P4ha1 (prolyl 4-hydroxylase subunit alpha 1) - Rat Genome Database
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Gene: P4ha1 (prolyl 4-hydroxylase subunit alpha 1) Rattus norvegicus
Analyze
Symbol: P4ha1
Name: prolyl 4-hydroxylase subunit alpha 1
RGD ID: 621000
Description: Predicted to contribute to procollagen-proline 4-dioxygenase activity. Predicted to be involved in collagen fibril organization and peptidyl-proline hydroxylation to 4-hydroxy-L-proline. Predicted to localize to mitochondrion and procollagen-proline 4-dioxygenase complex. Orthologous to human P4HA1 (prolyl 4-hydroxylase subunit alpha 1); PARTICIPATES IN arginine and proline metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 4-PH alpha-1; PHalphaI; procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide; procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I; procollagen-proline,2-oxoglutarate-4-dioxygenase subunit alpha-1; prolyl 4-hydroxylase alpha subunit; prolyl 4-hydroxylase subunit alpha-1; prolyl 4-hydroxylase, alpha polypeptide I
Orthologs:
Homo sapiens (human) : P4HA1 (prolyl 4-hydroxylase subunit alpha 1)  HGNC  Alliance
Mus musculus (house mouse) : P4ha1 (procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : P4ha1 (prolyl 4-hydroxylase subunit alpha 1)
Pan paniscus (bonobo/pygmy chimpanzee) : P4HA1 (prolyl 4-hydroxylase subunit alpha 1)
Canis lupus familiaris (dog) : P4HA1 (prolyl 4-hydroxylase subunit alpha 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : P4ha1 (prolyl 4-hydroxylase subunit alpha 1)
Sus scrofa (pig) : P4HA1 (prolyl 4-hydroxylase subunit alpha 1)
Chlorocebus sabaeus (African green monkey) : P4HA1 (prolyl 4-hydroxylase subunit alpha 1)
Heterocephalus glaber (naked mole-rat) : P4ha1 (prolyl 4-hydroxylase subunit alpha 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02028,920,616 - 28,972,576 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2028,920,616 - 28,971,966 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02030,726,604 - 30,776,891 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2028,745,570 - 28,795,338 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
adefovir pivoxil  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
benzoates  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A5  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
chloroacetaldehyde  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (EXP,ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
desferrioxamine B  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenofibrate  (EXP)
ferric ammonium citrate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gamma-hexachlorocyclohexane  (EXP)
glucose  (ISO)
hydrogen sulfide  (ISO)
ifosfamide  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
ketamine  (EXP)
leflunomide  (EXP)
lipopolysaccharide  (EXP)
mercury dichloride  (EXP)
methamphetamine  (EXP)
methapyrilene  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mitoxantrone  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
nickel dichloride  (EXP,ISO)
nitric oxide  (ISO)
oxaliplatin  (EXP,ISO)
ozone  (EXP,ISO)
paracetamol  (ISO)
phenobarbital  (EXP,ISO)
phenylephrine  (EXP)
pirinixic acid  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
ranitidine  (EXP)
resveratrol  (ISO)
rotenone  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
SCH 23390  (EXP)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
sodium fluoride  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
tolcapone  (EXP)
topotecan  (EXP)
valdecoxib  (EXP)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zinc atom  (EXP)
zinc dichloride  (ISO)
zinc(0)  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7753822   PMID:10799490   PMID:15489334   PMID:17135260   PMID:19946888   PMID:24207127  


Genomics

Comparative Map Data
P4ha1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02028,920,616 - 28,972,576 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2028,920,616 - 28,971,966 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02030,726,604 - 30,776,891 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2028,745,570 - 28,795,338 (+)NCBICelera
Cytogenetic Map20q11NCBI
P4HA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1073,007,217 - 73,096,974 (-)EnsemblGRCh38hg38GRCh38
GRCh381073,007,217 - 73,096,866 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371074,766,975 - 74,856,732 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361074,436,981 - 74,526,630 (-)NCBINCBI36hg18NCBI36
Build 341074,436,987 - 74,526,614NCBI
Celera1068,052,119 - 68,141,888 (-)NCBI
Cytogenetic Map10q22.1NCBI
HuRef1068,760,779 - 68,850,247 (-)NCBIHuRef
CHM1_11075,048,716 - 75,138,475 (-)NCBICHM1_1
P4ha1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391059,159,019 - 59,209,126 (+)NCBI
GRCm381059,323,197 - 59,373,304 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1059,323,296 - 59,373,304 (+)EnsemblGRCm38mm10GRCm38
MGSCv371058,786,044 - 58,836,052 (+)NCBIGRCm37mm9NCBIm37
MGSCv361058,718,730 - 58,767,701 (+)NCBImm8
Celera1060,423,571 - 60,473,579 (+)NCBICelera
Cytogenetic Map10B4NCBI
P4ha1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543718,604,525 - 18,668,800 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543718,604,525 - 18,668,800 (+)NCBIChiLan1.0ChiLan1.0
P4HA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11072,017,493 - 72,106,083 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1072,017,500 - 72,106,083 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01069,554,722 - 69,643,765 (-)NCBIMhudiblu_PPA_v0panPan3
P4HA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl423,601,636 - 23,677,762 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1423,600,399 - 23,677,820 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
P4ha1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365215,981,205 - 6,045,195 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
P4HA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1475,825,140 - 75,918,917 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11475,827,207 - 75,919,121 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21481,892,533 - 82,002,926 (-)NCBISscrofa10.2Sscrofa10.2susScr3
P4HA1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl958,178,461 - 58,259,802 (+)Ensembl
ChlSab1.1958,178,350 - 58,259,303 (+)NCBI
P4ha1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247546,707,429 - 6,802,333 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:134
Count of miRNA genes:109
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000070897
Prediction methods:Microtar, Miranda, Rnahybrid
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 1 43 44 28 19 28 8 11 74 35 40 11 8
Low 2 13 13 13 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000070897   ⟹   ENSRNOP00000064405
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2028,920,616 - 28,971,966 (+)Ensembl
RefSeq Acc Id: NM_172062   ⟹   NP_742059
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02028,920,616 - 28,971,984 (+)NCBI
Rnor_5.02030,726,604 - 30,776,891 (+)NCBI
Celera2028,745,570 - 28,795,338 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256424   ⟹   XP_006256486
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02028,920,631 - 28,972,576 (+)NCBI
Rnor_5.02030,726,604 - 30,776,891 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256425   ⟹   XP_006256487
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02028,920,622 - 28,972,576 (+)NCBI
Rnor_5.02030,726,604 - 30,776,891 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_742059   ⟸   NM_172062
- Peptide Label: precursor
- UniProtKB: P54001 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256487   ⟸   XM_006256425
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006256486   ⟸   XM_006256424
- Peptide Label: isoform X2
- UniProtKB: P54001 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064405   ⟸   ENSRNOT00000070897
Protein Domains
Fe2OG dioxygenase

Transcriptome

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

Promoters
RGD ID:13701587
Promoter ID:EPDNEW_R12111
Type:multiple initiation site
Name:P4ha1_1
Description:prolyl 4-hydroxylase subunit alpha 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_6.02028,920,711 - 28,920,771EPDNEW

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621000 AgrOrtholog
Ensembl Genes ENSRNOG00000050655 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000064405 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000070897 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7115543 IMAGE-MGC_LOAD
InterPro Oxoglu/Fe-dep_dioxygenase UniProtKB/Swiss-Prot
  Pro_4_hyd_alph UniProtKB/Swiss-Prot
  Pro_4_hyd_alph_N UniProtKB/Swiss-Prot
  TPR-contain_dom UniProtKB/Swiss-Prot
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot
  TPR_repeat UniProtKB/Swiss-Prot
KEGG Report rno:64475 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93107 IMAGE-MGC_LOAD
NCBI Gene 64475 ENTREZGENE
Pfam 2OG-FeII_Oxy_3 UniProtKB/Swiss-Prot
  P4Ha_N UniProtKB/Swiss-Prot
PhenoGen P4ha1 PhenoGen
PROSITE FE2OG_OXY UniProtKB/Swiss-Prot
  TPR UniProtKB/Swiss-Prot
  TPR_REGION UniProtKB/Swiss-Prot
SMART P4Hc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot
UniGene Rn.8531 ENTREZGENE
UniProt P4HA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6AZ74 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 P4ha1  prolyl 4-hydroxylase subunit alpha 1  P4ha1  prolyl 4-hydroxylase, alpha polypeptide I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-23 P4ha1  prolyl 4-hydroxylase, alpha polypeptide I  P4ha1  procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 P4ha1  procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I  P4ha1  procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 P4ha1  procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide    prolyl 4-hydroxylase alpha subunit  Name updated 1299863 APPROVED
2002-08-07 P4ha1  prolyl 4-hydroxylase alpha subunit      Symbol and Name status set to provisional 70820 PROVISIONAL