Pdpr (pyruvate dehydrogenase phosphatase regulatory subunit) - Rat Genome Database

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Gene: Pdpr (pyruvate dehydrogenase phosphatase regulatory subunit) Rattus norvegicus
Analyze
Symbol: Pdpr
Name: pyruvate dehydrogenase phosphatase regulatory subunit
RGD ID: 1308307
Description: Predicted to be active in mitochondrial matrix. Orthologous to human PDPR (pyruvate dehydrogenase phosphatase regulatory subunit); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC307852; pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial; RGD1308307; similar to pyruvate dehydrogenase phosphatase regulatory subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81955,974,611 - 56,019,045 (+)NCBIGRCr8
mRatBN7.21939,065,226 - 39,109,695 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1939,065,157 - 39,109,688 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1945,876,107 - 45,909,545 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01946,529,449 - 46,562,895 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01948,840,033 - 48,873,118 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01943,107,852 - 43,149,243 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1943,109,427 - 43,149,210 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01953,933,343 - 53,973,781 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41941,025,633 - 41,058,989 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11941,030,532 - 41,063,855 (+)NCBI
Celera1938,462,557 - 38,495,915 (+)NCBICelera
Cytogenetic Map19q12NCBI
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

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9651365   PMID:18614015   PMID:34800366  


Genomics

Comparative Map Data
Pdpr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81955,974,611 - 56,019,045 (+)NCBIGRCr8
mRatBN7.21939,065,226 - 39,109,695 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1939,065,157 - 39,109,688 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1945,876,107 - 45,909,545 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01946,529,449 - 46,562,895 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01948,840,033 - 48,873,118 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01943,107,852 - 43,149,243 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1943,109,427 - 43,149,210 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01953,933,343 - 53,973,781 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41941,025,633 - 41,058,989 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11941,030,532 - 41,063,855 (+)NCBI
Celera1938,462,557 - 38,495,915 (+)NCBICelera
Cytogenetic Map19q12NCBI
PDPR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381670,113,626 - 70,163,427 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1670,114,332 - 70,162,537 (+)EnsemblGRCh38hg38GRCh38
GRCh371670,147,529 - 70,196,440 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361668,705,030 - 68,752,685 (+)NCBINCBI36Build 36hg18NCBI36
Celera1655,305,783 - 55,318,599 (+)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1656,000,281 - 56,034,180 (+)NCBIHuRef
CHM1_11671,555,144 - 71,602,818 (+)NCBICHM1_1
T2T-CHM13v2.01675,922,058 - 75,974,584 (+)NCBIT2T-CHM13v2.0
Pdpr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398111,821,232 - 111,866,402 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8111,821,262 - 111,863,706 (+)EnsemblGRCm39 Ensembl
GRCm388111,094,609 - 111,139,781 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8111,094,630 - 111,137,074 (+)EnsemblGRCm38mm10GRCm38
MGSCv378113,618,645 - 113,659,044 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368113,981,418 - 114,021,817 (+)NCBIMGSCv36mm8
Celera8115,325,916 - 115,359,375 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map857.95NCBI
Pdpr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554843,010,918 - 3,044,004 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554843,007,435 - 3,044,060 (-)NCBIChiLan1.0ChiLan1.0
PDPR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21884,017,672 - 84,067,296 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11689,953,418 - 90,002,934 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01654,868,840 - 54,919,077 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PDPR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1576,210,472 - 76,239,837 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl576,213,566 - 76,239,852 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha576,166,902 - 76,196,312 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0576,646,289 - 76,682,979 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1576,468,772 - 76,505,252 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0576,280,014 - 76,316,315 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0576,772,087 - 76,808,437 (+)NCBIUU_Cfam_GSD_1.0
Pdpr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934936,215,965 - 36,257,021 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647523,332,093 - 23,373,340 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647523,332,093 - 23,373,151 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDPR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl613,187,427 - 13,227,033 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1613,187,377 - 13,230,601 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2613,272,323 - 13,289,911 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDPR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1553,296,772 - 53,341,206 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604716,082,058 - 16,128,130 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdpr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474612,423,917 - 12,492,966 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474612,426,081 - 12,492,966 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pdpr
184 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:145
Count of miRNA genes:102
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000038452
Prediction methods:Microtar, Miranda, Rnahybrid
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
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat

