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

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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 several functions, including 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

Alliance Genes

More Info

more info ...

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	19,676,384 - 19,686,945 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	19,676,386 - 19,686,960 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	20,814,848 - 20,825,421 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	21,427,553 - 21,438,126 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	20,492,753 - 20,503,314 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	22,716,421 - 22,726,982 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	22,716,423 - 22,726,982 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	24,728,205 - 24,738,766 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	20,856,527 - 20,867,088 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	20,846,399 - 20,856,690 (+)	NCBI
Celera	12	21,452,299 - 21,462,860 (-)	NCBI		Celera
Cytogenetic Map	12	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Bone Fragility with Contractures, Arterial Rupture, and Deafness (ISO)

Cerebral Hemorrhage (ISO)

genetic disease (ISO)

hepatocellular carcinoma (ISO)

hypothyroidism (IEP)

Plasminogen Activator Inhibitor-1 Deficiency (ISO)

pleomorphic xanthoastrocytoma (ISO)

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

Biological Process

basement membrane assembly (IEA,ISO)

cellular response to hormone stimulus (IEP)

collagen fibril organization (IEA,ISO)

collagen metabolic process (IEA,ISO)

endothelial cell morphogenesis (IEA,ISO)

epidermis morphogenesis (IEA,ISO)

hydroxylysine biosynthetic process (IEA,ISO)

in utero embryonic development (IEA,ISO)

lung morphogenesis (IEA,ISO)

neural tube development (IEA,ISO)

protein localization (IEA,ISO)

protein O-linked glycosylation (IEA,ISO)

vasodilation (IEA,ISO)

Cellular Component

collagen-containing extracellular matrix (IEA,ISO)

endoplasmic reticulum (IBA,ISO,ISS)

endoplasmic reticulum lumen (IEA)

endoplasmic reticulum membrane (IEA)

extracellular space (IEA,ISO,ISS)

Golgi apparatus (ISO)

rough endoplasmic reticulum (IEA)

trans-Golgi network (IEA,ISO)

Molecular Function

iron ion binding (IEA,ISO)

L-ascorbic acid binding (IEA)

metal ion binding (ISO)

procollagen galactosyltransferase activity (IEA,ISO,ISS)

procollagen glucosyltransferase activity (IBA,IEA,ISO,ISS)

procollagen-lysine 5-dioxygenase activity (IBA,IEA,ISO,ISS)

protein binding (ISO)

small molecule binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

lysine degradation pathway (IEA)

O-linked glycan biosynthetic pathway (IEA)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	12	19,676,384 - 19,686,945 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	19,676,386 - 19,686,960 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	20,814,848 - 20,825,421 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	21,427,553 - 21,438,126 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	20,492,753 - 20,503,314 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	22,716,421 - 22,726,982 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	22,716,423 - 22,726,982 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	24,728,205 - 24,738,766 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	20,856,527 - 20,867,088 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	20,846,399 - 20,856,690 (+)	NCBI
Celera	12	21,452,299 - 21,462,860 (-)	NCBI		Celera
Cytogenetic Map	12	q12	NCBI

PLOD3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	101,205,984 - 101,217,581 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	101,205,977 - 101,218,420 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	100,849,265 - 100,860,862 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	100,635,978 - 100,647,731 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	7	100,442,700 - 100,454,303	NCBI
Celera	7	95,858,417 - 95,870,169 (-)	NCBI		Celera
Cytogenetic Map	7	q22.1	NCBI
HuRef	7	95,442,117 - 95,454,228 (-)	NCBI		HuRef
CHM1_1	7	100,779,662 - 100,791,414 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	7	102,529,447 - 102,541,882 (-)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	100,207,645 - 100,219,398 (-)	NCBI

Plod3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	137,015,873 - 137,025,500 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	137,015,873 - 137,025,502 (+)	Ensembl		GRCm39 Ensembl
GRCm38	5	136,987,019 - 136,996,646 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	136,987,019 - 136,996,648 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	137,462,889 - 137,472,516 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	137,271,649 - 137,281,166 (+)	NCBI		MGSCv36	mm8
Celera	5	134,003,006 - 134,012,645 (+)	NCBI		Celera
Cytogenetic Map	5	G2	NCBI
cM Map	5	76.09	NCBI

