Pgk1 (phosphoglycerate kinase 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pgk1 (phosphoglycerate kinase 1) Rattus norvegicus
Analyze
Symbol: Pgk1
Name: phosphoglycerate kinase 1
RGD ID: 619878
Description: Exhibits ADP binding activity; ATP binding activity; and phosphoglycerate kinase activity. Involved in gluconeogenesis and glycolytic process. Localizes to cytosol. Human ortholog(s) of this gene implicated in hemolytic anemia and phosphoglycerate kinase 1 deficiency. Orthologous to human PGK1 (phosphoglycerate kinase 1); PARTICIPATES IN gluconeogenesis pathway; glycolysis pathway; hypoxia inducible factor pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MGC105265; Pgk
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X71,271,454 - 71,287,429 (+)NCBI
Rnor_6.0 EnsemblX77,263,359 - 77,279,367 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X77,263,399 - 77,279,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X56,383,459 - 56,399,433 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X94,324,219 - 94,340,193 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X94,397,574 - 94,413,625 (+)NCBI
CeleraX72,583,654 - 72,599,628 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-alpha-tocopherol  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(Z)-3-butylidenephthalide  (ISO)
1,10-phenanthroline  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
5-chloro-7-iodoquinolin-8-ol  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
amphotericin B  (ISO)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (ISO)
Azaspiracid  (ISO)
beauvericin  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorohydrocarbon  (EXP)
chloropicrin  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clozapine  (EXP)
cobalt dichloride  (EXP,ISO)
cobalt(2+) sulfate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
delphinidin  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dihydroartemisinin  (ISO)
dimercaprol  (ISO)
dioxygen  (EXP,ISO)
diuron  (EXP)
dopamine  (EXP)
doxorubicin  (ISO)
enniatin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenoldopam  (EXP)
ferric ammonium citrate  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (EXP,ISO)
gentamycin  (EXP)
glyphosate  (ISO)
graphite  (ISO)
haloperidol  (EXP)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP,ISO)
lithocholic acid  (ISO)
menadione  (ISO)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
Monobutylphthalate  (ISO)
motexafin gadolinium  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP,ISO)
nickel sulfate  (ISO)
ochratoxin A  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phenylpropanolamine  (ISO)
potassium dichromate  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
prostaglandin A1  (ISO)
quartz  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
Salinomycin  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
Soman  (EXP)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (EXP,ISO)
Tesaglitazar  (EXP)
tetraethylenepentamine  (ISO)
thapsigargin  (ISO)
thimerosal  (ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (EXP)
tungsten  (ISO)
tunicamycin  (ISO)
undecane  (EXP)
valproic acid  (ISO)
vandetanib  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
Yessotoxin  (ISO)
zearalenone  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:943046   PMID:5009693   PMID:6852525   PMID:7391028   PMID:11130727   PMID:11487543   PMID:15277470   PMID:15489334   PMID:15665293   PMID:17248765   PMID:19199708   PMID:19946888  
PMID:20458337   PMID:21492153   PMID:22082260   PMID:22420779   PMID:22871113   PMID:23376485   PMID:23533145   PMID:23904609   PMID:25204797   PMID:26316108   PMID:29476059  


Genomics

Comparative Map Data
Pgk1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X71,271,454 - 71,287,429 (+)NCBI
Rnor_6.0 EnsemblX77,263,359 - 77,279,367 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X77,263,399 - 77,279,373 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X56,383,459 - 56,399,433 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X94,324,219 - 94,340,193 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X94,397,574 - 94,413,625 (+)NCBI
CeleraX72,583,654 - 72,599,628 (+)NCBICelera
Cytogenetic MapXq22NCBI
PGK1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX77,910,739 - 78,129,295 (+)EnsemblGRCh38hg38GRCh38
GRCh38X78,104,248 - 78,129,295 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X77,359,745 - 77,384,792 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X77,246,425 - 77,268,980 (+)NCBINCBI36hg18NCBI36
Build 34X77,165,913 - 77,188,467NCBI
CeleraX77,600,747 - 77,623,405 (+)NCBI
Cytogenetic MapXq21.1NCBI
HuRefX70,945,945 - 70,968,603 (+)NCBIHuRef
CHM1_1X77,252,363 - 77,275,021 (+)NCBICHM1_1
Pgk1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X105,230,706 - 105,247,305 (+)NCBIGRCm39mm39
GRCm39 EnsemblX105,230,706 - 105,247,305 (+)Ensembl
GRCm38X106,187,100 - 106,203,699 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX106,187,100 - 106,203,699 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X103,382,463 - 103,399,038 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X102,389,843 - 102,406,418 (+)NCBImm8
CeleraX93,040,533 - 93,057,028 (+)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.36NCBI
Pgk1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555571,566,534 - 1,584,799 (+)NCBIChiLan1.0ChiLan1.0
PGK1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X77,391,639 - 77,413,786 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX77,391,805 - 77,414,459 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X67,280,269 - 67,302,307 (+)NCBIMhudiblu_PPA_v0panPan3
PGK1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X60,374,743 - 60,396,244 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX60,374,754 - 60,423,947 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX51,387,842 - 51,409,348 (+)NCBI
ROS_Cfam_1.0X61,613,473 - 61,634,977 (+)NCBI
UMICH_Zoey_3.1X59,319,607 - 59,341,115 (+)NCBI
UNSW_CanFamBas_1.0X60,929,381 - 60,951,098 (+)NCBI
UU_Cfam_GSD_1.0X60,517,684 - 60,539,186 (+)NCBI
Pgk1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X53,965,864 - 53,989,650 (+)NCBI
SpeTri2.0NW_004936547286,267 - 310,062 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PGK1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX62,187,431 - 62,212,244 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X62,187,472 - 62,210,321 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X71,339,754 - 71,351,768 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig CytomapXq1.2NCBI
PGK1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X67,072,029 - 67,093,881 (+)NCBI
Pgk1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248362,657,320 - 2,676,124 (-)NCBI

Position Markers
AA892797  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map2206.3UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:282
Count of miRNA genes:186
Interacting mature miRNAs:211
Transcripts:ENSRNOT00000003390
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 6 4 4 4 3 2
Medium 3 37 53 37 19 37 8 8 72 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077604   ⟹   ENSRNOP00000073523
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,263,359 - 77,279,367 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085653   ⟹   ENSRNOP00000073614
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX77,278,240 - 77,279,367 (+)Ensembl
RefSeq Acc Id: NM_053291   ⟹   NP_445743
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X71,271,454 - 71,287,429 (+)NCBI
Rnor_6.0X77,263,399 - 77,279,373 (+)NCBI
Rnor_5.0X56,383,459 - 56,399,433 (+)NCBI
RGSC_v3.4X94,324,219 - 94,340,193 (+)RGD
CeleraX72,583,654 - 72,599,628 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_445743   ⟸   NM_053291
- UniProtKB: P16617 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073614   ⟸   ENSRNOT00000085653
RefSeq Acc Id: ENSRNOP00000073523   ⟸   ENSRNOT00000077604

Transcriptome

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

Promoters
RGD ID:13701902
Promoter ID:EPDNEW_R12426
Type:initiation region
Name:Pgk1_1
Description:phosphoglycerate kinase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X77,263,359 - 77,263,419EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619878 AgrOrtholog
Ensembl Genes ENSRNOG00000058249 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000073523 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073614 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077604 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000085653 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1260 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Phosphoglycerate_kinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Phosphoglycerate_kinase_CS UniProtKB/Swiss-Prot
  Phosphoglycerate_kinase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Phosphoglycerate_kinase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24644 UniProtKB/Swiss-Prot
NCBI Gene 24644 ENTREZGENE
PANTHER PTHR11406 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PGK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pgk1 PhenoGen
PIRSF Pgk UniProtKB/Swiss-Prot
PRINTS PHGLYCKINASE UniProtKB/Swiss-Prot
PROSITE PGLYCERATE_KINASE UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53748 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A096MJL6_RAT UniProtKB/TrEMBL
  P16617 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5M945 UniProtKB/Swiss-Prot
  Q6P508 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Pgk1  phosphoglycerate kinase 1      Symbol and Name updated 629477 APPROVED
2003-03-06 Pgk1  phosphoglycerate kinase 1  Pgk  Phosphoglycerate kinase 1  Data Merged 628472 PROVISIONAL
2002-08-07 Pgk1        Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Pgk  Phosphoglycerate kinase 1      Symbol and Name status set to approved 70586 APPROVED