Pdhb (pyruvate dehydrogenase E1 subunit beta) - Rat Genome Database

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Gene: Pdhb (pyruvate dehydrogenase E1 subunit beta) Rattus norvegicus
Analyze
Symbol: Pdhb
Name: pyruvate dehydrogenase E1 subunit beta
RGD ID: 1359146
Description: Exhibits pyruvate dehydrogenase (acetyl-transferring) activity. Is predicted to contribute to pyruvate dehydrogenase (NAD+) activity. Involved in acetyl-CoA biosynthetic process from pyruvate. Localizes to mitochondrion and pyruvate dehydrogenase complex. Human ortholog(s) of this gene implicated in pyruvate decarboxylase deficiency. Orthologous to human PDHB (pyruvate dehydrogenase E1 subunit beta); PARTICIPATES IN citric acid cycle pathway; fumaric aciduria pathway; Leigh disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC94149; PDHE1-B; pyruvate dehydrogenase (lipoamide) beta; pyruvate dehydrogenase E1 beta subunit; pyruvate dehydrogenase E1 component subunit beta, mitochondrial
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
mRatBN7.21516,752,561 - 16,758,503 (+)NCBI
Rnor_6.0 Ensembl1518,539,210 - 18,546,854 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01518,540,826 - 18,546,855 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01522,507,861 - 22,513,890 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41518,737,449 - 18,743,391 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11518,737,448 - 18,743,390 (+)NCBI
Celera1516,710,789 - 16,716,731 (+)NCBICelera
Cytogenetic Map15p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
2-hydroxypropanoic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP)
aristolochic acid  (ISO)
aspartame  (ISO)
Azaspiracid  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chromium trinitrate  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
D-glucose  (EXP)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
dicrotophos  (ISO)
doxorubicin  (EXP,ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
ferric ammonium citrate  (ISO)
flutamide  (EXP)
folic acid  (ISO)
glucose  (EXP)
heparin  (EXP)
isotretinoin  (ISO)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
monosodium L-glutamate  (ISO)
morphine  (EXP)
ochratoxin A  (ISO)
oxidopamine  (ISO)
paracetamol  (ISO)
perfluorododecanoic acid  (EXP)
pirinixic acid  (EXP)
potassium chromate  (ISO)
quartz  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
sarin  (EXP,ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulforaphane  (EXP)
T-2 toxin  (EXP)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vincaleukoblastine  (ISO)
vinclozolin  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:2025639   PMID:14651853   PMID:15489334   PMID:18164639   PMID:18614015   PMID:19081061   PMID:21630459   PMID:22569713   PMID:23376485   PMID:25002582   PMID:25451023   PMID:26316108  
PMID:29476059  


Genomics

Candidate Gene Status
Pdhb is a candidate Gene for QTL Bmd62
Comparative Map Data
Pdhb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21516,752,561 - 16,758,503 (+)NCBI
Rnor_6.0 Ensembl1518,539,210 - 18,546,854 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01518,540,826 - 18,546,855 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01522,507,861 - 22,513,890 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41518,737,449 - 18,743,391 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11518,737,448 - 18,743,390 (+)NCBI
Celera1516,710,789 - 16,716,731 (+)NCBICelera
Cytogenetic Map15p14NCBI
PDHB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl358,427,630 - 58,433,857 (-)EnsemblGRCh38hg38GRCh38
GRCh38358,427,630 - 58,433,832 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37358,413,357 - 58,419,559 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36358,388,394 - 58,394,605 (-)NCBINCBI36hg18NCBI36
Build 34358,388,397 - 58,394,594NCBI
Celera358,427,174 - 58,433,398 (-)NCBI
Cytogenetic Map3p14.3NCBI
HuRef358,509,470 - 58,515,692 (-)NCBIHuRef
CHM1_1358,363,623 - 58,369,848 (-)NCBICHM1_1
Pdhb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391414,296,470 - 14,303,782 (+)NCBIGRCm39mm39
GRCm39 Ensembl1414,296,748 - 14,303,777 (+)Ensembl
GRCm38148,165,991 - 8,173,303 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl148,165,996 - 8,173,025 (-)EnsemblGRCm38mm10GRCm38
MGSCv37148,998,505 - 9,005,506 (-)NCBIGRCm37mm9NCBIm37
MGSCv36146,956,612 - 6,964,490 (-)NCBImm8
Celera143,789,851 - 3,797,024 (-)NCBICelera
Cytogenetic Map14A1NCBI
Pdhb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554301,707,615 - 1,713,541 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554301,707,615 - 1,713,541 (+)NCBIChiLan1.0ChiLan1.0
PDHB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1359,776,216 - 59,782,461 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl359,776,618 - 59,782,411 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0358,359,753 - 58,366,094 (-)NCBIMhudiblu_PPA_v0panPan3
PDHB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12032,185,420 - 32,191,592 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2032,110,558 - 32,116,683 (+)NCBI
ROS_Cfam_1.02032,453,097 - 32,459,222 (+)NCBI
UMICH_Zoey_3.12031,909,791 - 31,915,922 (+)NCBI
UNSW_CanFamBas_1.02032,266,176 - 32,272,302 (+)NCBI
UU_Cfam_GSD_1.02032,438,275 - 32,444,406 (+)NCBI
Pdhb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118169,442,034 - 169,447,686 (+)NCBI
SpeTri2.0NW_0049364732,580,642 - 2,586,266 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDHB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1340,160,546 - 40,167,476 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11340,161,519 - 40,167,502 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21344,121,821 - 44,127,805 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDHB
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12219,718,610 - 19,725,037 (-)NCBI
ChlSab1.1 Ensembl2219,718,353 - 19,725,036 (-)Ensembl
Vero_WHO_p1.0NW_023666041147,098,867 - 147,105,329 (+)NCBI
Pdhb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248225,482,177 - 5,488,218 (-)NCBI