Plod3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955456	16,082,437 - 16,093,389 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955456	16,082,424 - 16,090,773 (+)	NCBI	ChiLan1.0	ChiLan1.0

PLOD3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	7	167,483,838 - 167,495,393 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	93,347,335 - 93,358,921 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	106,587,858 - 106,599,605 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	106,587,858 - 106,599,605 (-)	Ensembl	panpan1.1		panPan2

PLOD3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	8,664,135 - 8,671,637 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	8,664,358 - 8,671,620 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	10,361,502 - 10,368,957 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	6	8,483,656 - 8,491,120 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	6	8,483,333 - 8,491,117 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	6	8,443,884 - 8,451,311 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	6	8,414,481 - 8,421,939 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	6	8,579,093 - 8,586,540 (+)	NCBI		UU_Cfam_GSD_1.0

Plod3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409344	132,939,235 - 132,946,261 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936543	1,090,253 - 1,097,301 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936543	1,090,268 - 1,097,170 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PLOD3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	8,911,791 - 8,919,516 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	8,911,787 - 8,919,525 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PLOD3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	28	11,962,394 - 11,974,206 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	28	11,962,286 - 11,975,228 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666070	4,378,287 - 4,390,520 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Plod3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624740	16,074,141 - 16,082,223 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624740	16,074,027 - 16,082,139 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Plod3
156 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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
10755457	Coatc14	Coat color QTL 14		0.01759	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	12	1	22591684	Rat
6893681	Bw109	Body weight QTL 109	2.3	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	12	1	23297788	Rat
1581516	Cm56	Cardiac mass QTL 56	4.2	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	12	1	29333307	Rat
1598855	Bp294	Blood pressure QTL 294	3.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	1	34851688	Rat
7411660	Foco28	Food consumption QTL 28	10.9	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
9590086	Insglur6	Insulin/glucose ratio QTL 6	18.97	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	12	1	42110980	Rat
8694179	Bw150	Body weight QTL 150	2.9	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
7411586	Foco5	Food consumption QTL 5	5.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411595	Foco9	Food consumption QTL 9	4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	1	42110980	Rat
7411545	Bw128	Body weight QTL 128	5.2	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	12	1	42110980	Rat
9590147	Scort7	Serum corticosterone level QTL 7	13.61	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	12	1	42110980	Rat
2303575	Insul14	Insulin level QTL 14	4		blood insulin amount (VT:0001560)	blood insulin level (CMO:0000349)	12	1	42450532	Rat
737979	Pia22	Pristane induced arthritis QTL 22	53.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	1	44465750	Rat
634351	Apr5	Acute phase response QTL 5	6.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	12	1	44503507	Rat
2302042	Pia38	Pristane induced arthritis QTL 38	3.5	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	1	44503507	Rat
634350	Apr4	Acute phase response QTL 4	6		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	1172005	46172005	Rat
8552918	Pigfal7	Plasma insulin-like growth factor 1 level QTL 7			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
7411547	Bw129	Body weight QTL 129		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	5564495	46669029	Rat
7411597	Foco10	Food consumption QTL 10		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
7411641	Foco19	Food consumption QTL 19	27.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
8552964	Pigfal17	Plasma insulin-like growth factor 1 level QTL 17	3.5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564495	46669029	Rat
7411588	Foco6	Food consumption QTL 6		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	12	5564495	46669029	Rat
8552912	Pigfal6	Plasma insulin-like growth factor 1 level QTL 6	5		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	12	5564498	46669029	Rat
10059594	Kidm46	Kidney mass QTL 46	3.79	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	12	6107579	46669029	Rat
1302792	Scl21	Serum cholesterol level QTL 21	3.8	0.0011	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	12	7196730	46669029	Rat
2293086	Iddm30	Insulin dependent diabetes mellitus QTL 30	3.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	8449490	28302290	Rat
61331	Eau2	Experimental allergic uveoretinitis QTL 2		0.0005	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	12	8525423	28064601	Rat
1300157	Rf21	Renal function QTL 21	4.4		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	12	9318216	32103380	Rat
1549829	Scl48	Serum cholesterol level QTL 48	5		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	12	9603277	46669029	Rat
2293699	Bss49	Bone structure and strength QTL 49	5.61	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	12	10474137	46669029	Rat
2300186	Bmd59	Bone mineral density QTL 59	7.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	12	10474137	46669029	Rat
1331786	Kidm11	Kidney mass QTL 11	3.571		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	12	11073825	24234895	Rat
1331755	Bp219	Blood pressure QTL 219	3.041		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	28064557	Rat
1331761	Bp218	Blood pressure QTL 218	2.973		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	12	11073825	45055165	Rat
61404	Bw120	Body weight QTL 120	5.1		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	12	12351619	46669029	Rat
1641928	Alcrsp5	Alcohol response QTL 5			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	12	12812385	46669029	Rat
2303569	Gluco44	Glucose level QTL 44	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	12	12812385	46669029	Rat
1549902	Bp269	Blood pressure QTL 269			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	13182736	46669029	Rat
1549912	Bp268	Blood pressure QTL 268			arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	13182736	46669029	Rat
2302060	Pia37	Pristane induced arthritis QTL 37	6.1	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	12	13198157	46669029	Rat
61416	Pia4	Pristane induced arthritis QTL 4	8.4		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	12	13635523	30827399	Rat
61421	Cia12	Collagen induced arthritis QTL 12	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	13635523	35682913	Rat
61443	Btemp2	Thermal response to stress QTL 2	3.3	0.000094	body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	12	15025183	20794014	Rat
631543	Bp83	Blood pressure QTL 83	5.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	12	15550826	38478808	Rat
2293684	Bmd26	Bone mineral density QTL 26	4.4	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	12	15872653	32974238	Rat
631560	Apr1	Acute phase response QTL 1	6.1		orosomucoid 1 amount (VT:0010541)	plasma orosomucoid 1 level (CMO:0001467)	12	19144362	46669029	Rat
2306789	Ean6	Experimental allergic neuritis QTL 6	4.9		nervous system integrity trait (VT:0010566)	experimental autoimmune neuritis severity score (CMO:0001528)	12	19610870	24139202	Rat
737822	Alc10	Alcohol consumption QTL 10	2.2		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	12	19610870	40218516	Rat
5684888	Pia42	Pristane induced arthritis QTL 42			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	19610870	42828880	Rat
61324	Eae5	Experimental allergic encephalomyelitis QTL 5	14		nervous system integrity trait (VT:0010566)	percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)	12	19610870	46669029	Rat
1298081	Cia25	Collagen induced arthritis QTL 25	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	12	19610889	35682913	Rat

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_178101	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AJ430859	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC085683	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473973	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CO386873	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000227	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M18864	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000001921 ⟹ ENSRNOP00000001921

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	19,676,386 - 19,686,960 (-)	Ensembl
Rnor_6.0 Ensembl	12	22,716,423 - 22,726,982 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000111361 ⟹ ENSRNOP00000088013

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	12	19,676,386 - 19,686,960 (-)	Ensembl

RefSeq Acc Id:

NM_178101 ⟹ NP_835202

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	12	19,676,384 - 19,686,945 (-)	NCBI
Rnor_6.0	12	22,716,421 - 22,726,982 (-)	NCBI
Rnor_5.0	12	24,728,205 - 24,738,766 (-)	NCBI
RGSC_v3.4	12	20,856,527 - 20,867,088 (+)	RGD
Celera	12	21,452,299 - 21,462,860 (-)	RGD

Sequence:

show sequence

CGGTTCCTCAGGCGTGAGTCGGGCTGTGTCGGGGACCAGACCCTCGGCTCCTCCCCACCCTCCA
GCCCGCGCCCGCGCGACAATCCTTGCCTTGTCTCGCCGTCTGCATCTCGGGTTTTAGGTGGCCT
CGGGTTACGCCTTTTTTCCAGGGCGGAGTCCGGAGCACAGCTCCTCCTCTCAGCGGGCTCGGCT
TCCCTTTCCCAGAATCTTCCTGGGGACTCGGAATCTAGGCGCTAAGCTCAGCCCTGGTGCGGGC
CTGGGTGTAGCCTAAGCGTGCTGCTAGCCATGGCAGCGTCAGTCCCGGAACCCCGGCTTTTGCT
CCTGCTCCTGCTGCTGCTGCCGCCGCTGCCCCCGGTAACTTCTGCCTCCGATCGACCCCGGGGC
GCCAATCCTGTCAACCCTGACAAACTGCTGGTGATCACCGTGGCTACAGCAGAGACAGAGGGGT
ACCGGCGTTTTCTGCAGTCTGCCGAGTTCTTTAACTACACTGTACGGACCCTGGGACTGGGACA
GGAGTGGCGAGGGGGTGATGTCGCCCGAACAGTCGGTGGAGGCCAGAAGGTCAGGTGGCTCAAG
AAGGAAATGGAGAAATATGCGAGTCAGGAGGACATGATCATCATGTTTGTGGACAGCTACGATG
TGATTCTGGCGAGCAGCCCAACAGAGCTGCTGAAGAAGTTTGTTCAGAGTGGCAGTCATCTGCT
GTTCTCCGCTGAGAGCTTCTGCTGGCCTGACTGGGGGCTGGCAGAGCAGTACCCTGAGGTGGGC
GTGGGGAAGCGCTTCCTCAACTCTGGTGGATTCATTGGCTTCGCTCCCACCATCCATCGGATTG
TCCGCCAGTGGAAGTACAAGGACGACGACGATGATCAGTTGTTCTATACTCAACTCTACCTGGA
CCCAGGGCTGCGGGAGAAACTCAAACTTAGCCTGGACCATAAATCCCGGATCTTCCAGAACCTC
AATGGAGCCTTAGATGAAGTGGTCTTAAAGTTCGACCAGAACCGTGTGCGCATCCGAAATGTGG