Markers in Region
RH135168  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21939,096,595 - 39,096,805 (-)MAPPERmRatBN7.2
Rnor_6.01943,117,720 - 43,117,929NCBIRnor6.0
Rnor_5.01953,943,211 - 53,943,420UniSTSRnor5.0
RGSC_v3.41941,050,526 - 41,050,735UniSTSRGSC3.4
Celera1938,487,554 - 38,487,763UniSTS
RH 3.4 Map5964.8UniSTS
Cytogenetic Map19q12UniSTS
RH136833  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21939,080,211 - 39,080,357 (-)MAPPERmRatBN7.2
Rnor_6.01943,134,054 - 43,134,199NCBIRnor6.0
Rnor_5.01953,959,545 - 53,959,690UniSTSRnor5.0
RGSC_v3.41941,034,145 - 41,034,290UniSTSRGSC3.4
Celera1938,471,171 - 38,471,316UniSTS
RH 3.4 Map19475.1UniSTS
Cytogenetic Map7q34UniSTS
Cytogenetic Map19q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000038452   ⟹   ENSRNOP00000032023
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1939,066,480 - 39,106,958 (+)Ensembl
Rnor_6.0 Ensembl1943,109,427 - 43,149,210 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000107538   ⟹   ENSRNOP00000083707
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1939,065,157 - 39,109,688 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000119660   ⟹   ENSRNOP00000080468
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1939,065,682 - 39,106,958 (+)Ensembl
RefSeq Acc Id: NM_001107430   ⟹   NP_001100900
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,981,059 - 56,014,415 (+)NCBI
mRatBN7.21939,071,700 - 39,105,059 (+)NCBI
Rnor_6.01943,109,466 - 43,142,711 (-)NCBI
Rnor_5.01953,933,343 - 53,973,781 (-)NCBI
RGSC_v3.41941,025,633 - 41,058,989 (+)RGD
Celera1938,462,557 - 38,495,915 (+)RGD
Sequence:
RefSeq Acc Id: XM_008772514   ⟹   XP_008770736
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,974,611 - 56,019,045 (+)NCBI
mRatBN7.21939,065,226 - 39,109,695 (+)NCBI
Rnor_6.01943,107,852 - 43,149,243 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601299   ⟹   XP_017456788
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,982,889 - 56,019,045 (+)NCBI
mRatBN7.21939,081,642 - 39,109,695 (+)NCBI
Rnor_6.01943,107,852 - 43,132,718 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100900 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770736 (Get FASTA)   NCBI Sequence Viewer  
  XP_017456788 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92561 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032023.5
  ENSRNOP00000080468.1
  ENSRNOP00000083707.1
RefSeq Acc Id: NP_001100900   ⟸   NM_001107430
- UniProtKB: D3ZXA6 (UniProtKB/TrEMBL),   A6IZ83 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770736   ⟸   XM_008772514
- Peptide Label: isoform X1
- UniProtKB: D3ZXA6 (UniProtKB/TrEMBL),   A6IZ83 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456788   ⟸   XM_017601299
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000032023   ⟸   ENSRNOT00000038452
Ensembl Acc Id: ENSRNOP00000083707   ⟸   ENSRNOT00000107538
Ensembl Acc Id: ENSRNOP00000080468   ⟸   ENSRNOT00000119660
Protein Domains
Aminomethyltransferase folate-binding   FAD dependent oxidoreductase   FAD dependent oxidoreductase central   Glycine cleavage T-protein C-terminal barrel

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZXA6-F1-model_v2 AlphaFold D3ZXA6 1-878 view protein structure

Transcriptome

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

Promoters
RGD ID:13701138
Promoter ID:EPDNEW_R11662
Type:single initiation site
Name:Pdpr_1
Description:pyruvate dehydrogenase phosphatase regulatory subunit
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_6.01943,149,220 - 43,149,280EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308307 AgrOrtholog
BioCyc Gene G2FUF-5659 BioCyc
Ensembl Genes ENSRNOG00000022593 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038452.7 UniProtKB/TrEMBL
  ENSRNOT00000107538.1 UniProtKB/TrEMBL
  ENSRNOT00000119660.1 UniProtKB/TrEMBL
Gene3D-CATH 3.50.50.60 UniProtKB/TrEMBL
  Aminomethyltransferase beta-barrel domains UniProtKB/TrEMBL
  Aminomethyltransferase beta-barrel domains UniProtKB/TrEMBL
  D-Amino Acid Oxidase, subunit A, domain 2 UniProtKB/TrEMBL
InterPro FAD-dep_OxRdtase UniProtKB/TrEMBL
  FAD/NAD-bd_sf UniProtKB/TrEMBL
  FAO_M UniProtKB/TrEMBL
  GCV_T_C UniProtKB/TrEMBL
  GCV_T_N UniProtKB/TrEMBL
  GcvT/YgfZ_C UniProtKB/TrEMBL
  TrmE/GcvT_dom1 UniProtKB/TrEMBL
KEGG Report rno:307852 UniProtKB/TrEMBL
NCBI Gene 307852 ENTREZGENE
PANTHER PYRUVATE DEHYDROGENASE PHOSPHATASE REGULATORY SUBUNIT, MITOCHONDRIAL UniProtKB/TrEMBL
  SARCOSINE DEHYDROGENASE-RELATED UniProtKB/TrEMBL
Pfam DAO UniProtKB/TrEMBL
  FAO_M UniProtKB/TrEMBL
  GCV_T UniProtKB/TrEMBL
  GCV_T_C UniProtKB/TrEMBL
PhenoGen Pdpr PhenoGen
RatGTEx ENSRNOG00000022593 RatGTEx
Superfamily-SCOP FAD-linked reductases, C-terminal domain UniProtKB/TrEMBL
  Folate-binding domain UniProtKB/TrEMBL
  SSF101790 UniProtKB/TrEMBL
  SSF51905 UniProtKB/TrEMBL
UniProt A0A8I5ZQQ3_RAT UniProtKB/TrEMBL
  A0A8I5ZVU4_RAT UniProtKB/TrEMBL
  A6IZ83 ENTREZGENE, UniProtKB/TrEMBL
  D3ZXA6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-26 Pdpr  pyruvate dehydrogenase phosphatase regulatory subunit  RGD1308307_predicted  similar to pyruvate dehydrogenase phosphatase regulatory subunit (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1308307_predicted  similar to pyruvate dehydrogenase phosphatase regulatory subunit (predicted)  LOC307852_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC307852_predicted  similar to pyruvate dehydrogenase phosphatase regulatory subunit (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL