Plod3 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3) - Rat Genome Database

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Gene: Plod3 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3) Rattus norvegicus
Analyze
Symbol: Plod3
Name: procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3
RGD ID: 631339
Description: Predicted to enable hexosyltransferase activity; iron ion binding activity; and procollagen-lysine 5-dioxygenase activity. Involved in cellular response to hormone stimulus. Predicted to be located in collagen-containing extracellular matrix; extracellular space; and trans-Golgi network. Predicted to be active in endoplasmic reticulum. Biomarker of hypothyroidism. Orthologous to human PLOD3 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 3); PARTICIPATES IN lysine degradation pathway; O-linked glycan biosynthetic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; aconitine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: bone protein I (BP-I); LH3; lysyl hydroxylase 3; MGC93055; multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3; procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
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
GRCr81225,313,070 - 25,323,631 (-)NCBIGRCr8
mRatBN7.21219,676,384 - 19,686,945 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1219,676,386 - 19,686,960 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1220,814,848 - 20,825,421 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01221,427,553 - 21,438,126 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01220,492,753 - 20,503,314 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01222,716,421 - 22,726,982 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1222,716,423 - 22,726,982 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01224,728,205 - 24,738,766 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41220,856,527 - 20,867,088 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11220,846,399 - 20,856,690 (+)NCBI
Celera1221,452,299 - 21,462,860 (-)NCBICelera
Cytogenetic Map12q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,10-phenanthroline  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-dithiothreitol  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
2,6-dinitrotoluene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
aconitine  (EXP)
acrylamide  (ISO)
allethrin  (EXP)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (EXP,ISO)
carbon nanotube  (ISO)
chlorogenic acid  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
Cuprizon  (EXP)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
decabromodiphenyl ether  (ISO)
dicrotophos  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
fenthion  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
ivermectin  (ISO)
kainic acid  (ISO)
L-1,4-dithiothreitol  (ISO)
L-methionine  (ISO)
miconazole  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (ISO)
nicotine  (ISO)
Osajin  (ISO)
paracetamol  (ISO)
piperonyl butoxide  (ISO)
Pomiferin  (ISO)
potassium chromate  (ISO)
puerarin  (ISO)
pyrethrins  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
Rosavin  (ISO)
rotenone  (EXP)
simvastatin  (EXP)
Soman  (EXP)
thapsigargin  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Identification, expression, and tissue distribution of the three rat lysyl hydroxylase isoforms. Mercer DK, etal., Biochem Biophys Res Commun 2003 Aug 8;307(4):803-9.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
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.
11. Barrier to autointegration factor 1, procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3, and splicing factor 3b subunit 4 as early-stage cancer decision markers and drivers of hepatocellular carcinoma. Shen Q, etal., Hepatology. 2018 Apr;67(4):1360-1377. doi: 10.1002/hep.29606. Epub 2018 Feb 20.
Additional References at PubMed
PMID:3162363   PMID:9582318   PMID:9724729   PMID:10934207   PMID:12477932   PMID:15489334   PMID:16447251   PMID:16467571   PMID:18298658   PMID:19056867   PMID:19199708   PMID:27435297  


Genomics

Comparative Map Data
Plod3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81225,313,070 - 25,323,631 (-)NCBIGRCr8
mRatBN7.21219,676,384 - 19,686,945 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1219,676,386 - 19,686,960 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1220,814,848 - 20,825,421 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01221,427,553 - 21,438,126 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01220,492,753 - 20,503,314 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01222,716,421 - 22,726,982 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1222,716,423 - 22,726,982 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01224,728,205 - 24,738,766 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41220,856,527 - 20,867,088 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11220,846,399 - 20,856,690 (+)NCBI
Celera1221,452,299 - 21,462,860 (-)NCBICelera
Cytogenetic Map12q12NCBI
PLOD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387101,205,984 - 101,217,581 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7101,205,977 - 101,218,420 (-)EnsemblGRCh38hg38GRCh38
GRCh377100,849,265 - 100,860,862 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367100,635,978 - 100,647,731 (-)NCBINCBI36Build 36hg18NCBI36
Build 347100,442,700 - 100,454,303NCBI
Celera795,858,417 - 95,870,169 (-)NCBICelera
Cytogenetic Map7q22.1NCBI
HuRef795,442,117 - 95,454,228 (-)NCBIHuRef
CHM1_17100,779,662 - 100,791,414 (-)NCBICHM1_1
T2T-CHM13v2.07102,529,447 - 102,541,882 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27100,207,645 - 100,219,398 (-)NCBI
Plod3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395137,015,873 - 137,025,500 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5137,015,873 - 137,025,502 (+)EnsemblGRCm39 Ensembl
GRCm385136,987,019 - 136,996,646 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5136,987,019 - 136,996,648 (+)EnsemblGRCm38mm10GRCm38
MGSCv375137,462,889 - 137,472,516 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365137,271,649 - 137,281,166 (+)NCBIMGSCv36mm8
Celera5134,003,006 - 134,012,645 (+)NCBICelera
Cytogenetic Map5G2NCBI
cM Map576.09NCBI
Plod3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545616,082,437 - 16,093,389 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545616,082,424 - 16,090,773 (+)NCBIChiLan1.0ChiLan1.0
PLOD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26119,219,216 - 119,230,857 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17167,483,838 - 167,495,393 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0793,347,335 - 93,358,921 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17106,587,858 - 106,599,605 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7106,587,858 - 106,599,605 (-)Ensemblpanpan1.1panPan2
PLOD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.168,664,135 - 8,671,637 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl68,664,358 - 8,671,620 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha610,361,502 - 10,368,957 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.068,483,656 - 8,491,120 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl68,483,333 - 8,491,117 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.168,443,884 - 8,451,311 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.068,414,481 - 8,421,939 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.068,579,093 - 8,586,540 (+)NCBIUU_Cfam_GSD_1.0
Plod3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344132,939,235 - 132,946,261 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365431,090,253 - 1,097,301 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365431,090,268 - 1,097,170 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLOD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl38,911,791 - 8,919,516 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.138,911,787 - 8,919,525 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PLOD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12811,962,394 - 11,974,206 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2811,962,286 - 11,975,228 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660704,378,287 - 4,390,520 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Plod3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474016,074,141 - 16,082,223 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474016,074,027 - 16,082,139 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Plod3
181 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:40
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000001921
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121363552330827399Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
61443Btemp2Thermal response to stress QTL 23.30.000094body temperature trait (VT:0005535)core body temperature (CMO:0001036)121502518320794014Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)121961087024139202Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat


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 3 36 53 37 19 37 1 3 68 35 40 11 1
Low 7 4 4 4 7 8 6 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001921   ⟹   ENSRNOP00000001921
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1219,676,386 - 19,686,960 (-)Ensembl
Rnor_6.0 Ensembl1222,716,423 - 22,726,982 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111361   ⟹   ENSRNOP00000088013
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1219,676,386 - 19,686,960 (-)Ensembl
RefSeq Acc Id: NM_178101   ⟹   NP_835202
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81225,313,070 - 25,323,631 (-)NCBI
mRatBN7.21219,676,384 - 19,686,945 (-)NCBI
Rnor_6.01222,716,421 - 22,726,982 (-)NCBI
Rnor_5.01224,728,205 - 24,738,766 (-)NCBI
RGSC_v3.41220,856,527 - 20,867,088 (+)RGD
Celera1221,452,299 - 21,462,860 (-)RGD
Sequence:
RefSeq Acc Id: XM_063271149   ⟹   XP_063127219
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81225,318,656 - 25,323,363 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_835202   ⟸   NM_178101
- Peptide Label: precursor
- UniProtKB: Q811A5 (UniProtKB/Swiss-Prot),   Q5U367 (UniProtKB/Swiss-Prot),   A6J056 (UniProtKB/TrEMBL),   A0A8I6A8W8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001921   ⟸   ENSRNOT00000001921
RefSeq Acc Id: ENSRNOP00000088013   ⟸   ENSRNOT00000111361
RefSeq Acc Id: XP_063127219   ⟸   XM_063271149
- Peptide Label: isoform X1
Protein Domains
Fe2OG dioxygenase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U367-F1-model_v2 AlphaFold Q5U367 1-741 view protein structure

Transcriptome

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

Promoters
RGD ID:13698528
Promoter ID:EPDNEW_R9052
Type:initiation region
Name:Plod3_1
Description:procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R9053  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01222,726,780 - 22,726,840EPDNEW
RGD ID:13698529
Promoter ID:EPDNEW_R9053
Type:initiation region
Name:Plod3_2
Description:procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R9052  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01222,726,985 - 22,727,045EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:631339 AgrOrtholog
BioCyc Gene G2FUF-19674 BioCyc
Ensembl Genes ENSRNOG00000001417 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001921 ENTREZGENE
  ENSRNOT00000001921.5 UniProtKB/Swiss-Prot
  ENSRNOT00000111361.1 UniProtKB/TrEMBL
Gene3D-CATH q2cbj1_9rhob like domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7110561 IMAGE-MGC_LOAD
InterPro 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:288583 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93055 IMAGE-MGC_LOAD
NCBI Gene 288583 ENTREZGENE
PANTHER MULTIFUNCTIONAL PROCOLLAGEN LYSINE HYDROXYLASE AND GLYCOSYLTRANSFERASE LH3 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 Plod3 PhenoGen
PROSITE FE2OG_OXY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYS_HYDROXYLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001417 RatGTEx
SMART P4Hc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53448 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A8W8 ENTREZGENE, UniProtKB/TrEMBL
  A6J056 ENTREZGENE, UniProtKB/TrEMBL
  PLOD3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q811A5 ENTREZGENE
UniProt Secondary Q811A5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-11 Plod3  procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3      Symbol and Name status set to approved 625702 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression ubiquitously expressed 633907