca_2
Description:peptidase, mitochondrial processing alpha subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R2430  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.033,833,989 - 3,834,049EPDNEW
RGD ID:13691912
Promoter ID:EPDNEW_R2430
Type:multiple initiation site
Name:Pmpca_1
Description:peptidase, mitochondrial processing alpha subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R2428  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.033,834,251 - 3,834,311EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727897 AgrOrtholog
BioCyc Gene G2FUF-50381 BioCyc
Ensembl Genes ENSRNOG00000026775 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037642 ENTREZGENE
  ENSRNOP00000037642.2 UniProtKB/TrEMBL
  ENSRNOP00000038295.5 UniProtKB/TrEMBL
  ENSRNOP00000090125.1 UniProtKB/TrEMBL
  ENSRNOP00000091234 ENTREZGENE
  ENSRNOP00000091234.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031607 ENTREZGENE
  ENSRNOT00000031607.5 UniProtKB/TrEMBL
  ENSRNOT00000031622.6 UniProtKB/TrEMBL
  ENSRNOT00000105584.1 UniProtKB/TrEMBL
  ENSRNOT00000108671 ENTREZGENE
  ENSRNOT00000108671.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7112945 IMAGE-MGC_LOAD
InterPro Metalloenz_LuxS/M16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M16_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M16_Zn_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_M16_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PMPCA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:296588 UniProtKB/TrEMBL
MGC_CLONE MGC:93916 IMAGE-MGC_LOAD
NCBI Gene 296588 ENTREZGENE
PANTHER PTHR11851:SF192 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Peptidase_M16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_M16_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pmpca PhenoGen
PROSITE INSULINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF63411 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AB79 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GHY3_RAT UniProtKB/TrEMBL
  F1M964_RAT UniProtKB/TrEMBL
  MPPA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q68FX8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-12-06 Pmpca  peptidase, mitochondrial processing subunit alpha  Pmpca  peptidase, mitochondrial processing alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-22 Pmpca  peptidase, mitochondrial processing alpha subunit  Pmpca  peptidase (mitochondrial processing) alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Pmpca  peptidase (mitochondrial processing) alpha    mitochondrial processing peptidase alpha subunit, mitochondrial precursor  Name updated 1299863 APPROVED