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 serine family amino acid 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82188,595,700 - 188,624,789 (-)NCBIGRCr8
mRatBN7.22185,906,962 - 185,936,054 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2185,906,966 - 185,935,944 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2193,556,309 - 193,584,839 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02191,364,666 - 191,393,755 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02186,188,892 - 186,217,422 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02200,484,245 - 200,513,564 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2200,484,246 - 200,513,564 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02219,959,693 - 219,989,012 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42193,147,943 - 193,177,137 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12193,110,696 - 193,139,891 (-)NCBI
Celera2178,395,133 - 178,424,307 (-)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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-amino-14,16-dimethyloctadecan-3-ol  (ISO)
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)
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)
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-naphthoflavone  (ISO)
bisphenol A  (EXP,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)
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)
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)
glafenine  (EXP)
glucose  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
ifosfamide  (ISO)
indole-3-methanol  (EXP)
indometacin  (EXP)
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)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nicotine  (ISO)
ochratoxin A  (ISO)
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 fluoride  (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)
titanium dioxide  (EXP)
trichloroethene  (EXP,ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
trovafloxacin  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

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 (-)NCBIGRCr8
mRatBN7.22185,906,962 - 185,936,054 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2185,906,966 - 185,935,944 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2193,556,309 - 193,584,839 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02191,364,666 - 191,393,755 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02186,188,892 - 186,217,422 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02200,484,245 - 200,513,564 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2200,484,246 - 200,513,564 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02219,959,693 - 219,989,012 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42193,147,943 - 193,177,137 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12193,110,696 - 193,139,891 (-)NCBI
Celera2178,395,133 - 178,424,307 (-)NCBICelera
Cytogenetic Map2q34NCBI
PHGDH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381119,711,934 - 119,744,215 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1119,648,411 - 119,744,218 (+)EnsemblGRCh38hg38GRCh38
GRCh371120,254,557 - 120,286,838 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361120,056,033 - 120,088,361 (+)NCBINCBI36Build 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 Ensembl
GRCm38398,313,171 - 98,339,969 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl398,313,170 - 98,339,990 (-)EnsemblGRCm38mm10GRCm38
MGSCv37398,117,094 - 98,143,892 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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_Tasha
ROS_Cfam_1.01757,523,903 - 57,551,298 (+)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477215,473,609 - 15,514,392 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Phgdh
279 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2157142078192625452Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2184114274202447032Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
7488929Bp366Blood pressure QTL 3660.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2184974550193094998Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
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)2157142078226277316Rat
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)281689826221035911Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2143657411190602963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 26 44 28 19 28 74 35 41 1
Low 17 13 13 13 8 11 10 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000056173   ⟹   ENSRNOP00000053019
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq Acc Id: ENSRNOP00000053019   ⟸   ENSRNOT00000056173
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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056173 ENTREZGENE
  ENSRNOT00000056173.3 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7115765 IMAGE-MGC_LOAD
InterPro ASB_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  D-isomer_2_OHA_DH_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  D-isomer_DH_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  D-isomer_DH_CS1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  D-isomer_DH_NAD-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PGDH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PGDH_ASB_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:58835 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105399 IMAGE-MGC_LOAD
NCBI Gene 58835 ENTREZGENE
PANTHER D-3-PHOSPHOGLYCERATE DEHYDROGENASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FORMATE DEHYDROGENASE 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam 2-Hacid_dh UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2-Hacid_dh_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PGDH_inter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Phgdh PhenoGen
PROSITE D_2_HYDROXYACID_DH_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  D_2_HYDROXYACID_DH_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  D_2_HYDROXYACID_DH_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019328 RatGTEx
Superfamily-SCOP Formate/glycerate dehydrogenase catalytic domain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF143548 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51735 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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