Position Markers
RH127408  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21516,758,210 - 16,758,390 (+)MAPPER
Rnor_6.01518,546,563 - 18,546,742NCBIRnor6.0
Rnor_5.01522,513,598 - 22,513,777UniSTSRnor5.0
RGSC_v3.41518,743,099 - 18,743,278UniSTSRGSC3.4
Celera1516,716,439 - 16,716,618UniSTS
RH 3.4 Map15145.48UniSTS
Cytogenetic Map15p14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15130597196Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15232787726288802Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15232787726288802Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151582824233657761Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:38
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000010545
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.


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: ENSRNOT00000010545   ⟹   ENSRNOP00000010545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1518,540,913 - 18,546,854 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000083212   ⟹   ENSRNOP00000075450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1518,539,210 - 18,546,673 (+)Ensembl
RefSeq Acc Id: NM_001007620   ⟹   NP_001007621
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21516,752,561 - 16,758,503 (+)NCBI
Rnor_6.01518,540,913 - 18,546,855 (+)NCBI
Rnor_5.01522,507,861 - 22,513,890 (+)NCBI
RGSC_v3.41518,737,449 - 18,743,391 (+)RGD
Celera1516,710,789 - 16,716,731 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251754   ⟹   XP_006251816
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01518,540,826 - 18,546,855 (+)NCBI
Rnor_5.01522,507,861 - 22,513,890 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001007621 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79137 (Get FASTA)   NCBI Sequence Viewer  
  EDL94164 (Get FASTA)   NCBI Sequence Viewer  
  P49432 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001007621   ⟸   NM_001007620
- Peptide Label: precursor
- UniProtKB: P49432 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251816   ⟸   XM_006251754
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000010545   ⟸   ENSRNOT00000010545
RefSeq Acc Id: ENSRNOP00000075450   ⟸   ENSRNOT00000083212
Protein Domains
Transket_pyr

Transcriptome

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

Promoters
RGD ID:13699589
Promoter ID:EPDNEW_R10112
Type:multiple initiation site
Name:Pdhb_1
Description:pyruvate dehydrogenase E1 beta 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_6.01518,541,210 - 18,541,270EPDNEW

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)
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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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: 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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359146 AgrOrtholog
Ensembl Genes ENSRNOG00000007895 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010545 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075450 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010545 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000083212 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.920 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127701 IMAGE-MGC_LOAD
InterPro PDHB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THDP-binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transketo_C/PFOR_II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transketolase-like_Pyr-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transketolase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:289950 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94149 IMAGE-MGC_LOAD
NCBI Gene 289950 ENTREZGENE
PANTHER PTHR11624 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Transket_pyr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transketolase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdhb PhenoGen
SMART Transket_pyr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52518 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52922 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KAM3_RAT UniProtKB/TrEMBL
  ODPB_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6AY95 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-12-06 Pdhb  pyruvate dehydrogenase E1 subunit beta  Pdhb  pyruvate dehydrogenase E1 beta subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-08-22 Pdhb  pyruvate dehydrogenase E1 beta subunit  Pdhb  pyruvate dehydrogenase (lipoamide) beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Pdhb  pyruvate dehydrogenase (lipoamide) beta      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Pdhb  pyruvate dehydrogenase (lipoamide) beta      Symbol and Name status set to provisional 70820 PROVISIONAL