Plod1 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Plod1 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1) Rattus norvegicus
Analyze
Symbol: Plod1
Name: procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1
RGD ID: 621382
Description: Enables several functions, including L-ascorbic acid binding activity; ferrous iron binding activity; and procollagen-lysine 5-dioxygenase activity. Involved in cellular response to hormone stimulus; peptidyl-lysine hydroxylation; and response to hypoxia. Predicted to be located in rough endoplasmic reticulum membrane. Predicted to be part of catalytic complex. Predicted to be active in several cellular components, including Golgi apparatus; endoplasmic reticulum; and extracellular space. Biomarker of hypothyroidism. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome kyphoscoliotic type 1. Orthologous to human PLOD1 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 1); PARTICIPATES IN lysine degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LH1; lysyl hydroxylase 1; Plod; procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1; procollagen-lysine 2-oxoglutarate 5-dioxygenase (lysine hydroxylase Ehlers-Danlos syndrome type VI); procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI); procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Plod1em1Mcwi
Genetic Models: SS-Plod1em1Mcwi
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85163,623,847 - 163,650,737 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5163,623,848 - 163,651,110 (-)EnsemblGRCr8
mRatBN7.25158,340,674 - 158,367,581 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5158,340,490 - 158,367,620 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5161,057,429 - 161,084,332 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05162,884,948 - 162,911,870 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05162,841,286 - 162,868,216 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05164,720,629 - 164,747,071 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5164,720,587 - 164,747,083 (-)Ensemblrn6Rnor6.0
Rnor_5.05168,379,092 - 168,405,534 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45164,987,252 - 165,012,581 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5156,623,980 - 156,649,807 (-)NCBICelera
RGSC_v3.15164,997,439 - 165,022,772 (-)NCBI
Cytogenetic Map5q36NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calciol  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
deoxynivalenol  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (EXP)
diuron  (EXP)
doxorubicin  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
finasteride  (EXP)
genistein  (ISO)
gentamycin  (EXP)
GSK-J4  (ISO)
inulin  (ISO)
isoniazide  (ISO)
ivermectin  (ISO)
methapyrilene  (ISO)
nefazodone  (EXP)
Nivalenol  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
pirinixic acid  (ISO)
rotenone  (EXP)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
Soman  (EXP)
temozolomide  (ISO)
thimerosal  (ISO)
thiram  (ISO)
triphenyl phosphate  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Rat lysyl hydroxylase: molecular cloning, mRNA distribution and expression in a baculovirus system. Armstrong LC and Last JA, Biochim Biophys Acta 1995 Oct 17;1264(1):93-102.
2. Thyroid hormone decreases thyrotropin subunit mRNA levels in rat anterior pituitary. Croyle ML and Maurer RA, DNA 1984 Jun;3(3):231-6.
3. Analysis of the organization and nucleotide sequence of the chromosomal gene for the beta-subunit of rat thyrotropin. Croyle ML, etal., DNA 1986 Aug;5(4):299-304.
4. Identifying multiple causative genes at a single GWAS locus. Flister MJ, etal., Genome Res. 2013 Dec;23(12):1996-2002. doi: 10.1101/gr.160283.113. Epub 2013 Sep 4.
5. 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.
6. Oxygen tension regulates the expression of a group of procollagen hydroxylases. Hofbauer KH, etal., Eur J Biochem 2003 Nov;270(22):4515-22.
7. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG 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. Differential expression of procollagen lysine 2-oxoglutarate 5-deoxygenase and matrix metalloproteinase isoforms in hypothyroid rat ovary and disintegration of extracellular matrix. Saha SK, etal., Endocrinology. 2005 Jul;146(7):2963-75. Epub 2005 Apr 7.
16. Mechanism of inhibition of lysyl hydroxylase activity by the organophosphates malathion and malaoxon. Samimi A and Last JA, Toxicol Appl Pharmacol. 2001 Nov 1;176(3):181-6.
Additional References at PubMed
PMID:8449506   PMID:8621606   PMID:8889548   PMID:9724729   PMID:10934207   PMID:15174142   PMID:19056867   PMID:27119146   PMID:36695693  


