Pgam5 (PGAM family member 5, mitochondrial serine/threonine protein phosphatase) - Rat Genome Database

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Gene: Pgam5 (PGAM family member 5, mitochondrial serine/threonine protein phosphatase) Rattus norvegicus
Analyze
Symbol: Pgam5
Name: PGAM family member 5, mitochondrial serine/threonine protein phosphatase
RGD ID: 1312028
Description: Predicted to enable GTPase activator activity and protein serine/threonine phosphatase activity. Predicted to be involved in several processes, including negative regulation of cold-induced thermogenesis; peptidyl-threonine dephosphorylation; and positive regulation of mitochondrial fission. Predicted to be located in mitochondrial outer membrane. Predicted to be active in mitochondrion. Orthologous to human PGAM5 (PGAM family member 5, mitochondrial serine/threonine protein phosphatase); PARTICIPATES IN mitochondrial autophagy pathway; nuclear factor, erythroid 2 like 2 signaling pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC288731; phosphoglycerate mutase family member 5; RGD1312028; serine/threonine-protein phosphatase PGAM5, mitochondrial; similar to hypothetical protein MGC5352
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
mRatBN7.21246,409,324 - 46,416,410 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1246,409,369 - 46,416,420 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1247,585,056 - 47,592,113 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01248,190,483 - 48,197,540 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01247,251,009 - 47,258,066 (+)NCBIRnor_WKY
Rnor_6.01252,467,417 - 52,474,533 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1252,467,450 - 52,474,511 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01254,202,823 - 54,210,153 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41246,555,416 - 46,562,477 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11246,422,347 - 46,429,409 (+)NCBI
Celera1247,965,707 - 47,972,769 (+)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

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. The Nrf2 regulatory network provides an interface between redox and intermediary metabolism. Hayes JD and Dinkova-Kostova AT, Trends Biochem Sci. 2014 Apr;39(4):199-218. doi: 10.1016/j.tibs.2014.02.002. Epub 2014 Mar 16.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. The Ablation of Mitochondrial Protein Phosphatase Pgam5 Confers Resistance Against Metabolic Stress. Sekine S, etal., EBioMedicine. 2016 Jan 29;5:82-92. doi: 10.1016/j.ebiom.2016.01.031. eCollection 2016 Mar.
8. Selective removal of mitochondria via mitophagy: distinct pathways for different mitochondrial stresses. Wei H, etal., Biochim Biophys Acta. 2015 Oct;1853(10 Pt B):2784-90. doi: 10.1016/j.bbamcr.2015.03.013. Epub 2015 Apr 1.
Additional References at PubMed
PMID:12477932   PMID:19590015   PMID:22265414   PMID:25002582   PMID:27815660   PMID:29476059   PMID:32580628   PMID:33681349  


Genomics

Comparative Map Data
Pgam5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21246,409,324 - 46,416,410 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1246,409,369 - 46,416,420 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1247,585,056 - 47,592,113 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01248,190,483 - 48,197,540 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01247,251,009 - 47,258,066 (+)NCBIRnor_WKY
Rnor_6.01252,467,417 - 52,474,533 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1252,467,450 - 52,474,511 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01254,202,823 - 54,210,153 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41246,555,416 - 46,562,477 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11246,422,347 - 46,429,409 (+)NCBI
Celera1247,965,707 - 47,972,769 (+)NCBICelera
Cytogenetic Map12q16NCBI
PGAM5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812132,710,842 - 132,722,734 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12132,710,819 - 132,722,734 (+)EnsemblGRCh38hg38GRCh38
GRCh3712133,287,428 - 133,299,320 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612131,797,509 - 131,805,825 (+)NCBINCBI36Build 36hg18NCBI36
Celera12132,987,362 - 133,009,550 (+)NCBICelera
Cytogenetic Map12q24.33NCBI
HuRef12130,043,032 - 130,078,592 (+)NCBIHuRef
CHM1_112133,107,383 - 133,119,182 (+)NCBICHM1_1
T2T-CHM13v2.012132,759,704 - 132,771,989 (+)NCBIT2T-CHM13v2.0
Pgam5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395110,407,001 - 110,417,765 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5110,406,996 - 110,417,779 (-)EnsemblGRCm39 Ensembl
GRCm385110,259,135 - 110,269,899 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5110,259,130 - 110,269,913 (-)EnsemblGRCm38mm10GRCm38
MGSCv375110,688,154 - 110,698,918 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365110,499,457 - 110,510,184 (-)NCBIMGSCv36mm8
Celera5107,382,715 - 107,393,630 (-)NCBICelera
Cytogenetic Map5FNCBI
Pgam5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955482356,863 - 363,862 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955482356,863 - 363,666 (-)NCBIChiLan1.0ChiLan1.0
PGAM5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v05105,233,821 - 105,237,475 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PGAM5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.126406,871 - 414,874 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl26407,174 - 414,860 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha26448,802 - 456,805 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.026464,504 - 472,485 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl26464,505 - 485,472 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.126405,826 - 413,824 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.026492,873 - 500,882 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.026424,108 - 432,107 (-)NCBIUU_Cfam_GSD_1.0
PGAM5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1422,773,136 - 22,780,720 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11422,773,135 - 22,780,904 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PGAM5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111128,053,176 - 128,064,030 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11128,053,795 - 128,065,720 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037116,802,167 - 116,811,028 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pgam5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474728,078,368 - 28,085,437 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474728,078,138 - 28,084,920 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pgam5
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:386
Count of miRNA genes:215
Interacting mature miRNAs:260
Transcripts:ENSRNOT00000056675
Prediction methods:Microtar, Miranda, 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
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)122806443346669029Rat

