Phgdh (phosphoglycerate dehydrogenase) - Rat Genome Database

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Gene: Phgdh (phosphoglycerate dehydrogenase) Rattus norvegicus
Analyze
Symbol: Phgdh
Name: phosphoglycerate dehydrogenase
RGD ID: 61987
Description: Enables phosphoglycerate dehydrogenase activity. Predicted to be involved in L-serine biosynthetic process. Predicted to act upstream of or within several processes, including gamma-aminobutyric acid metabolic process; nervous system development; and proteinogenic amino acid metabolic process. Human ortholog(s) of this gene implicated in Neu-Laxova syndrome 1; PHGDH deficiency; and amino acid metabolic disorder. Orthologous to human PHGDH (phosphoglycerate dehydrogenase); PARTICIPATES IN dihydropyrimidine dehydrogenase deficiency pathway; dimethylglycine dehydrogenase deficiency pathway; nonketotic hyperglycinemia pathway; INTERACTS WITH (+)-schisandrin B; (R)-adrenaline; 1-bromopropane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 3-PGDH; 3-phosphoglycerate dehydrogenase; D-3-phosphoglycerate dehydrogenase; MGC105399
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82188,595,700 - 188,624,789 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2188,595,700 - 188,624,789 (-)EnsemblGRCr8
mRatBN7.22185,906,962 - 185,936,054 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2185,906,966 - 185,935,944 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2193,556,309 - 193,584,839 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02191,364,666 - 191,393,755 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02186,188,892 - 186,217,422 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02200,484,245 - 200,513,564 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2200,484,246 - 200,513,564 (-)Ensemblrn6Rnor6.0
Rnor_5.02219,959,693 - 219,989,012 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42193,147,943 - 193,177,137 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2178,395,133 - 178,424,307 (-)NCBICelera
RGSC_v3.12193,110,696 - 193,139,891 (-)NCBI
Cytogenetic Map2q34NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(R)-adrenaline  (EXP)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-bromopropane  (EXP)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
2,4-D  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2,5-hexanedione  (EXP)
2,6-dimethoxyphenol  (ISO)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
2-bromohexadecanoic acid  (ISO)
2-methoxyethanol  (EXP)
2-methylcholine  (ISO)
2-nitrofluorene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
alpha-Zearalanol  (EXP)
amitrole  (EXP)
ammonium chloride  (EXP)
antimycin A  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
azoxystrobin  (ISO)
beauvericin  (ISO)
benzatropine  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcium silicate  (ISO)
cantharidin  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
CGP 52608  (ISO)
chloroacetaldehyde  (ISO)
chlorophyllin  (ISO)
chloropicrin  (ISO)
choline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (EXP,ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (ISO)
deguelin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenzofurans  (ISO)
dibutyl phthalate  (EXP,ISO)
dichloroacetic acid  (ISO)
diethylstilbestrol  (EXP,ISO)
dimethyl sulfoxide  (ISO)
dioxygen  (ISO)
dobutamine  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
enniatin  (ISO)
enzyme inhibitor  (EXP,ISO)
ethanol  (EXP,ISO)
etoposide  (ISO)
fenamidone  (ISO)
fenofibrate  (EXP,ISO)
fenpyroximate  (ISO)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
fructose  (ISO)
furan  (EXP)
furfural  (ISO)
glafenine  (EXP)
glucose  (ISO)
glycine  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
ifosfamide  (ISO)
indole-3-methanol  (EXP)
indometacin  (EXP)
isoniazide  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
lucanthone  (ISO)
metformin  (EXP)
methamphetamine  (EXP)
methapyrilene  (EXP)
methimazole  (EXP)
methotrexate  (ISO)
mitoxantrone  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
naled  (ISO)
nefazodone  (EXP)
nicotine  (ISO)
nitrates  (ISO)
Nivalenol  (ISO)
ochratoxin A  (ISO)
orotic acid  (EXP)
ozone  (ISO)
paclitaxel  (EXP)
paracetamol  (EXP,ISO)
paraquat  (EXP)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenylephrine  (EXP)
PhIP  (EXP)
phorone  (EXP)
picoxystrobin  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
piroxicam  (ISO)
potassium bromate  (ISO)
potassium dichromate  (EXP)
prednisolone  (ISO)
prostaglandin A1  (ISO)
pyrazinecarboxamide  (EXP)
pyrimidifen  (ISO)
pyrogallol  (ISO)
quercetin  (ISO)
retinyl acetate  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium aurothiomalate  (ISO)
sodium chloride  (ISO)
sodium fluoride  (ISO)
streptozocin  (ISO)
sulfadimethoxine  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
Tanshinone I  (EXP)
tebufenpyrad  (ISO)
temozolomide  (ISO)
terbutaline  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
thifluzamide  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (EXP)
trichloroethene  (EXP,ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP,ISO)
troglitazone  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. Cloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase. Achouri Y, etal., Biochem J 1997 Apr 15;323 ( Pt 2):365-70.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
5. Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency--a neurometabolic disorder associated with reduced L-serine biosynthesis. Klomp LW, etal., Am J Hum Genet. 2000 Dec;67(6):1389-99. Epub 2000 Oct 27.