Genomics

Comparative Map Data
Plod1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85163,623,847 - 163,650,737 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5163,623,848 - 163,651,110 (-)EnsemblGRCr8
mRatBN7.25158,340,674 - 158,367,581 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5158,340,490 - 158,367,620 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5161,057,429 - 161,084,332 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05162,884,948 - 162,911,870 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05162,841,286 - 162,868,216 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05164,720,629 - 164,747,071 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5164,720,587 - 164,747,083 (-)Ensemblrn6Rnor6.0
Rnor_5.05168,379,092 - 168,405,534 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45164,987,252 - 165,012,581 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5156,623,980 - 156,649,807 (-)NCBICelera
RGSC_v3.15164,997,439 - 165,022,772 (-)NCBI
Cytogenetic Map5q36NCBI
PLOD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38111,934,717 - 11,975,537 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl111,934,205 - 11,975,542 (+)Ensemblhg38GRCh38
GRCh37111,994,774 - 12,035,594 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36111,917,333 - 11,958,181 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34111,929,011 - 11,969,860NCBI
Celera111,108,411 - 11,149,258 (+)NCBICelera
Cytogenetic Map1p36.22NCBI
HuRef111,149,615 - 11,190,362 (+)NCBIHuRef
CHM1_1111,982,590 - 12,023,381 (+)NCBICHM1_1
T2T-CHM13v2.0111,478,837 - 11,519,656 (+)NCBIT2T-CHM13v2.0
Plod1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394147,994,210 - 148,021,233 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4147,994,210 - 148,021,224 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm384147,909,753 - 147,936,776 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4147,909,753 - 147,936,767 (-)Ensemblmm10GRCm38
MGSCv374147,283,862 - 147,310,885 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364146,753,861 - 146,780,504 (-)NCBIMGSCv36mm8
Celera4150,174,511 - 150,201,195 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map478.57NCBI
Plod1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554861,967,167 - 1,990,561 (-)Ensembl
ChiLan1.0NW_0049554861,967,771 - 1,990,561 (-)NCBIChiLan1.0ChiLan1.0
PLOD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21216,260,905 - 216,301,738 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11214,904,976 - 214,948,943 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0110,684,608 - 10,725,376 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1111,900,881 - 11,941,308 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl111,900,881 - 11,941,308 (+)EnsemblpanPan2panpan1.1
PLOD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1284,320,529 - 84,343,562 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl284,320,529 - 84,343,562 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha280,853,098 - 80,876,054 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0284,981,087 - 85,004,061 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl284,980,603 - 85,004,654 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1281,730,741 - 81,753,653 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0282,730,771 - 82,753,652 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0283,796,533 - 83,819,467 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Plod1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505834,916,884 - 34,938,512 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936474746,922 - 765,585 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936474740,582 - 763,294 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLOD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl671,988,459 - 72,021,804 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1671,987,938 - 72,019,712 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2665,898,212 - 65,928,890 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PLOD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120119,824,380 - 119,865,866 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605423,682,782 - 23,725,813 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Plod1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248181,071,505 - 1,092,237 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248181,070,841 - 1,092,346 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Plod1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1112,838,657 - 12,865,087 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Plod1
91 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:72
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000010433
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
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5141212838172190305Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149642129171146538Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5160111176171146538Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5133789363172190305Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5156396728172190305Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)551657967166600247Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138002522170842766Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5160071170172129029Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5141764300172190305Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5148093485172129029Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5156396728167181764Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5149661912166600247Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5156289283171137955Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat

Markers in Region
BI275190  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25158,340,889 - 158,341,054 (+)MAPPERmRatBN7.2
Rnor_6.05164,720,845 - 164,721,009NCBIRnor6.0
Rnor_5.05168,379,308 - 168,379,472UniSTSRnor5.0
RGSC_v3.45164,987,463 - 164,987,627UniSTSRGSC3.4
Celera5156,624,196 - 156,624,360UniSTS
RH 3.4 Map51106.9UniSTS
Cytogenetic Map5q36UniSTS
MARC_65458-65459:1186500885:3  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr85163,631,059 - 163,631,796 (+)Marker Load Pipeline
mRatBN7.25158,347,887 - 158,348,624 (+)MAPPERmRatBN7.2
Rnor_6.05164,727,842 - 164,728,578NCBIRnor6.0
Rnor_5.05168,386,305 - 168,387,041UniSTSRnor5.0
RGSC_v3.45164,994,460 - 164,995,196UniSTSRGSC3.4
Celera5156,631,193 - 156,631,929UniSTS
Cytogenetic Map5q36UniSTS


Genetic Models
This gene Plod1 is modified in the following models/strains:
SS-Plod1em1Mcwi    


