Plod2 (procollagen lysine, 2-oxoglutarate 5-dioxygenase 2) - Rat Genome Database

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Gene: Plod2 (procollagen lysine, 2-oxoglutarate 5-dioxygenase 2) Rattus norvegicus
Analyze
Symbol: Plod2
Name: procollagen lysine, 2-oxoglutarate 5-dioxygenase 2
RGD ID: 3353
Description: Predicted to enable procollagen-lysine 5-dioxygenase activity. Involved in cellular response to hormone stimulus and response to hypoxia. Predicted to be located in rough endoplasmic reticulum membrane. Predicted to be active in several cellular components, including Golgi apparatus; endoplasmic reticulum; and extracellular space. Biomarker of hypothyroidism. Orthologous to human PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2); PARTICIPATES IN lysine degradation pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LH2; lysyl hydroxylase 2; Procollagen-lysine 2-oxoglutarate 5-dioxygenase (Lysine hydroxylase) 2; Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (Lysine hydroxylase) 2; procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2; procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88101,964,318 - 102,047,022 (+)NCBIGRCr8
mRatBN7.2893,084,548 - 93,167,255 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl893,084,513 - 93,167,255 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx898,757,951 - 98,827,969 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0896,957,203 - 97,027,220 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0894,787,446 - 94,864,034 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0899,977,334 - 100,059,736 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl899,977,334 - 100,059,736 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0899,462,925 - 99,529,696 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0899,543,695 - 99,545,578 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4897,525,279 - 97,623,152 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1897,544,733 - 97,642,604 (+)NCBI
Celera892,602,361 - 92,678,608 (+)NCBICelera
Cytogenetic Map8q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-bromohexadecanoic acid  (ISO)
2-hydroxypropanoic acid  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
aflatoxin M1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
beta-naphthoflavone  (EXP,ISO)
bexarotene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloropicrin  (ISO)
choline  (ISO)
ciglitazone  (EXP)
cisplatin  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diallyl trisulfide  (EXP)
dicrotophos  (ISO)
dimethyl sulfoxide  (EXP)
dioxygen  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxifluridine  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
enzalutamide  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
fonofos  (ISO)
fulvestrant  (ISO)
furan  (EXP)
genistein  (EXP)
glucose  (ISO)
isoniazide  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
parathion  (ISO)
pentane-2,3-dione  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
phosgene  (ISO)
progesterone  (EXP)
protein kinase inhibitor  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
Salinomycin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenate  (ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
Tanshinone I  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
testosterone  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
Tungsten carbide  (ISO)
valproic acid  (ISO)
vandetanib  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
Yessotoxin  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. PLOD2 regulated by transcription factor FOXA1 promotes metastasis in NSCLC. Du H, etal., Cell Death Dis. 2017 Oct 26;8(10):e3143. doi: 10.1038/cddis.2017.553.
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. Oxygen tension regulates the expression of a group of procollagen hydroxylases. Hofbauer KH, etal., Eur J Biochem 2003 Nov;270(22):4515-22.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. 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.
Additional References at PubMed
PMID:10934207   PMID:15174142   PMID:19199708   PMID:37670228   PMID:37981258  


Genomics

Comparative Map Data
Plod2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88101,964,318 - 102,047,022 (+)NCBIGRCr8
mRatBN7.2893,084,548 - 93,167,255 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl893,084,513 - 93,167,255 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx898,757,951 - 98,827,969 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0896,957,203 - 97,027,220 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0894,787,446 - 94,864,034 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0899,977,334 - 100,059,736 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl899,977,334 - 100,059,736 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0899,462,925 - 99,529,696 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0899,543,695 - 99,545,578 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4897,525,279 - 97,623,152 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1897,544,733 - 97,642,604 (+)NCBI
Celera892,602,361 - 92,678,608 (+)NCBICelera
Cytogenetic Map8q31NCBI
PLOD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383146,069,440 - 146,161,184 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3146,035,139 - 146,163,725 (-)EnsemblGRCh38hg38GRCh38
GRCh373145,787,227 - 145,878,971 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363147,269,917 - 147,361,972 (-)NCBINCBI36Build 36hg18NCBI36
Celera3144,204,566 - 144,296,620 (-)NCBICelera
Cytogenetic Map3q24NCBI
HuRef3143,164,166 - 143,256,088 (-)NCBIHuRef
CHM1_13145,750,160 - 145,842,267 (-)NCBICHM1_1
T2T-CHM13v2.03148,824,992 - 148,916,735 (-)NCBIT2T-CHM13v2.0
Plod2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39992,421,828 - 92,490,481 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl992,424,276 - 92,490,481 (+)EnsemblGRCm39 Ensembl
GRCm38992,539,636 - 92,608,428 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl992,542,223 - 92,608,428 (+)EnsemblGRCm38mm10GRCm38
MGSCv37992,437,061 - 92,503,266 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36992,346,223 - 92,412,195 (+)NCBIMGSCv36mm8
Celera992,126,694 - 92,192,758 (+)NCBICelera
Cytogenetic Map9E3.3NCBI
cM Map948.4NCBI
Plod2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547411,392,163 - 11,475,508 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547411,392,163 - 11,473,918 (+)NCBIChiLan1.0ChiLan1.0
PLOD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22143,960,509 - 144,050,676 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13143,965,240 - 144,055,393 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03143,091,833 - 143,181,831 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13150,675,423 - 150,764,939 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3150,675,424 - 150,764,939 (-)Ensemblpanpan1.1panPan2
PLOD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12341,290,183 - 41,382,917 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2341,290,567 - 41,382,807 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.02341,914,649 - 42,007,609 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2341,915,768 - 42,007,611 (-)EnsemblROS_Cfam_1.0 Ensembl
Plod2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560280,594,496 - 80,680,880 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365199,053,033 - 9,140,059 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365199,053,192 - 9,139,221 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLOD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1386,401,244 - 86,513,105 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11386,402,673 - 86,513,167 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21394,175,156 - 94,243,446 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PLOD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11544,489,804 - 44,590,284 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1544,490,042 - 44,591,526 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604117,375,187 - 17,466,565 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Plod2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473022,944,184 - 23,034,231 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473022,944,710 - 23,034,200 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Plod2
902 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:266
Count of miRNA genes:133
Interacting mature miRNAs:146
Transcripts:ENSRNOT00000041859, ENSRNOT00000056704
Prediction methods:Microtar, Miranda, 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
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
8693654Alc32Alcohol consumption QTL 3220.755drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)888612425107550209Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
1578755Pur5Proteinuria QTL 53.30.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat

Markers in Region
RH130034  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2893,166,948 - 93,167,128 (+)MAPPERmRatBN7.2
Rnor_6.08100,059,430 - 100,059,609NCBIRnor6.0
Rnor_5.0899,545,272 - 99,545,451UniSTSRnor5.0
RGSC_v3.4897,622,846 - 97,623,025UniSTSRGSC3.4
Celera892,678,302 - 92,678,481UniSTS
RH 3.4 Map81039.6UniSTS
Cytogenetic Map8q31UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000041859   ⟹   ENSRNOP00000047828
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl893,084,513 - 93,167,251 (+)Ensembl
Rnor_6.0 Ensembl899,977,334 - 100,059,736 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000056704   ⟹   ENSRNOP00000053546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl893,084,546 - 93,167,255 (+)Ensembl
Rnor_6.0 Ensembl899,977,334 - 100,059,736 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000085808   ⟹   ENSRNOP00000069407
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl899,977,334 - 100,059,728 (+)Ensembl
RefSeq Acc Id: NM_001142915   ⟹   NP_001136387
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88101,964,318 - 102,047,022 (+)NCBI
mRatBN7.2893,084,548 - 93,167,255 (+)NCBI
Rnor_6.0899,977,334 - 100,059,736 (+)NCBI
Rnor_5.0899,462,925 - 99,529,696 (+)NCBI
Rnor_5.0899,543,695 - 99,545,578 (+)NCBI
RGSC_v3.4897,525,279 - 97,623,152 (+)RGD
Celera892,602,361 - 92,678,608 (+)RGD
Sequence:
RefSeq Acc Id: NM_175869   ⟹   NP_787065
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88101,964,318 - 102,047,022 (+)NCBI
mRatBN7.2893,084,548 - 93,167,255 (+)NCBI
Rnor_6.0899,977,334 - 100,059,736 (+)NCBI
Rnor_5.0899,462,925 - 99,529,696 (+)NCBI
Rnor_5.0899,543,695 - 99,545,578 (+)NCBI
RGSC_v3.4897,525,279 - 97,623,152 (+)RGD
Celera892,602,361 - 92,678,608 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001136387 (Get FASTA)   NCBI Sequence Viewer  
  NP_787065 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAD23629 (Get FASTA)   NCBI Sequence Viewer  
  CAD23630 (Get FASTA)   NCBI Sequence Viewer  
  EDL77532 (Get FASTA)   NCBI Sequence Viewer  
  EDL77533 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000047828.3
  ENSRNOP00000053546.1
GenBank Protein Q811A3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_787065   ⟸   NM_175869
- Peptide Label: isoform 1 precursor
- UniProtKB: Q811A4 (UniProtKB/Swiss-Prot),   Q811A3 (UniProtKB/Swiss-Prot),   A6I244 (UniProtKB/TrEMBL),   D3ZQR7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001136387   ⟸   NM_001142915
- Peptide Label: isoform 2 precursor
- UniProtKB: Q811A4 (UniProtKB/Swiss-Prot),   Q811A3 (UniProtKB/Swiss-Prot),   A6I245 (UniProtKB/TrEMBL),   G3V9I0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000047828   ⟸   ENSRNOT00000041859
Ensembl Acc Id: ENSRNOP00000053546   ⟸   ENSRNOT00000056704
Ensembl Acc Id: ENSRNOP00000069407   ⟸   ENSRNOT00000085808
Protein Domains
Fe2OG dioxygenase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q811A3-F1-model_v2 AlphaFold Q811A3 1-737 view protein structure

Transcriptome

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

Promoters
RGD ID:13696182
Promoter ID:EPDNEW_R6707
Type:multiple initiation site
Name:Plod2_1
Description:procollagen lysine, 2-oxoglutarate 5-dioxygenase 2
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_6.0899,977,336 - 99,977,396EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3353 AgrOrtholog
BioCyc Gene G2FUF-29544 BioCyc
Ensembl Genes ENSRNOG00000030183 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041859.5 UniProtKB/TrEMBL
  ENSRNOT00000056704.4 UniProtKB/TrEMBL
Gene3D-CATH q2cbj1_9rhob like domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Collagen_mod_GT25 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IPNS-like_FE2OG_OXY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Oxoglu/Fe-dep_dioxygenase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pro_4_hyd_alph UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Procol_lys_dOase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300901 UniProtKB/TrEMBL
NCBI Gene Plod2 ENTREZGENE
PANTHER PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE/GLYCOSYLTRANSFERASE 25 FAMILY MEMBER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam 2OG-FeII_Oxy UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Plod2 PhenoGen
PROSITE FE2OG_OXY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYS_HYDROXYLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030183 RatGTEx
SMART P4Hc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53448 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6I244 ENTREZGENE, UniProtKB/TrEMBL
  A6I245 ENTREZGENE, UniProtKB/TrEMBL
  D3ZQR7 ENTREZGENE, UniProtKB/TrEMBL
  G3V9I0 ENTREZGENE, UniProtKB/TrEMBL
  PLOD2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q811A4 ENTREZGENE
UniProt Secondary Q811A4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-11-06 Plod2  procollagen lysine, 2-oxoglutarate 5-dioxygenase 2    Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (Lysine hydroxylase) 2  Name updated 625702 APPROVED
2002-06-10 Plod2  Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (Lysine hydroxylase) 2      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA is highly induced in a time-dependent manner by hypoxia in vascular smooth muscle cell line A7r5 1303932
gene_function indispensible for collagen fiber formation 1303932
gene_homology human homologue PLOD2 is an important enzyme in fibrotic processes 1303933
gene_transcript expression during hypoxia may be regulated by hypoxia-inducible transcription factor 1 (HIF-1), a binding site of which is located in the promoter region 1303932