Pdha1 (pyruvate dehydrogenase E1 subunit alpha 1)

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Gene: Pdha1 (pyruvate dehydrogenase E1 subunit alpha 1) Rattus norvegicus

Analyze

Symbol:

Pdha1

Name:

pyruvate dehydrogenase E1 subunit alpha 1

RGD ID:

3286

Description:

Enables pyruvate dehydrogenase (acetyl-transferring) activity. Involved in acetyl-CoA biosynthetic process from pyruvate. Located in mitochondrion. Part of pyruvate dehydrogenase complex. Used to study pyruvate decarboxylase deficiency. Human ortholog(s) of this gene implicated in pyruvate decarboxylase deficiency. Orthologous to human PDHA1 (pyruvate dehydrogenase E1 subunit alpha 1); PARTICIPATES IN citric acid cycle pathway; fumaric aciduria pathway; Leigh disease pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

MGC114215; MGC94854; PDHE1-A type I; pyruvate dehydrogenase (lipoamide) alpha 1; pyruvate dehydrogenase alpha 1; pyruvate dehydrogenase E1 alpha 1; pyruvate dehydrogenase E1 alpha 1 subunit; pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial; pyruvate dehydrogenase E1alpha subunit

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PDHA1 (pyruvate dehydrogenase E1 subunit alpha 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Pdha1 (pyruvate dehydrogenase E1 alpha 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Pdha1 (pyruvate dehydrogenase E1 alpha 1 subunit)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PDHA1 (pyruvate dehydrogenase E1 subunit alpha 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PDHA1 (pyruvate dehydrogenase E1 subunit alpha 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pdha1 (pyruvate dehydrogenase E1 subunit alpha 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PDHA1 (pyruvate dehydrogenase E1 subunit alpha 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PDHA1 (pyruvate dehydrogenase E1 subunit alpha 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pdha1 (pyruvate dehydrogenase E1 subunit alpha 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PDHA2 (pyruvate dehydrogenase E1 subunit alpha 2)	HGNC	OrthoDB, Panther
Alliance orthologs ³
Homo sapiens (human):	PDHA1 (pyruvate dehydrogenase E1 subunit alpha 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Mus musculus (house mouse):	Pdha1 (pyruvate dehydrogenase E1 alpha 1)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Danio rerio (zebrafish):	pdha1b (pyruvate dehydrogenase E1 alpha 1 subunit b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Danio rerio (zebrafish):	pdha1a (pyruvate dehydrogenase E1 alpha 1 subunit a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	PDA1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Drosophila melanogaster (fruit fly):	CG7024	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Pdha	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)
Caenorhabditis elegans (roundworm):	pdha-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|sonicParanoid)

Related Pseudogenes:

Pdha1l1

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	34,700,481 - 34,714,309 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	X	34,700,409 - 34,714,311 (+)	Ensembl
Rnor_6.0	X	37,329,779 - 37,343,410 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	37,329,779 - 37,343,410 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	37,640,725 - 37,654,356 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	55,899,491 - 55,913,319 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	55,952,967 - 55,966,789 (+)	NCBI
Celera	X	35,373,056 - 35,386,884 (+)	NCBI		Celera
Cytogenetic Map	X	q14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

developmental and epileptic encephalopathy 2 (ISO)

Disease Progression (ISO)

genetic disease (ISO)

lactic acidosis (ISO)

Leigh Syndrome, X-Linked (ISO)

Myocardial Ischemia (ISO)

Neurodevelopmental Disorders (ISO)

osteoarthritis (ISO)

Prostatic Neoplasms (ISO)

pyruvate decarboxylase deficiency (IMP,ISO)

Pyruvate Dehydrogenase E1 Alpha Deficiency (ISO)

Pyruvate Metabolism, Inborn Errors (ISO)

Stomach Neoplasms (ISO)

sudden infant death syndrome (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

visual epilepsy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

(-)-epigallocatechin 3-gallate (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP)

2,3,7,8-tetrabromodibenzodioxine (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

3-chloropropane-1,2-diol (EXP)

4,4'-diaminodiphenylmethane (ISO)

aflatoxin B1 (ISO)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bezafibrate (EXP)

bisphenol A (EXP,ISO)

cadmium atom (ISO)

ciguatoxin CTX1B (ISO)

cobalt dichloride (ISO)

D-glucose (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

dichloroacetic acid (ISO)

dinophysistoxin 1 (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

duvoglustat (ISO)

ethanol (EXP,ISO)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

fulvestrant (ISO)

Fusaric acid (ISO)

genistein (EXP)

gentamycin (EXP)

glucose (ISO)

hydrogen peroxide (ISO)

isotretinoin (ISO)

ivermectin (ISO)

kojic acid (ISO)

maneb (ISO)

metformin (ISO)

methamphetamine (EXP)

methyl methanesulfonate (ISO)

Methylazoxymethanol acetate (EXP)

methylmercury chloride (ISO)

methylparaben (ISO)

mitoxantrone (ISO)

N-acetyl-L-cysteine (ISO)

nefazodone (EXP)

okadaic acid (ISO)

paracetamol (ISO)

paraquat (ISO)

PCB138 (EXP)

perfluorooctanoic acid (ISO)

picoxystrobin (ISO)

pirinixic acid (EXP,ISO)

pregnenolone 16alpha-carbonitrile (ISO)

quinoline (ISO)

resveratrol (EXP,ISO)

sodium dodecyl sulfate (ISO)

sodium fluoride (ISO)

superoxide (ISO)

temozolomide (ISO)

titanium dioxide (ISO)

triclosan (ISO)

valproic acid (ISO)

zearalenone (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

acetyl-CoA biosynthetic process from pyruvate (IBA,IDA,IEA,ISO)

glucose metabolic process (IEA)

mitochondrial acetyl-CoA biosynthetic process from pyruvate (ISO)

tricarboxylic acid cycle (IEA)

Cellular Component

intracellular membrane-bounded organelle (IEA)

mitochondrial pyruvate dehydrogenase complex (ISO,TAS)

mitochondrion (IDA,ISO)

nucleolus (ISO)

pyruvate dehydrogenase complex (IDA,ISO)

Molecular Function

protein binding (ISO)

pyruvate dehydrogenase (acetyl-transferring) activity (IBA,IDA,IEA,ISO,ISS,TAS)

pyruvate dehydrogenase (NAD+) activity (ISO)

pyruvate dehydrogenase activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

butanoate metabolic pathway (IEA)

citric acid cycle pathway (IEA,ISO)

fumaric aciduria pathway (ISO)

gluconeogenesis pathway (IEA)

glycolysis pathway (IEA)

glycolysis/gluconeogenesis pathway (IEA)

Leigh disease pathway (ISO)

mitochondrial complex II deficiency pathway (ISO)

primary hyperoxaluria type 2 pathway (ISO)

pyruvate decarboxylase deficiency pathway (ISO)

pyruvate dehydrogenase E1 deficiency pathway (ISO)

pyruvate dehydrogenase E2 deficiency pathway (ISO)

pyruvate dehydrogenase E3 deficiency pathway (ISO)

pyruvate kinase deficiency of red cells pathway (ISO)

pyruvate metabolic pathway (IEA,ISO)

valine, leucine and isoleucine biosynthetic pathway (IEA)

References

References - curated


1.	Cullingford TE, etal., J Neurochem 1994 May;62(5):1682-90.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	KEGG
5.	Lissens W, etal., Hum Mutat 2000;15(3):209-19.
6.	Maury J, etal., Biochem J. 1995 Oct 15;311 ( Pt 2):531-5.
7.	MGD data from the GO Consortium
8.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	Ojano-Dirain C, etal., Mol Genet Metab. 2010 Oct-Nov;101(2-3):183-91. doi: 10.1016/j.ymgme.2010.07.008. Epub 2010 Jul 15.
10.	OMIM Disease Annotation Pipeline
11.	Patel MS and Korotchkina LG, Exp Mol Med. 2001 Dec 31;33(4):191-7.
12.	Pipeline to import KEGG annotations from KEGG into RGD
13.	Pipeline to import SMPDB annotations from SMPDB into RGD
14.	Quintana E, etal., Clin Genet. 2010 May;77(5):474-82. doi: 10.1111/j.1399-0004.2009.01313.x. Epub 2009 Dec 10.
15.	RGD automated data pipeline
16.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17.	RGD automated import pipeline for gene-chemical interactions
18.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:2025639	PMID:11708858	PMID:14651853	PMID:16641100	PMID:17634366	PMID:18586888	PMID:18614015	PMID:19081061	PMID:19429050	PMID:20833797	PMID:21630459	PMID:22809973
PMID:26503465	PMID:27871875	PMID:28376086	PMID:29476059

Genomics

Comparative Map Data

Pdha1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	34,700,481 - 34,714,309 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	X	34,700,409 - 34,714,311 (+)	Ensembl
Rnor_6.0	X	37,329,779 - 37,343,410 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	37,329,779 - 37,343,410 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	37,640,725 - 37,654,356 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	55,899,491 - 55,913,319 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	55,952,967 - 55,966,789 (+)	NCBI
Celera	X	35,373,056 - 35,386,884 (+)	NCBI		Celera
Cytogenetic Map	X	q14	NCBI

PDHA1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	X	19,343,927 - 19,361,718 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	X	19,343,893 - 19,361,718 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	X	19,362,045 - 19,379,836 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	19,271,972 - 19,287,886 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	19,121,707 - 19,137,622	NCBI
Celera	X	23,483,337 - 23,501,163 (+)	NCBI
Cytogenetic Map	X	p22.12	NCBI
HuRef	X	17,111,170 - 17,129,001 (+)	NCBI		HuRef
CHM1_1	X	19,393,050 - 19,410,882 (+)	NCBI		CHM1_1

Pdha1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	158,905,215 - 158,921,426 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	X	158,905,205 - 158,921,409 (-)	Ensembl
GRCm38	X	160,122,219 - 160,138,430 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	160,122,209 - 160,138,413 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	156,560,151 - 156,576,268 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	155,466,324 - 155,482,441 (-)	NCBI			mm8
Celera	X	143,366,647 - 143,382,812 (-)	NCBI		Celera
Cytogenetic Map	X	F4	NCBI
cM Map	X	73.95	NCBI

Pdha1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955586	97,172 - 114,928 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955586	98,492 - 114,927 (-)	NCBI	ChiLan1.0	ChiLan1.0

PDHA1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	X	19,330,622 - 19,348,443 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	19,330,508 - 19,348,443 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	11,967,944 - 11,985,837 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PDHA1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	15,338,364 - 15,354,011 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	15,338,202 - 15,387,458 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
ROS_Cfam_1.0	X	15,298,232 - 15,314,012 (+)	NCBI
ROS_Cfam_1.0 Ensembl	X	15,298,193 - 15,314,012 (+)	Ensembl
UMICH_Zoey_3.1	X	15,346,993 - 15,362,754 (+)	NCBI
UNSW_CanFamBas_1.0	X	15,348,770 - 15,364,534 (+)	NCBI
UU_Cfam_GSD_1.0	X	15,416,047 - 15,431,830 (+)	NCBI

Pdha1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	X	8,400,113 - 8,416,930 (+)	NCBI
SpeTri2.0	NW_004936844	889,720 - 906,631 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDHA1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	15,700,050 - 15,718,904 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	15,699,924 - 15,718,908 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	16,947,200 - 16,966,053 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PDHA1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	17,804,123 - 17,820,087 (+)	NCBI	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666056	19,671,536 - 19,689,681 (+)	NCBI	Vero_WHO_p1.0

Pdha1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624829	4,154,143 - 4,170,726 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

AI170398

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	X	34,714,460 - 34,714,644 (+)	MAPPER	mRatBN7.2
Rnor_6.0	X	37,343,562 - 37,343,745	NCBI	Rnor6.0
Rnor_5.0	X	37,654,508 - 37,654,691	UniSTS	Rnor5.0
RGSC_v3.4	X	55,913,471 - 55,913,654	UniSTS	RGSC3.4
Celera	X	35,387,036 - 35,387,219	UniSTS
RH 3.4 Map	X	500.8	UniSTS
Cytogenetic Map	X	q21	UniSTS

RH144218

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	X	34,712,636 - 34,712,737 (+)	MAPPER	mRatBN7.2
Rnor_6.0	X	37,341,738 - 37,341,838	NCBI	Rnor6.0
Rnor_5.0	X	37,652,684 - 37,652,784	UniSTS	Rnor5.0
RGSC_v3.4	X	55,911,647 - 55,911,747	UniSTS	RGSC3.4
Celera	X	35,385,212 - 35,385,312	UniSTS
Cytogenetic Map	X	q21	UniSTS

AA819807

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	X	34,713,892 - 34,714,106 (+)	MAPPER	mRatBN7.2
mRatBN7.2	16	82,511,694 - 82,511,908 (-)	MAPPER	mRatBN7.2
mRatBN7.2	X	34,713,892 - 34,714,106 (-)	MAPPER	mRatBN7.2
mRatBN7.2	16	82,511,694 - 82,511,908 (+)	MAPPER	mRatBN7.2
Rnor_6.0	X	37,342,994 - 37,343,207	NCBI	Rnor6.0
Rnor_6.0	16	88,344,652 - 88,344,865	NCBI	Rnor6.0
Rnor_5.0	16	87,741,383 - 87,741,596	UniSTS	Rnor5.0
Rnor_5.0	X	37,653,940 - 37,654,153	UniSTS	Rnor5.0
RGSC_v3.4	X	55,912,903 - 55,913,116	UniSTS	RGSC3.4
RGSC_v3.4	16	87,958,417 - 87,958,630	UniSTS	RGSC3.4
Celera	16	80,231,365 - 80,231,578	UniSTS
Celera	X	35,386,468 - 35,386,681	UniSTS
Cytogenetic Map	X	q21	UniSTS

RH141520

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	16	82,512,559 - 82,512,740 (-)	MAPPER	mRatBN7.2
mRatBN7.2	16	82,512,559 - 82,512,740 (+)	MAPPER	mRatBN7.2
mRatBN7.2	X	34,713,049 - 34,713,230 (-)	MAPPER	mRatBN7.2
mRatBN7.2	X	34,713,049 - 34,713,230 (+)	MAPPER	mRatBN7.2
Rnor_6.0	X	37,342,151 - 37,342,331	NCBI	Rnor6.0
Rnor_6.0	16	88,345,517 - 88,345,697	NCBI	Rnor6.0
Rnor_5.0	X	37,653,097 - 37,653,277	UniSTS	Rnor5.0
Rnor_5.0	16	87,742,248 - 87,742,428	UniSTS	Rnor5.0
RGSC_v3.4	X	55,912,060 - 55,912,240	UniSTS	RGSC3.4
RGSC_v3.4	16	87,959,282 - 87,959,462	UniSTS	RGSC3.4
Celera	16	80,232,230 - 80,232,410	UniSTS
Celera	X	35,385,625 - 35,385,805	UniSTS
RH 3.4 Map	X	503.51	UniSTS
Cytogenetic Map	16	q12.5	UniSTS
Cytogenetic Map	X	q21	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
731181	Uae27	Urinary albumin excretion QTL 27	2.7	0.0059	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	X	1	43491017	Rat
1298071	Edpm12	Estrogen-dependent pituitary mass QTL 12	3.2		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	X	2927898	47927898	Rat
10755455	Coatc13	Coat color QTL 13		0	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	7	4406000	49406000	Rat
631666	Iddm5	Insulin dependent diabetes mellitus QTL 5			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	X	4494549	49494549	Rat
61430	Cia18	Collagen induced arthritis QTL 18	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	14843113	120568734	Rat
71116	Niddm16	Non-insulin dependent diabetes mellitus QTL 16	7.81		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	X	15297802	60297802	Rat
1598873	Memor2	Memory QTL 2	2.5		exploratory behavior trait (VT:0010471)	average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)	X	20990947	41052531	Rat
2290375	Gluco34	Glucose level QTL 34	2.75		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	X	20990947	41203591	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	339
Count of miRNA genes:	219
Interacting mature miRNAs:	257
Transcripts:	ENSRNOT00000038352
Prediction methods:	Miranda, Pita
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	34	11	8
Low											7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001004072	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099538	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC079369	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC098897	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473966	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214890	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ235262	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000386	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000038352 ⟹ ENSRNOP00000030279

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	X	34,700,409 - 34,714,311 (+)	Ensembl
Rnor_6.0 Ensembl	X	37,329,779 - 37,343,410 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000088802 ⟹ ENSRNOP00000069789

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	X	34,704,381 - 34,714,299 (+)	Ensembl
Rnor_6.0 Ensembl	X	37,329,817 - 37,341,807 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000110948 ⟹ ENSRNOP00000094690

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	X	34,704,570 - 34,714,299 (+)	Ensembl

RefSeq Acc Id:

NM_001004072 ⟹ NP_001004072

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	34,700,481 - 34,714,309 (+)	NCBI
Rnor_6.0	X	37,329,779 - 37,343,410 (+)	NCBI
Rnor_5.0	X	37,640,725 - 37,654,356 (+)	NCBI
RGSC_v3.4	X	55,899,491 - 55,913,319 (+)	RGD
Celera	X	35,373,056 - 35,386,884 (+)	RGD

Sequence:

show sequence

CTGGGTGCCGCGGCTGCCGCGTCAGTCTGCTGCGCTCCATGAGGAAGATGCTTGCCGCTGTGTC
CCGCGTGTTGGCAGGCGCTGCGCAGAAGCCGGCAAGCAGAGTGCTGGTAGCTTCCCGTAATTTC
GCAAATGATGCTACATTTGAGATTAAGAAATGTGACCTTCATCGTCTAGAAGAGGGCCCTCCAG
TCACCACAGTGCTCACCAGAGAGGATGGGCTCAAGTACTACAGGATGATGCAGACCGTGCGCCG
GATGGAGCTCAAGGCGGATCAGCTGTATAAGCAGAAAATTATTCGTGGTTTCTGTCACTTGTGT
GATGGTCAGGAAGCCTGCTGTGTGGGCCTGGAGGCTGGCATAAACCCCACGGACCATCTCATCA
CTGCCTATCGAGCCCATGGCTTCACCTTCACTCGGGGCCTGCCTGTCCGAGCAATTCTTGCAGA
ATTAACAGGACGAAGAGGAGGCTGTGCTAAGGGGAAAGGCGGATCAATGCACATGTACGCCAAG
AACTTCTATGGCGGCAACGGTATCGTTGGAGCTCAGGTGCCCCTGGGTGCAGGAATTGCTCTGG
CCTGCAAGTATAATGGCAAAGATGAGGTCTGTTTGACATTATATGGTGATGGTGCTGCTAACCA
GGGTCAGATATTTGAAGCTTACAATATGGCAGCATTGTGGAAATTACCTTGTATTTTCATCTGT
GAGAATAACCGCTATGGCATGGGCACATCTGTTGAGAGAGCAGCAGCCAGCACGGATTACTACA
AAAGAGGAGATTTCATTCCTGGACTGAGGGTAGATGGAATGGATATCTTGTGTGTCCGAGAGGC
AACAAAGTTTGCAGCTGCCTACTGCAGGTCTGGTAAGGGGCCTATCCTGATGGAGCTACAGACT
TACCGCTACCATGGACATAGTATGAGTGACCCTGGAGTCAGTTATCGCACTCGAGAAGAAATCC
AGGAAGTAAGAAGTAAGAGTGACCCTATTATGCTTCTCAAGGATAGAATGGTGAACAGCAATCT
