Jmjd6 (jumonji domain containing 6, arginine demethylase and lysine hydroxylase) - Rat Genome Database

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Gene: Jmjd6 (jumonji domain containing 6, arginine demethylase and lysine hydroxylase) Rattus norvegicus
Analyze
Symbol: Jmjd6
Name: jumonji domain containing 6, arginine demethylase and lysine hydroxylase
RGD ID: 1305395
Description: Predicted to enable several functions, including 2-oxoglutarate-dependent dioxygenase activity; P-TEFb complex binding activity; and transcription regulator activator activity. Predicted to be involved in several processes, including oxidative RNA demethylation; peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine; and regulation of RNA metabolic process. Predicted to act upstream of or within several processes, including circulatory system development; hemopoiesis; and recognition of apoptotic cell. Predicted to be located in cytosol; nuclear lumen; and plasma membrane. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human JMJD6 (jumonji domain containing 6, arginine demethylase and lysine hydroxylase); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: arginine demethylase and lysine hydroxylase; bifunctional arginine demethylase and lysyl-hydroxylase JMJD6; histone arginine demethylase JMJD6; jmjC domain-containing protein 6; jumonji domain containing 6; jumonji domain-containing protein 6; LOC360665; lysyl-hydroxylase JMJD6; peptide-lysine 5-dioxygenase JMJD6; phosphatidylserine receptor; Ptdsr
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810102,539,935 - 102,545,986 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl10102,539,894 - 102,545,986 (-)EnsemblGRCr8
mRatBN7.210102,041,131 - 102,047,182 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10102,041,120 - 102,047,182 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx10107,145,069 - 107,151,158 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010106,608,158 - 106,614,247 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010101,961,962 - 101,968,013 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.010105,781,752 - 105,787,803 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10105,781,753 - 105,787,803 (-)Ensemblrn6Rnor6.0
Rnor_5.010105,440,305 - 105,446,356 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.410106,942,942 - 106,948,652 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera10100,609,595 - 100,615,642 (-)NCBICelera
RGSC_v3.110106,957,446 - 106,963,156 (-)NCBI
Cytogenetic Map10q32.2NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
2-palmitoylglycerol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
antimycin A  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-hexachlorocyclohexane  (ISO)
beta-lapachone  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (EXP,ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
diazinon  (EXP)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP)
dieldrin  (EXP)
diethyl malate  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
fenpyroximate  (ISO)
flusilazole  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
GSK-J4  (ISO)
Heptachlor epoxide  (ISO)
hexaconazole  (ISO)
hexadecanoic acid  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
Licochalcone B  (ISO)
methamphetamine  (ISO)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nicotine  (ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
ozone  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chloride  (ISO)
pyrimidifen  (ISO)
rac-lactic acid  (ISO)
senecionine  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
tebufenpyrad  (ISO)
tert-butyl hydroperoxide  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP,ISO)
thifluzamide  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
triadimefon  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,IEA,ISO,ISS)
cytosol  (IEA,ISO)
nucleolus  (IEA,ISO,ISS)
nucleoplasm  (IEA,ISO,ISS)
nucleus  (IBA,IEA,ISO,ISS)
plasma membrane  (IEA,ISO)
ribonucleoprotein complex  (IEA,ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8889548   PMID:10811223   PMID:12477932   PMID:14645847   PMID:14715629   PMID:14729065   PMID:15057822   PMID:15345036   PMID:15489334   PMID:15615595   PMID:15647754   PMID:17534701  
PMID:17947579   PMID:19574390   PMID:20679243   PMID:21060799   PMID:21300889   PMID:21555454   PMID:22189873   PMID:24360279   PMID:24498420   PMID:29176719   PMID:29620141  


Genomics

Comparative Map Data
Jmjd6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810102,539,935 - 102,545,986 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl10102,539,894 - 102,545,986 (-)EnsemblGRCr8