Markers in Region
RH139349  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21246,416,199 - 46,416,276 (+)MAPPERmRatBN7.2
Rnor_6.01252,474,301 - 52,474,377NCBIRnor6.0
Rnor_5.01254,209,943 - 54,210,019UniSTSRnor5.0
RGSC_v3.41246,562,267 - 46,562,343UniSTSRGSC3.4
Celera1247,972,559 - 47,972,635UniSTS
RH 3.4 Map12811.41UniSTS
Cytogenetic Map12q16UniSTS
BE103934  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21246,407,544 - 46,407,694 (+)MAPPERmRatBN7.2
Rnor_6.01252,465,647 - 52,465,796NCBIRnor6.0
Rnor_5.01254,201,022 - 54,201,171UniSTSRnor5.0
RGSC_v3.41246,553,613 - 46,553,762UniSTSRGSC3.4
Celera1247,963,904 - 47,964,053UniSTS
RH 3.4 Map12801.0UniSTS
Cytogenetic Map12q16UniSTS


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 36 51 35 19 35 6 9 74 35 35 11 6
Low 7 6 6 6 2 2 6 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000056675   ⟹   ENSRNOP00000053513
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1246,409,369 - 46,416,420 (+)Ensembl
Rnor_6.0 Ensembl1252,467,450 - 52,474,511 (+)Ensembl
RefSeq Acc Id: NM_001025272   ⟹   NP_001020443
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21246,409,348 - 46,416,410 (+)NCBI
Rnor_6.01252,467,450 - 52,474,511 (+)NCBI
Rnor_5.01254,202,823 - 54,210,153 (+)NCBI
RGSC_v3.41246,555,416 - 46,562,477 (+)RGD
Celera1247,965,707 - 47,972,769 (+)RGD
Sequence:
RefSeq Acc Id: XM_006249534   ⟹   XP_006249596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21246,409,324 - 46,416,410 (+)NCBI
Rnor_6.01252,467,417 - 52,474,533 (+)NCBI
Rnor_5.01254,202,823 - 54,210,153 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001020443 (Get FASTA)   NCBI Sequence Viewer  
  XP_006249596 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH92607 (Get FASTA)   NCBI Sequence Viewer  
  EDM14059 (Get FASTA)   NCBI Sequence Viewer  
  Q562B5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001020443   ⟸   NM_001025272
- UniProtKB: Q562B5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006249596   ⟸   XM_006249534
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000053513   ⟸   ENSRNOT00000056675

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q562B5-F1-model_v2 AlphaFold Q562B5 1-288 view protein structure

Transcriptome

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

Promoters
RGD ID:13698739
Promoter ID:EPDNEW_R9264
Type:initiation region
Name:Pgam5_1
Description:PGAM family member 5, mitochondrial serine/threonine proteinphosphatase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01252,467,453 - 52,467,513EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1312028 AgrOrtholog
BioCyc Gene G2FUF-18802 BioCyc
Ensembl Genes ENSRNOG00000037443 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053513 ENTREZGENE
  ENSRNOP00000053513.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056675 ENTREZGENE
  ENSRNOT00000056675.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1240 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7309810 IMAGE-MGC_LOAD
InterPro His_Pase_superF_clade-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  His_PPase_superfam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:288731 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109239 IMAGE-MGC_LOAD
NCBI Gene 288731 ENTREZGENE
Pfam His_Phos_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pgam5 PhenoGen
SMART PGAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53254 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V9N1_RAT UniProtKB/TrEMBL
  PGAM5_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-29 Pgam5  PGAM family member 5, mitochondrial serine/threonine protein phosphatase  Pgam5  phosphoglycerate mutase family member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Pgam5  phosphoglycerate mutase family member 5  RGD1312028  similar to hypothetical protein MGC5352  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1312028  similar to hypothetical protein MGC5352  RGD1312028_predicted  similar to hypothetical protein MGC5352 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1312028_predicted  similar to hypothetical protein MGC5352 (predicted)  LOC288731_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC288731_predicted  similar to hypothetical protein MGC5352 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL