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: GRCr8 - GRCr8 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



  
Object Symbol
Species
Term
Qualifier
Evidence
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Reference
Notes
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Original Reference(s)
Plod2Rathypothyroidism  IEP 2314536mRNA:decreased expression:multiple organsRGD 
Plod2Ratlung adenocarcinoma disease_progressionISOPLOD2 (Homo sapiens)151665822 RGD 
Plod2RatNeoplasm Metastasis amelioratesISOPLOD2 (Homo sapiens)151665822associated with lung non-small cell carcinomaRGD 
Object Symbol
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Original Reference(s)
Plod2RatBruck syndrome  ISOPLOD2 (Homo sapiens)8554872ClinVar Annotator: match by term: OSTEOGENESIS IMPERFECTA WITH CONGENITAL JOINT CONTRACTURESClinVarPMID:25086671 more ...
Plod2RatBruck Syndrome 2  ISOPLOD2 (Homo sapiens)8554872ClinVar more ...ClinVarPMID:12881513 more ...
Plod2Ratcleft soft palate  ISOPLOD2 (Homo sapiens)8554872ClinVar Annotator: match by term: Cleft soft palateClinVarPMID:22689593 more ...
Plod2Ratgenetic disease  ISOPLOD2 (Homo sapiens)8554872ClinVar Annotator: match by term: Inborn genetic diseasesClinVarPMID:25741868 and PMID:28492532
Plod2Ratosteogenesis imperfecta  ISOPLOD2 (Homo sapiens)8554872ClinVar Annotator: match by term: Osteogenesis imperfectaClinVarPMID:22689593 more ...
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Original Reference(s)
Plod2RatBone Neoplasms  ISOPLOD2 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:15865105
Plod2RatBruck Syndrome 2  ISOPLOD2 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTD 
Plod2RatExperimental Liver Cirrhosis  ISOPLOD2 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:25380136
Plod2Ratjuvenile rheumatoid arthritis  ISOPLOD2 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:19565504
Plod2Ratliver cirrhosis  ISOPLOD2 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:26396155
Plod2Ratosteoarthritis  ISOPLOD2 (Homo sapiens)11554173CTD Direct Evidence: marker/mechanismCTDPMID:18784066
Object Symbol
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Original Reference(s)
Plod2RatBruck syndrome  ISSPlod2 (Mus musculus)13592920OMIM:259450 more ...MouseDO 
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Original Reference(s)
Plod2RatBruck Syndrome 2  ISOPLOD2 (Homo sapiens)7240710 OMIM 

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Original Reference(s)
Plod2Rat1,1-dichloroethene decreases expressionISOPlod2 (Mus musculus)6480464vinylidene chloride results in decreased expression of PLOD2 mRNACTDPMID:26682919
Plod2Rat1,2-dimethylhydrazine increases expressionISOPlod2 (Mus musculus)64804641 and 2-Dimethylhydrazine results in increased expression of PLOD2 mRNACTDPMID:22206623
Plod2Rat1-naphthyl isothiocyanate increases expressionEXP 64804641-Naphthylisothiocyanate results in increased expression of PLOD2 mRNACTDPMID:25380136 and PMID:30723492
Plod2Rat17alpha-ethynylestradiol increases expressionEXP 6480464Ethinyl Estradiol results in increased expression of PLOD2 mRNACTDPMID:12075121
Plod2Rat17beta-estradiol increases expressionISOPLOD2 (Homo sapiens)6480464Estradiol results in increased expression of PLOD2 mRNACTDPMID:20106945
Plod2Rat17beta-estradiol multiple interactionsEXP 6480464[estradiol 3-benzoate co-treated with [Testosterone co-treated with Estradiol]] results in increased expression of PLOD2 mRNACTDPMID:32741896
Plod2Rat17beta-estradiol increases expressionISOPlod2 (Mus musculus)6480464Estradiol results in increased expression of PLOD2 mRNACTDPMID:19484750
Plod2Rat17beta-estradiol multiple interactionsISOPLOD2 (Homo sapiens)6480464[Estradiol binds to ESR2 protein] which results in increased expression of PLOD2 mRNA and [Estradiol co-treated with TGFB1 protein] results in increased expression of PLOD2 mRNACTDPMID:20404318 and PMID:30165855
Plod2Rat17beta-estradiol affects expressionISOPLOD2 (Homo sapiens)6480464Estradiol affects the expression of PLOD2 mRNACTDPMID:14699072
Plod2Rat17beta-estradiol 3-benzoate multiple interactionsEXP 6480464[estradiol 3-benzoate co-treated with [Testosterone co-treated with Estradiol]] results in increased expression of PLOD2 mRNACTDPMID:32741896
Plod2Rat17beta-hydroxy-5alpha-androstan-3-one increases expressionISOPLOD2 (Homo sapiens)6480464Dihydrotestosterone results in increased expression of PLOD2 mRNACTDPMID:29581250
Plod2Rat2,3,7,8-tetrachlorodibenzodioxine decreases expressionISOPlod2 (Mus musculus)6480464Tetrachlorodibenzodioxin results in decreased expression of PLOD2 mRNACTDPMID:18691609 and PMID:19770486
Plod2Rat2,3,7,8-tetrachlorodibenzodioxine affects expressionEXP 6480464Tetrachlorodibenzodioxin affects the expression of PLOD2 mRNACTDPMID:34747641
Plod2Rat2,4,6-trinitrobenzenesulfonic acid increases expressionISOPlod2 (Mus musculus)6480464Trinitrobenzenesulfonic Acid results in increased expression of PLOD2 mRNACTDPMID:18200517
Plod2Rat2,4,6-trinitrobenzenesulfonic acid multiple interactionsISOPlod2 (Mus musculus)6480464Curcumin inhibits the reaction [Trinitrobenzenesulfonic Acid results in increased expression of PLOD2 mRNA]CTDPMID:18200517
Plod2Rat2-bromohexadecanoic acid multiple interactionsISOPLOD2 (Homo sapiens)64804642-bromopalmitate inhibits the reaction [[Cadmium Chloride results in increased abundance of Cadmium] which results in increased palmitoylation of PLOD2 protein]CTDPMID:38195004
Plod2Rat2-hydroxypropanoic acid decreases expressionISOPLOD2 (Homo sapiens)6480464Lactic Acid results in decreased expression of PLOD2 mRNACTDPMID:30851411
Plod2Rat4,4'-diaminodiphenylmethane increases expressionEXP 64804644 and 4'-diaminodiphenylmethane results in increased expression of PLOD2 mRNACTDPMID:25380136
Plod2Rat4,4'-diaminodiphenylmethane increases expressionISOPlod2 (Mus musculus)64804644 and 4'-diaminodiphenylmethane results in increased expression of PLOD2 mRNACTDPMID:18648102
Plod2Rat4,4'-sulfonyldiphenol increases expressionISOPlod2 (Mus musculus)6480464bisphenol S results in increased expression of PLOD2 mRNACTDPMID:30951980

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Biological Process
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Cellular Component
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Original Reference(s)
Plod2Ratcollagen-containing extracellular matrix is_active_inIBAMGI:1347008 and PANTHER:PTN0008429621600115GO_REF:0000033GO_CentralGO_REF:0000033
Plod2Ratendoplasmic reticulum located_inIEAUniProtKB-KW:KW-02561600115GO_REF:0000043UniProtGO_REF:0000043
Plod2Ratendoplasmic reticulum is_active_inIBAFB:FBgn0036147 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Plod2Ratendoplasmic reticulum membrane located_inIEAUniProtKB-SubCell:SL-00971600115GO_REF:0000044UniProtGO_REF:0000044
Plod2Ratextracellular space is_active_inIBAFB:FBgn0036147 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Plod2RatGolgi apparatus is_active_inIBAMGI:1347008 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Plod2Ratmembrane located_inIEAUniProtKB-KW:KW-04721600115GO_REF:0000043UniProtGO_REF:0000043
Plod2Ratrough endoplasmic reticulum located_inIEAUniProtKB-SubCell:SL-02351600115GO_REF:0000044UniProtGO_REF:0000044
Plod2Ratrough endoplasmic reticulum membrane located_inIEAUniProtKB-SubCell:SL-02371600115GO_REF:0000044UniProtGO_REF:0000044
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Molecular Function
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Object Symbol
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Original Reference(s)
Plod2Ratdioxygenase activity enablesIEAUniProtKB-KW:KW-02231600115GO_REF:0000043UniProtGO_REF:0000043
Plod2Ratiron ion binding enablesIEAInterPro:IPR0066201600115GO_REF:0000002InterProGO_REF:0000002
Plod2RatL-ascorbic acid binding enablesIEAUniProtKB-KW:KW-08471600115GO_REF:0000043UniProtGO_REF:0000043
Plod2RatL-ascorbic acid binding enablesIEAInterPro:IPR0066201600115GO_REF:0000002InterProGO_REF:0000002
Plod2Ratmetal ion binding enablesIEAUniProtKB-KW:KW-04791600115GO_REF:0000043UniProtGO_REF:0000043
Plod2Ratoxidoreductase activity enablesIEAUniProtKB-KW:KW-05601600115GO_REF:0000043UniProtGO_REF:0000043
Plod2Ratoxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen enablesIEAInterPro:IPR0066201600115GO_REF:0000002InterProGO_REF:0000002
Plod2Ratprocollagen glucosyltransferase activity NOT|enablesISOPLOD2 (Homo sapiens)1624291 PMID:10934207RGDPMID:10934207
Plod2Ratprocollagen-lysine 5-dioxygenase activity enablesIEAEC:1.14.11.41600115GO_REF:0000003UniProtGO_REF:0000003
Plod2Ratprocollagen-lysine 5-dioxygenase activity enablesIEAUniProtKB:O00469 and ensembl:ENSP000002829031600115GO_REF:0000107EnsemblGO_REF:0000107
Plod2Ratprocollagen-lysine 5-dioxygenase activity enablesIEARHEA:165691600115GO_REF:0000116RHEAGO_REF:0000116
Plod2Ratprocollagen-lysine 5-dioxygenase activity enablesIBAMGI:1347008 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Plod2Ratprocollagen-lysine 5-dioxygenase activity enablesIEAInterPro:IPR0010061600115GO_REF:0000002InterProGO_REF:0000002
Plod2Ratprocollagen-lysine 5-dioxygenase activity enablesISOPLOD2 (Homo sapiens)1624291 PMID:10934207RGDPMID:10934207
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Imported Annotations - KEGG (archival)

Object Symbol
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Original Reference(s)
Plod2Ratlysine degradation pathway  IEA 6907045 KEGGrno:00310

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#
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.
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PMID:10934207   PMID:15174142   PMID:19199708   PMID:37670228   PMID:37981258  



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

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Variants in Plod2
902 total Variants

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.


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The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
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

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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




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



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:
1 to 9 of 9 rows
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
  ENSRNOP00000053546
GenBank Protein Q811A3 (Get FASTA)   NCBI Sequence Viewer  
1 to 9 of 9 rows
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
Fe2OG dioxygenase

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


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

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


1 to 29 of 29 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-29544 BioCyc
Ensembl Genes ENSRNOG00000030183 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000041859 ENTREZGENE
  ENSRNOT00000056704 ENTREZGENE
Gene3D-CATH q2cbj1_9rhob like domain UniProtKB/Swiss-Prot
  Spore Coat Polysaccharide Biosynthesis Protein SpsA, Chain A 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 Plod2 ENTREZGENE
PANTHER PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE 2 UniProtKB/Swiss-Prot
  PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE/GLYCOSYLTRANSFERASE 25 FAMILY MEMBER UniProtKB/Swiss-Prot
Pfam 2OG-FeII_Oxy UniProtKB/Swiss-Prot
PhenoGen Plod2 PhenoGen
PROSITE FE2OG_OXY UniProtKB/Swiss-Prot
  LYS_HYDROXYLASE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000030183 RatGTEx
SMART P4Hc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53448 UniProtKB/Swiss-Prot
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
1 to 29 of 29 rows


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

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