mRatBN7.210102,041,131 - 102,047,182 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10102,041,120 - 102,047,182 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx10107,145,069 - 107,151,158 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010106,608,158 - 106,614,247 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010101,961,962 - 101,968,013 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.010105,781,752 - 105,787,803 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10105,781,753 - 105,787,803 (-)Ensemblrn6Rnor6.0
Rnor_5.010105,440,305 - 105,446,356 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.410106,942,942 - 106,948,652 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera10100,609,595 - 100,615,642 (-)NCBICelera
RGSC_v3.110106,957,446 - 106,963,156 (-)NCBI
Cytogenetic Map10q32.2NCBI
JMJD6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381776,712,836 - 76,726,606 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1776,712,832 - 76,726,784 (-)Ensemblhg38GRCh38
GRCh371774,708,918 - 74,722,688 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361772,220,509 - 72,234,476 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341772,224,004 - 72,234,152NCBI
Celera1771,301,287 - 71,315,250 (-)NCBICelera
Cytogenetic Map17q25.1NCBI
HuRef1770,136,605 - 70,150,592 (-)NCBIHuRef
CHM1_11774,773,704 - 74,787,689 (-)NCBICHM1_1
T2T-CHM13v2.01777,609,799 - 77,623,589 (-)NCBIT2T-CHM13v2.0
Jmjd6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911116,728,258 - 116,734,593 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11116,728,258 - 116,734,275 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm3811116,837,432 - 116,843,767 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11116,837,432 - 116,843,449 (-)Ensemblmm10GRCm38
MGSCv3711116,698,746 - 116,704,763 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3611116,653,522 - 116,659,465 (-)NCBIMGSCv36mm8
Celera11128,577,896 - 128,583,930 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1181.49NCBI
Jmjd6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555065,577,437 - 5,588,372 (+)Ensembl
ChiLan1.0NW_0049555065,577,735 - 5,588,307 (+)NCBIChiLan1.0ChiLan1.0
JMJD6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21992,762,647 - 92,776,315 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11797,588,347 - 97,602,333 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01770,789,922 - 70,803,791 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11776,356,142 - 76,370,117 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1776,356,142 - 76,370,117 (-)EnsemblpanPan2panpan1.1
JMJD6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.194,037,307 - 4,076,119 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl94,037,439 - 4,076,123 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha94,718,621 - 4,729,606 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.094,712,963 - 4,722,109 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl94,713,060 - 4,721,010 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.194,738,827 - 4,749,810 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.094,858,470 - 4,869,452 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.094,939,522 - 4,950,508 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Jmjd6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056024,641,004 - 4,651,035 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365941,760,853 - 1,770,765 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365941,760,924 - 1,771,022 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JMJD6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl124,809,118 - 4,818,043 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1124,809,014 - 4,819,853 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2124,660,874 - 4,668,712 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JMJD6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11644,955,617 - 44,970,136 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1644,955,778 - 44,970,133 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607715,693,816 - 15,702,798 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Jmjd6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248016,563,756 - 6,571,196 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248016,560,746 - 6,571,190 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Jmjd6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1967,236,380 - 67,242,405 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Jmjd6
49 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:36
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000064671