TGCAAGTGTTGAAGAATTAAAGGAGATTGATGTGGAAGTGAGGAAAGAAATCGAGGATGCTGCC
CAGTTTGCCACGGCTGATCCGGAGCCGCCATTGGAGGAGCTAGGCTATCATATCTACAGCAGTG
ACCCACCCTTCGAAGTGCGTGGTGCCAACCAGTGGATCAAGTTTAAGTCAGTCAGTTAATGGGA
GAGTATTAGATGGATGGGCGTTTCTCATCCGTTGTAAGAAACTCTTTGTGCTCTCAACTTTGAC
AGGAAATACCCAGACAACAAAAGTCTTGAAAACATGTAAATTAAGGGAGAGTAAAATTGCATGC
AGTTTGTACATTGTTGTATTCGGTGTATTCATGTGAATAAGAGTGTATAGGATTGGAGATGGGT
AATGCAGTTTATAACCTTCATCATGTCCTAGGTCAGTTACTAAAAGGAACAACTCTGCCATTTG
GTGATGTGATCATAGCTTTGAATGACCTTGTGGAGGCATGCTGGGATTAATGCAAAGCACAGGT
TAGAAGTGTATGGTCACCATGAATTGTGGAGGCTGGACTCTGTTTGGCACTGACCGTTATGTCT
TTGATCAAAGGCTATATATAATCATGTGTTTTAAAATAAGGGTACTTCAGTCACTTCAAAGGTA
AAATAATTTAATTTTCTCCATTTAGACATTTAACAAACACAAAATTGTACTCCCATTCCAAGGC
ACACTTTTTAACTTTTCACATTTAAGTAATTACACTGGTTTATAAAATACTTAGGCTTTATCTT
TCCAGCAACTGCTATAAGGTATGCTGACATTTTAAATACTAGGTCAGGAGAGACATTACTTACA
ATCCGGTTTATAAACAAGTATGCTCTAAATCACATGTGCTTGAATGAAACGAACAAGGGTCTTT
CTGTGTAAACGCAGGATTTGTGTGTGCACTAACAGAAGCTTTAATCGTGAGCAGGTGTAGGGTA
CTTTTTGCTCATTCTCCCCAGCTTGGCTTATTGTGAGGACTCCTGCATTTGTCTTCTGTGCTGG
GAGACTGCATGCCAGAGCCTACAGAGGACACCACCACTGCAAAACAATAATTTTCATAAGAAAA
GCAAACTTGAAGCCACCCATCTACTCTTCAAATGTAATCTCTAACTTAAAAGTATGTAACCTTT
TCCTAGACATGGTACCATAGGAACACTGGGTGATCTGGGTAGAGGTGTGGGCATTTAAACAATG
TAAAGAAAGGTCTGGCACCTCATGCCTTGCCAACCTGAGAAAATGAGCTGTGCTTGCTACAACA
TAGGAAAGATAAATTTCAAAGATCGGGGAAACTACCAGCATTAAAAATAAAAGTATTCACATAA
AAAAGCCCCATTTTATTATTTAAATTGTTTGCAGGCTCTCTTACCGTAGTCTGAGGCACCTTAG
GTCTTCCTTAGTGATATCATTGAGAATATCAGAAAGTGTGTAATCTTCTTCAACAATCTGAAAG
ATTCAACATACATTCAACAACATAAGCAGCTTTTCAACAGTATCATAGGAATCCTTTGATTTAG
AAATTTACCTTTTCTATTGTATTTGCATCCACTCCTTGTAGCTGCAACCAGTCTATAAGCTCTC
TGTTGGTTCCCAGTCCGTCATGGGGTGGTGGGTTCTCTGTTCCACCTATAAAGATTCCAATTTT
GTTTTATTGTATAGTAATGTATAACCATAAAATGCTTCAAAAATAACAAAGTGGATGTAATCAT
GTATCCAAACAGAAATGTAAATGTGCTGTGAAAAGGAAATGAATTAAACTTGTTTGACCCGCAA
AAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039099538 ⟹ XP_038955466