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 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000010433   ⟹   ENSRNOP00000010433
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5163,623,848 - 163,651,110 (-)Ensembl
mRatBN7.2 Ensembl5158,340,490 - 158,367,582 (-)Ensembl
Rnor_6.0 Ensembl5164,720,587 - 164,747,083 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000097241   ⟹   ENSRNOP00000080105
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5163,641,437 - 163,650,738 (-)Ensembl
mRatBN7.2 Ensembl5158,358,267 - 158,367,620 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000114261   ⟹   ENSRNOP00000088453
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5158,340,490 - 158,364,025 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000117604   ⟹   ENSRNOP00000087676
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5163,623,848 - 163,647,018 (-)Ensembl
mRatBN7.2 Ensembl5158,340,490 - 158,363,862 (-)Ensembl
RefSeq Acc Id: NM_053827   ⟹   NP_446279
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85163,623,847 - 163,650,737 (-)NCBI
mRatBN7.25158,340,674 - 158,367,581 (-)NCBI
Rnor_6.05164,720,629 - 164,747,071 (-)NCBI
Rnor_5.05168,379,092 - 168,405,534 (-)NCBI
RGSC_v3.45164,987,252 - 165,012,581 (-)RGD
Celera5156,623,980 - 156,649,807 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109144   ⟹   XP_038965072
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85163,623,851 - 163,643,108 (-)NCBI
mRatBN7.25158,340,678 - 158,359,944 (-)NCBI
Protein Sequences
Protein RefSeqs NP_446279 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965072 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL81085 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000010433
GenBank Protein Q63321 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_446279   ⟸   NM_053827
- Peptide Label: precursor
- UniProtKB: Q63321 (UniProtKB/Swiss-Prot),   D3ZQ74 (UniProtKB/TrEMBL),   A6IU34 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000010433   ⟸   ENSRNOT00000010433
RefSeq Acc Id: XP_038965072   ⟸   XM_039109144
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000080105   ⟸   ENSRNOT00000097241
Ensembl Acc Id: ENSRNOP00000087676   ⟸   ENSRNOT00000117604
Ensembl Acc Id: ENSRNOP00000088453   ⟸   ENSRNOT00000114261
Protein Domains
Fe2OG dioxygenase   PLOD1-3-like GT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63321-F1-model_v2 AlphaFold Q63321 1-728 view protein structure

Transcriptome

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

Promoters
RGD ID:13694251
Promoter ID:EPDNEW_R4776
Type:multiple initiation site
Name:Plod1_1
Description:procollagen-lysine, 2-oxoglutarate 5-dioxygenase 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_6.05164,747,054 - 164,747,114EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621382 AgrOrtholog
BioCyc Gene G2FUF-39204 BioCyc
Ensembl Genes ENSRNOG00000007763 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000010433 ENTREZGENE
Gene3D-CATH q2cbj1_9rhob like domain UniProtKB/Swiss-Prot
InterPro Collagen_mod_GT25 UniProtKB/Swiss-Prot
  IPNS-like_FE2OG_OXY UniProtKB/Swiss-Prot
  Nucleotide-diphossugar_trans UniProtKB/Swiss-Prot
  Oxoglu/Fe-dep_dioxygenase UniProtKB/Swiss-Prot
  Pro_4_hyd_alph UniProtKB/Swiss-Prot
  Procol_lys_dOase UniProtKB/Swiss-Prot
NCBI Gene 116552 ENTREZGENE
PANTHER PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE 1 UniProtKB/Swiss-Prot
  PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE/GLYCOSYLTRANSFERASE 25 FAMILY MEMBER UniProtKB/Swiss-Prot
Pfam 2OG-FeII_Oxy UniProtKB/Swiss-Prot
  GT_PLOD UniProtKB/Swiss-Prot
  OGFOD2-like UniProtKB/Swiss-Prot
PhenoGen Plod1 PhenoGen
PROSITE FE2OG_OXY UniProtKB/Swiss-Prot
  LYS_HYDROXYLASE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000007763 RatGTEx
SMART P4Hc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53448 UniProtKB/Swiss-Prot
UniProt A0A8I5ZPY4_RAT UniProtKB/TrEMBL
  A0A8I6GFD5_RAT UniProtKB/TrEMBL
  A6IU34 ENTREZGENE, UniProtKB/TrEMBL
  D3ZQ74 ENTREZGENE, UniProtKB/TrEMBL
  PLOD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Plod1  procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1  Plod1  procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Plod1  procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1  Plod  procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)  Symbol and Name updated 1299863 APPROVED
2002-08-07 Plod  procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)      Symbol and Name status set to provisional 70820 PROVISIONAL