6. Improved radiation hybrid map of rat chromosome 2: colocalization of the genes encoding corticotropin-releasing hormone and IL6-receptor with quantitative trait loci regulating the inflammatory response. Laes JF, etal., Cytogenet Cell Genet 2001;92(1-2):130-3.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
11. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:17634366   PMID:19056867   PMID:19114063   PMID:19199708   PMID:20458337   PMID:22871113   PMID:23376485   PMID:23533145   PMID:29476059   PMID:33846783  


Genomics

Comparative Map Data
Phgdh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82188,595,700 - 188,624,789 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2188,595,700 - 188,624,789 (-)EnsemblGRCr8
mRatBN7.22185,906,962 - 185,936,054 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2185,906,966 - 185,935,944 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2193,556,309 - 193,584,839 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02191,364,666 - 191,393,755 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02186,188,892 - 186,217,422 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02200,484,245 - 200,513,564 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2200,484,246 - 200,513,564 (-)Ensemblrn6Rnor6.0
Rnor_5.02219,959,693 - 219,989,012 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42193,147,943 - 193,177,137 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2178,395,133 - 178,424,307 (-)NCBICelera
RGSC_v3.12193,110,696 - 193,139,891 (-)NCBI
Cytogenetic Map2q34NCBI
PHGDH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381119,711,934 - 119,744,215 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1119,648,411 - 119,744,227 (+)Ensemblhg38GRCh38
GRCh371120,254,557 - 120,286,838 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361120,056,033 - 120,088,361 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341119,966,551 - 119,998,878NCBI
Celera1118,485,152 - 118,517,585 (+)NCBICelera
Cytogenetic Map1p12NCBI
HuRef1118,112,949 - 118,145,389 (+)NCBIHuRef
CHM1_11120,369,927 - 120,402,393 (+)NCBICHM1_1
T2T-CHM13v2.01119,725,174 - 119,757,460 (+)NCBIT2T-CHM13v2.0
Phgdh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39398,220,487 - 98,247,285 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl398,220,486 - 98,247,306 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38398,313,171 - 98,339,969 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl398,313,170 - 98,339,990 (-)Ensemblmm10GRCm38
MGSCv37398,117,094 - 98,143,892 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36398,398,576 - 98,425,374 (-)NCBIMGSCv36mm8
Celera399,712,302 - 99,738,644 (-)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map342.74NCBI
Phgdh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543522,757,454 - 22,803,123 (+)Ensembl
ChiLan1.0NW_00495543522,757,473 - 22,803,123 (+)NCBIChiLan1.0ChiLan1.0
PHGDH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21112,335,154 - 112,367,620 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11111,937,516 - 111,969,976 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0182,803,155 - 82,835,465 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11117,800,843 - 117,833,462 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1117,800,843 - 117,833,462 (-)EnsemblpanPan2panpan1.1
PHGDH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11756,806,912 - 56,833,765 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1756,444,352 - 56,472,916 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01757,523,903 - 57,551,298 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1757,523,906 - 57,714,022 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11756,560,319 - 56,586,083 (+)NCBIUMICH_Zoey_3.1
UU_Cfam_GSD_1.01757,181,718 - 57,206,990 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Phgdh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505810,040,659 - 10,074,835 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366274,414,122 - 4,448,623 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366274,414,122 - 4,448,347 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHGDH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4101,444,693 - 101,478,144 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.14101,445,977 - 101,478,144 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24111,436,317 - 111,468,486 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PHGDH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12014,045,395 - 14,075,935 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2014,045,346 - 14,076,177 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603816,675,443 - 16,706,180 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Phgdh
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477215,473,221 - 15,514,637 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462477215,473,609 - 15,514,392 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Phgdh
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1358,974,152 - 59,001,595 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Phgdh
277 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:56
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000056173
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2163997722225110681Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2169358774214358774Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170656145239614549Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2149957381221199885Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845370229470703Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283465462229820014Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2138595962205135428Rat
1581576Pur7Proteinuria QTL 70.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)280396178220931218Rat
152025245Scl81Serum cholesterol level QTL 813.49blood cholesterol amount (VT:0000180)2124537199209621565Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2145807215220931416Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)278269809208420281Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2122597372215234002Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2154723085199723085Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)280396178220931218Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2145807215190807215Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2154723085199723085Rat