CCTACGACACGCTTCCTGTTGTGGTCCATGGCAACGGTCCCACTAAGCTCCAGCTTAACTACCT
GGGGAACTATGTCCCCAATGGCTGGACTCCCCAGGGAGGCTGTGGATTCTGCAACTTGAACCGG
AGGACACTCCCGGGGGGGCAGCCTCCCCCCCGGGTGCTTCTGGCCGTGTTTGTGGAGCAGCCCA
CTCCCTTCCTACCTCGGTTCCTGCAGCGCCTACTGCTCCTGGATTACCCGCCGGACAGGATCTC
TCTTTTCCTTCACAACAACGAGGTGTACCACGAGCCTCACATTGCAGATGCCTGGCCACAGCTC
CAGGACCACTTCTCAGCTGTAAAGCTAGTGGGGCCAGAGGAGGCCCTGAGCTCAGGGGAGGCCA
GGGACATGGCCATGGATAGCTGTCGGCAGAACCCCGAGTGTGAGTTCTACTTTAGCCTGGATGC
CGATGCTGTCCTCACGAACCCGGAGACCTTGCGTATCTTGATTGAACAAAACAGGAAGGTAATA
GCTCCCATGCTTTCTCGCCACGGCAAGCTCTGGTCCAACTTCTGGGGGGCCCTGAGCCCCGATG
AGTACTATGCCCGCTCCGAAGACTACGTGGAATTGGTGCAGCGGAAGCGAGTGGGCTTGTGGAA
TGTACCCTACATATCCCAGGCATATGTGATCCGAGGAGAGACCCTGAGGACAGAGCTCCCCGAA
AAGGAAGTATTCTCCAGCAGCGACACAGACCCAGATATGGCTTTCTGCAGGAGTGTCCGGGACA
AGGGCATCTTCCTGCACCTCAGCAATCAGCACGAGTTTGGCCGGCTGCTGTCTACTTCCCACTA
TGACACTGACCACTTACACCCGGACCTCTGGCAGATCTTTGACAACCCTGTGGACTGGAGAGAA
CAGTACATCCATGAGAACTACAGCCGGGCCCTGGATGGGGAGGGGCTGGTAGAACAGCCATGCC
CAGATGTGTACTGGTTCCCACTGCTGACCGAGCAGATGTGTGATGAGCTGGTGGAGGAAATGGA
ACACTATGGCCAGTGGTCTGGAGGCCGGCATGAGGACTCCAGGTTGGCTGGAGGGTATGAGAAT
GTTCCCACCGTGGACATCCACATGAAGCAGGTGGGGTACGAGGACCAGTGGCTTCAGCTGCTGA
GGACATATGTGGGGCCCATGACGGAGCACCTGTTTCCTGGCTACCACACCAAGACACGGGCAGT
GATGAACTTTGTGGTCCGCTACCGGCCAGATGAGCAGCCCTCACTTCGGCCACACCATGACTCG
TCCACCTTCACGCTCAACGTTGCCCTCAATCACAAGGGTGTAGATTATGAGGGAGGTGGCTGCC
GCTTCCTGAGGTACGACTGCAGAGTCTCATCCCCGAGGAAGGGCTGGGCTCTCCTGCACCCTGG
TCGCCTCACACACTACCACGAGGGGCTGCCCACCACCAGGGGAACTCGATACATCATGGTGTCC
TTCGTTGACCCCTGACACTCAATCAGTCTGCCAAACCTTCTCTGCCACTGTGCCTTGTTGGGCC
ACCTGGGTTGTCATTCTCATCTCCTGAGTGTGTCTATGTGCCTGGGACAGAATGTGCTGGCCCC
AACAGCCCTCCCAGGAGGTCCCTAGAGTCTTCTATTTTCCCATTGACCCTTCTGAGGGTCCCCT
GCCTGATAAATTATTAAGCTTCCTCAGCCTCACTTTCAATAAAAGGATGTTTGTAACTGTTGAA
AAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_835202	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40820	(Get FASTA)	NCBI Sequence Viewer
	AAH85683	(Get FASTA)	NCBI Sequence Viewer
	CAD23628	(Get FASTA)	NCBI Sequence Viewer
	EDM13298	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000001921
	ENSRNOP00000088013.1
GenBank Protein	Q5U367	(Get FASTA)	NCBI Sequence Viewer

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:	show sequence MAASVPEPRLLLLLLLLLPPLPPVTSASDRPRGANPVNPDKLLVITVATAETEGYRRFLQSAEF FNYTVRTLGLGQEWRGGDVARTVGGGQKVRWLKKEMEKYASQEDMIIMFVDSYDVILASSPTEL LKKFVQSGSHLLFSAESFCWPDWGLAEQYPEVGVGKRFLNSGGFIGFAPTIHRIVRQWKYKDDD DDQLFYTQLYLDPGLREKLKLSLDHKSRIFQNLNGALDEVVLKFDQNRVRIRNVAYDTLPVVVH GNGPTKLQLNYLGNYVPNGWTPQGGCGFCNLNRRTLPGGQPPPRVLLAVFVEQPTPFLPRFLQR LLLLDYPPDRISLFLHNNEVYHEPHIADAWPQLQDHFSAVKLVGPEEALSSGEARDMAMDSCRQ NPECEFYFSLDADAVLTNPETLRILIEQNRKVIAPMLSRHGKLWSNFWGALSPDEYYARSEDYV ELVQRKRVGLWNVPYISQAYVIRGETLRTELPEKEVFSSSDTDPDMAFCRSVRDKGIFLHLSNQ HEFGRLLSTSHYDTDHLHPDLWQIFDNPVDWREQYIHENYSRALDGEGLVEQPCPDVYWFPLLT EQMCDELVEEMEHYGQWSGGRHEDSRLAGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTEH LFPGYHTKTRAVMNFVVRYRPDEQPSLRPHHDSSTFTLNVALNHKGVDYEGGGCRFLRYDCRVS SPRKGWALLHPGRLTHYHEGLPTTRGTRYIMVSFVDP hide sequence

RefSeq Acc Id:

ENSRNOP00000001921 ⟸ ENSRNOT00000001921

RefSeq Acc Id:

ENSRNOP00000088013 ⟸ ENSRNOT00000111361

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	22,726,780 - 22,726,840	EPDNEW

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	12	22,726,985 - 22,727,045	EPDNEW

Additional Information

External Database Links

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, 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	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
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
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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)