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	34,704,093 - 34,714,297 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001004072	(Get FASTA)	NCBI Sequence Viewer
	XP_038955466	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH98897	(Get FASTA)	NCBI Sequence Viewer
	EDL96148	(Get FASTA)	NCBI Sequence Viewer
	P26284	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001004072 ⟸ NM_001004072
- Peptide Label:	precursor
- UniProtKB:	Q4FZZ4 (UniProtKB/TrEMBL)
- Sequence:	show sequence MRKMLAAVSRVLAGAAQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKY YRMMQTVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRG LPVRAILAELTGRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLT LYGDGAANQGQIFEAYNMAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDG MDILCVREATKFAAAYCRSGKGPILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLL KDRMVNSNLASVEELKEIDVEVRKEIEDAAQFATADPEPPLEELGYHIYSSDPPFEVRGANQWI KFKSVS hide sequence

RefSeq Acc Id:

ENSRNOP00000030279 ⟸ ENSRNOT00000038352

RefSeq Acc Id:

ENSRNOP00000069789 ⟸ ENSRNOT00000088802

RefSeq Acc Id:	XP_038955466 ⟸ XM_039099538
- Peptide Label:	isoform X1

RefSeq Acc Id:

ENSRNOP00000094690 ⟸ ENSRNOT00000110948

Protein Domains

E1_dh

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P26284-F1-model_v2	AlphaFold	P26284	1-390	view protein structure

Transcriptome

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

Promoters

RGD ID:

13701816

Promoter ID:

EPDNEW_R12333

Type:

initiation region

Name:

Pdha1_1

Description:

pyruvate dehydrogenase E1 alpha 1 subunit

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	37,329,767 - 37,329,827	EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)

ACI/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN-Lx/CubMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BUF/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

DA/OlaHsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE16/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/FarMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB10/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF10A/StmMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/NRrrcMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MWF/Hsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHR/OlalpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WAG/RijCrl (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Damaging Variants

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
X	55911679	55911680	G	A	snv	ACI/EurMcwi (MCW), F344/NHsd (ICAHN), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SS/JrHsdMcwi (MDC), BUF/N (KNAW), M520/N (KNAW), GK/Ox (ICL), LEW/Crl (ICL), SHR/OlaIpcv (ICL), SHRSP/Gcrc (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), FHH/EurMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3286	AgrOrtholog
BioCyc Gene	G2FUF-2492	BioCyc
Ensembl Genes	ENSRNOG00000025383	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000030279	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOP00000069789	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000038352	ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOT00000088802	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7103543	IMAGE-MGC_LOAD
	IMAGE:7109678	IMAGE-MGC_LOAD
InterPro	DH_E1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Pyrv_DH_E1_asu_subgrp-y	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	THDP-binding	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:29554	UniProtKB/TrEMBL
MGC_CLONE	MGC:114215	IMAGE-MGC_LOAD
	MGC:94854	IMAGE-MGC_LOAD
NCBI Gene	29554	ENTREZGENE
Pfam	E1_dh	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Pdha1	PhenoGen
Superfamily-SCOP	SSF52518	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs	PDH_E1_alph_y	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JW90_RAT	UniProtKB/TrEMBL
	F7FKI5_RAT	UniProtKB/TrEMBL
	ODPA_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q4FZZ4	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-12-06	Pdha1	pyruvate dehydrogenase E1 subunit alpha 1	Pdha1	pyruvate dehydrogenase E1 alpha 1 subunit	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2017-08-23	Pdha1	pyruvate dehydrogenase E1 alpha 1 subunit	Pdha1	pyruvate dehydrogenase alpha 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2017-06-20	Pdha1	pyruvate dehydrogenase alpha 1	Pdha1	pyruvate dehydrogenase (lipoamide) alpha 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2009-02-26	Pdha1	pyruvate dehydrogenase (lipoamide) alpha 1	Pdha1	pyruvate dehydrogenase E1 alpha 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Pdha1	Pyruvate dehydrogenase (lipoamide) alpha 1			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_disease	mutation of the human homolog is detected in patients with pyruvate dehydrogenase complex deficiency disease	731230

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)