Pdk3 (pyruvate dehydrogenase kinase 3) - Rat Genome Database

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Gene: Pdk3 (pyruvate dehydrogenase kinase 3) Rattus norvegicus
Analyze
Symbol: Pdk3
Name: pyruvate dehydrogenase kinase 3
RGD ID: 1593276
Description: Predicted to have ATP binding activity; protein serine/threonine kinase activity; and pyruvate dehydrogenase (acetyl-transferring) kinase activity. Involved in cellular response to glucose stimulus. Predicted to localize to mitochondrion and nucleolus. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease X-linked dominant 6. Orthologous to human PDK3 (pyruvate dehydrogenase kinase 3); PARTICIPATES IN pyruvate metabolic pathway; INTERACTS WITH acetamide; acrylamide; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3, mitochondrial; Pdk3_mapped; pyruvate dehydrogenase kinase, isoenzyme 3; pyruvate dehydrogenase kinase, isoenzyme 3 (mapped); pyruvate dehydrogenase kinase, isozyme 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X58,477,471 - 58,553,932 (-)NCBI
Rnor_6.0 EnsemblX62,836,131 - 62,903,554 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X62,836,131 - 62,904,114 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X63,428,816 - 63,497,161 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X81,104,667 - 81,171,536 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX58,924,116 - 58,991,740 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11485553   PMID:11486000   PMID:12477932   PMID:14651853   PMID:15861126   PMID:17669420   PMID:18614015   PMID:18718909   PMID:20715114   PMID:22865452  


Genomics

Comparative Map Data
Pdk3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X58,477,471 - 58,553,932 (-)NCBI
Rnor_6.0 EnsemblX62,836,131 - 62,903,554 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X62,836,131 - 62,904,114 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X63,428,816 - 63,497,161 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X81,104,667 - 81,171,536 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX58,924,116 - 58,991,740 (-)NCBICelera
Cytogenetic MapXq22NCBI
PDK3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX24,465,221 - 24,550,466 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX24,465,270 - 24,550,466 (+)EnsemblGRCh38hg38GRCh38
GRCh38X24,465,286 - 24,550,466 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X24,483,403 - 24,568,583 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X24,393,475 - 24,462,463 (+)NCBINCBI36hg18NCBI36
Build 34X24,243,210 - 24,312,199NCBI
CeleraX28,606,234 - 28,691,468 (+)NCBI
Cytogenetic MapXp22.11NCBI
HuRefX22,225,142 - 22,310,559 (+)NCBIHuRef
CHM1_1X24,514,817 - 24,600,156 (+)NCBICHM1_1
Pdk3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X92,798,923 - 92,875,756 (-)NCBIGRCm39mm39
GRCm39 EnsemblX92,808,213 - 92,875,807 (-)Ensembl
GRCm38X93,764,616 - 93,832,150 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX93,764,607 - 93,832,201 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X91,009,955 - 91,077,434 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X90,017,335 - 90,084,814 (-)NCBImm8
CeleraX80,688,439 - 80,755,738 (-)NCBICelera
Cytogenetic MapXC3NCBI
Pdk3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555094,809,399 - 4,878,976 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555094,809,422 - 4,888,802 (+)NCBIChiLan1.0ChiLan1.0
PDK3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X24,430,028 - 24,514,873 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX24,430,028 - 24,504,730 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X17,062,278 - 17,147,489 (+)NCBIMhudiblu_PPA_v0panPan3
PDK3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X19,994,383 - 20,058,979 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX19,994,393 - 20,058,485 (+)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X19,949,236 - 20,023,756 (+)NCBI
UMICH_Zoey_3.1X19,987,464 - 20,061,958 (+)NCBI
UNSW_CanFamBas_1.0X20,020,576 - 20,095,075 (+)NCBI
UU_Cfam_GSD_1.0X20,078,072 - 20,152,369 (+)NCBI
Pdk3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X12,944,337 - 13,025,336 (+)NCBI
SpeTri2.0NW_004936624141,745 - 213,495 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDK3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX20,436,815 - 20,602,716 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X20,486,205 - 20,598,492 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X21,996,492 - 22,076,913 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDK3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X22,948,162 - 23,030,542 (+)NCBI
ChlSab1.1 EnsemblX22,948,203 - 23,029,868 (+)Ensembl
Pdk3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624897759,367 - 833,947 (+)NCBI

Position Markers
DXGot133  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,488,321 - 58,488,469 (+)MAPPER
Rnor_6.0X62,837,899 - 62,838,046NCBIRnor6.0
Rnor_5.0X63,430,584 - 63,430,731UniSTSRnor5.0
RGSC_v3.4X81,106,435 - 81,106,582UniSTSRGSC3.4
CeleraX58,925,884 - 58,926,031UniSTS
Cytogenetic MapXq22UniSTS
AI035637  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,487,096 - 58,487,298 (+)MAPPER
Rnor_6.0X62,836,674 - 62,836,875NCBIRnor6.0
Rnor_5.0X63,429,359 - 63,429,560UniSTSRnor5.0
RGSC_v3.4X81,105,210 - 81,105,411UniSTSRGSC3.4
CeleraX58,924,659 - 58,924,860UniSTS
Cytogenetic MapXq22UniSTS
RH128023  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,486,992 - 58,487,188 (+)MAPPER
Rnor_6.0X62,836,570 - 62,836,765NCBIRnor6.0
Rnor_5.0X63,429,255 - 63,429,450UniSTSRnor5.0
RGSC_v3.4X81,105,106 - 81,105,301UniSTSRGSC3.4
CeleraX58,924,555 - 58,924,750UniSTS
Cytogenetic MapXq22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X6139809770352120Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:645
Count of miRNA genes:276
Interacting mature miRNAs:350
Transcripts:ENSRNOT00000017370
Prediction methods:Microtar, Miranda, Pita, 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.