10043139Iddm55Insulin dependent diabetes mellitus QTL 553.10.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2150313808195313808Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2154723085199723085Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2159440891205135267Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2154723085199723085Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170652929215652929Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2159440891220931218Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2171994826205135428Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2188565047233565047Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2154723085199723085Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2139067258192287892Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2184856304229856304Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2184856304229856304Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2159440760195313808Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2144882354205135428Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845182205135428Rat
1357991Ael2Aortic elastin QTL 24.20.000071aorta elastin amount (VT:0003905)aortic elastin2169227906214227906Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283400752223709938Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2184856304229856304Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)2175931416220931416Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)280396034220931416Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278269809205135428Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2182024327227024327Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2159440760228950743Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2184482291229482291Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2143746578205135428Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2114384617215381366Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150096616195096616Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2145306936212705578Rat
7488929Bp366Blood pressure QTL 3660.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2187663373195783351Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2113746222205135428Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2186850607231850607Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2147287892192287892Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2114384617215381366Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660223841096Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2117415288205135428Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150096616195096616Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2182635347227635347Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283465462225110681Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)247856345205135428Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2175008837220008837Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2184856304229856304Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2165453811210453811Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2163253030208253030Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166372086229820014Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)276328396209350714Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000056173   ⟹   ENSRNOP00000053019
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2188,595,700 - 188,624,789 (-)Ensembl
mRatBN7.2 Ensembl2185,906,966 - 185,935,944 (-)Ensembl
Rnor_6.0 Ensembl2200,484,246 - 200,513,564 (-)Ensembl
RefSeq Acc Id: NM_031620   ⟹   NP_113808
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82188,595,700 - 188,624,789 (-)NCBI
mRatBN7.22185,906,962 - 185,936,054 (-)NCBI
Rnor_6.02200,484,246 - 200,513,564 (-)NCBI
Rnor_5.02219,959,693 - 219,989,012 (-)NCBI
RGSC_v3.42193,147,943 - 193,177,137 (-)RGD
Celera2178,395,133 - 178,424,307 (-)RGD
Sequence:
RefSeq Acc Id: NP_113808   ⟸   NM_031620
- UniProtKB: Q546Q9 (UniProtKB/Swiss-Prot),   O08651 (UniProtKB/Swiss-Prot),   A6K3D6 (UniProtKB/TrEMBL),   A0A8L2UMI0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000053019   ⟸   ENSRNOT00000056173
Protein Domains
D-3-phosphoglycerate dehydrogenase ASB   D-isomer specific 2-hydroxyacid dehydrogenase   D-isomer specific 2-hydroxyacid dehydrogenase NAD-

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08651-F1-model_v2 AlphaFold O08651 1-533 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61987 AgrOrtholog
BioCyc Gene G2FUF-51916 BioCyc
BioCyc Pathway SERSYN-PWY [L-serine biosynthesis I] BioCyc
BioCyc Pathway Image SERSYN-PWY BioCyc
Ensembl Genes ENSRNOG00000019328 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000056173 ENTREZGENE
Gene3D-CATH D-3-phosphoglycerate dehydrogenase, domain 3 UniProtKB/Swiss-Prot
  NAD(P)-binding Rossmann-like Domain UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7115765 IMAGE-MGC_LOAD
InterPro ASB_dom_sf UniProtKB/Swiss-Prot
  D-isomer_2_OHA_DH_cat_dom UniProtKB/Swiss-Prot
  D-isomer_DH_CS UniProtKB/Swiss-Prot
  D-isomer_DH_CS1 UniProtKB/Swiss-Prot
  D-isomer_DH_NAD-bd UniProtKB/Swiss-Prot
  NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot
  PGDH UniProtKB/Swiss-Prot
  PGDH_ASB_dom UniProtKB/Swiss-Prot
KEGG Report rno:58835 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105399 IMAGE-MGC_LOAD
NCBI Gene 58835 ENTREZGENE
PANTHER D-3-PHOSPHOGLYCERATE DEHYDROGENASE UniProtKB/Swiss-Prot
  FORMATE DEHYDROGENASE 1 UniProtKB/Swiss-Prot
Pfam 2-Hacid_dh UniProtKB/Swiss-Prot
  2-Hacid_dh_C UniProtKB/Swiss-Prot
  PGDH_inter UniProtKB/Swiss-Prot
PhenoGen Phgdh PhenoGen
PROSITE D_2_HYDROXYACID_DH_1 UniProtKB/Swiss-Prot
  D_2_HYDROXYACID_DH_2 UniProtKB/Swiss-Prot
  D_2_HYDROXYACID_DH_3 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000019328 RatGTEx
Superfamily-SCOP Formate/glycerate dehydrogenase catalytic domain-like UniProtKB/Swiss-Prot
  SSF143548 UniProtKB/Swiss-Prot
  SSF51735 UniProtKB/Swiss-Prot
UniProt A0A8L2UMI0 ENTREZGENE, UniProtKB/TrEMBL
  A6K3D5_RAT UniProtKB/TrEMBL
  A6K3D6 ENTREZGENE, UniProtKB/TrEMBL
  O08651 ENTREZGENE
  Q546Q9 ENTREZGENE
  SERA_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q546Q9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-14 Phgdh  phosphoglycerate dehydrogenase  Phgdh  3-phosphoglycerate dehydrogenase   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Phgdh  3-phosphoglycerate dehydrogenase       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in kidney, brain, liver and testis  
gene_regulation activity is inhibited by 3-phosphohydroxypyruvate