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 26 34 22 18 22 74 35 41 11
Low 17 22 18 1 18 8 11 8
Below cutoff 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017370   ⟹   ENSRNOP00000017370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX62,836,131 - 62,903,554 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076652   ⟹   ENSRNOP00000068033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX62,836,276 - 62,903,530 (-)Ensembl
RefSeq Acc Id: NM_001106581   ⟹   NP_001100051
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,486,554 - 58,553,557 (-)NCBI
Rnor_6.0X62,836,131 - 62,903,554 (-)NCBI
Rnor_5.0X63,428,816 - 63,497,161 (-)NCBI
RGSC_v3.4X81,104,667 - 81,171,536 (-)RGD
CeleraX58,924,116 - 58,991,740 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257018   ⟹   XP_006257080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X62,836,256 - 62,903,584 (-)NCBI
Rnor_5.0X63,428,816 - 63,497,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257019   ⟹   XP_006257081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X62,836,256 - 62,904,114 (-)NCBI
Rnor_5.0X63,428,816 - 63,497,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257020   ⟹   XP_006257082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X62,836,256 - 62,903,635 (-)NCBI
Rnor_5.0X63,428,816 - 63,497,161 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099568   ⟹   XP_038955496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,477,471 - 58,553,932 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100051 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955496 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI69078 (Get FASTA)   NCBI Sequence Viewer  
  EDL96013 (Get FASTA)   NCBI Sequence Viewer  
  EDL96014 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100051   ⟸   NM_001106581
- UniProtKB: B5DFI9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257081   ⟸   XM_006257019
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257082   ⟸   XM_006257020
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006257080   ⟸   XM_006257018
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000017370   ⟸   ENSRNOT00000017370
RefSeq Acc Id: ENSRNOP00000068033   ⟸   ENSRNOT00000076652
RefSeq Acc Id: XP_038955496   ⟸   XM_039099568
- Peptide Label: isoform X1
Protein Domains
Histidine kinase

Transcriptome

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

Promoters
RGD ID:13701843
Promoter ID:EPDNEW_R12362
Type:multiple initiation site
Name:Pdk3_1
Description:pyruvate dehydrogenase kinase 3
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_6.0X62,903,509 - 62,903,569EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 62848432 62848433 C A snv LE/Stm (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 81151823 81151824 G A snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593276 AgrOrtholog
Ensembl Genes ENSRNOG00000012513 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017370 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068033 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017370 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076652 UniProtKB/TrEMBL
Gene3D-CATH 1.20.140.20 UniProtKB/TrEMBL
  3.30.565.10 UniProtKB/TrEMBL
InterPro AK/P_DHK_N_sf UniProtKB/TrEMBL
  ATPase-like_ATP-bd UniProtKB/TrEMBL
  BCDHK/PDK_mit UniProtKB/TrEMBL
  BCKD/PDK UniProtKB/TrEMBL
  HATPase_C_sf UniProtKB/TrEMBL
  Sig_transdc_His_kinase_core UniProtKB/TrEMBL
KEGG Report rno:296849 UniProtKB/TrEMBL
NCBI Gene 296849 ENTREZGENE
PANTHER PTHR11947 UniProtKB/TrEMBL
Pfam BCDHK_Adom3 UniProtKB/TrEMBL
  HATPase_c UniProtKB/TrEMBL
PhenoGen Pdk3 PhenoGen
PROSITE HIS_KIN UniProtKB/TrEMBL
SMART HATPase_c UniProtKB/TrEMBL
Superfamily-SCOP ATP_bd_ATPase UniProtKB/TrEMBL
  BCDHK/PDK_N UniProtKB/TrEMBL
UniProt B5DFI9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Pdk3  pyruvate dehydrogenase kinase 3  Pdk3  pyruvate dehydrogenase kinase, isozyme 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-10 Pdk3  pyruvate dehydrogenase kinase, isozyme 3  Pdk3  pyruvate dehydrogenase kinase, isoenzyme 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-13   pyruvate dehydrogenase kinase, isoenzyme 3  Pdk3  pyruvate dehydrogenase kinase, isoenzyme 3 (mapped)  Name updated 737654 APPROVED
2007-04-11 Pdk3  pyruvate dehydrogenase kinase, isoenzyme 3 (mapped)  Pdk3_mapped  pyruvate dehydrogenase kinase, isoenzyme 3 (mapped)  Data Merged 737654 APPROVED
2006-11-20 Pdk3  pyruvate dehydrogenase kinase, isoenzyme 3 (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Pdk3_mapped  pyruvate dehydrogenase kinase, isoenzyme 3 (mapped)  Pdk3  pyruvate dehydrogenase kinase, isoenzyme 3  Symbol and Name updated 1556543 APPROVED
2002-11-06 Pdk3  pyruvate dehydrogenase kinase, isoenzyme 3    Pyruvate dehydrogenase kinase 3  Name updated 625702 APPROVED
2002-06-10 Pdk3  Pyruvate dehydrogenase kinase 3      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_homology human PDK3 binds to the lipoyl domains of the dihydrolipoyl acetyltransferase (E2) to affect phosphorylation rates of the pyruvate dehydrogenase (E1) component 1302271