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093723381107556066Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1058073360103073360Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1079272424102982300Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1089039175107713808Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1061843496106843496Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)1097202388107556066Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062556066107556066Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1066108888107555881Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062556066107556066Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087807758107713808Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1091127270107556066Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)1061997479106997479Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091727883107713808Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1097202388107556066Rat

Markers in Region
RH131428  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210102,041,227 - 102,041,428 (+)MAPPERmRatBN7.2
Rnor_6.010105,781,849 - 105,782,049NCBIRnor6.0
Rnor_5.010105,440,402 - 105,440,602UniSTSRnor5.0
RGSC_v3.410106,943,039 - 106,943,239UniSTSRGSC3.4
Celera10100,609,692 - 100,609,892UniSTS
Cytogenetic Map10q32.3UniSTS
Jmjd6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210102,043,461 - 102,044,869 (+)MAPPERmRatBN7.2
Rnor_6.010105,784,083 - 105,785,490NCBIRnor6.0
Rnor_5.010105,442,636 - 105,444,043UniSTSRnor5.0
Celera10100,611,926 - 100,613,329UniSTS
Cytogenetic Map10q32.3UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000064671   ⟹   ENSRNOP00000062806
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl10102,539,894 - 102,545,986 (-)Ensembl
mRatBN7.2 Ensembl10102,041,120 - 102,047,182 (-)Ensembl
Rnor_6.0 Ensembl10105,781,753 - 105,787,803 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000109361   ⟹   ENSRNOP00000093570
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10102,042,040 - 102,047,182 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000116096   ⟹   ENSRNOP00000077039
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl10102,539,894 - 102,545,986 (-)Ensembl
mRatBN7.2 Ensembl10102,042,014 - 102,047,182 (-)Ensembl
RefSeq Acc Id: NM_001012143   ⟹   NP_001012143
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,539,935 - 102,545,986 (-)NCBI
mRatBN7.210102,041,131 - 102,047,182 (-)NCBI
Rnor_6.010105,781,752 - 105,787,803 (-)NCBI
Rnor_5.010105,440,305 - 105,446,356 (-)NCBI
RGSC_v3.410106,942,942 - 106,948,652 (-)RGD
Celera10100,609,595 - 100,615,642 (-)RGD
Sequence:
RefSeq Acc Id: XM_006247806   ⟹   XP_006247868
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,539,935 - 102,545,704 (-)NCBI
mRatBN7.210102,041,131 - 102,047,015 (-)NCBI
Rnor_6.010105,781,752 - 105,787,636 (-)NCBI
Rnor_5.010105,440,305 - 105,446,356 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063269473   ⟹   XP_063125543
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,540,823 - 102,545,704 (-)NCBI
RefSeq Acc Id: XM_063269474   ⟹   XP_063125544
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,540,823 - 102,545,704 (-)NCBI
RefSeq Acc Id: XM_063269475   ⟹   XP_063125545
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,539,935 - 102,545,704 (-)NCBI
RefSeq Acc Id: XM_063269476   ⟹   XP_063125546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,541,405 - 102,545,704 (-)NCBI
RefSeq Acc Id: XM_063269477   ⟹   XP_063125547
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,541,405 - 102,545,704 (-)NCBI
RefSeq Acc Id: XR_010055212
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,540,823 - 102,545,704 (-)NCBI
RefSeq Acc Id: XR_010055213
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810102,540,823 - 102,545,704 (-)NCBI
RefSeq Acc Id: NP_001012143   ⟸   NM_001012143
- UniProtKB: Q6AYK2 (UniProtKB/Swiss-Prot),   A6HKZ3 (UniProtKB/TrEMBL),   A0A8I6AJV5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006247868   ⟸   XM_006247806
- Peptide Label: isoform X1
- UniProtKB: A6HKZ2 (UniProtKB/TrEMBL),   A0A8I6AJV5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000062806   ⟸   ENSRNOT00000064671
Ensembl Acc Id: ENSRNOP00000077039   ⟸   ENSRNOT00000116096
Ensembl Acc Id: ENSRNOP00000093570   ⟸   ENSRNOT00000109361
RefSeq Acc Id: XP_063125545   ⟸   XM_063269475
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063125543   ⟸   XM_063269473
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AJV5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125544   ⟸   XM_063269474
- Peptide Label: isoform X3
- UniProtKB: A0A8I5Y5A5 (UniProtKB/TrEMBL),   A0A8I6AJV5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125547   ⟸   XM_063269477
- Peptide Label: isoform X6
- UniProtKB: A6HKZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125546   ⟸   XM_063269476
- Peptide Label: isoform X5
- UniProtKB: A0A8L2QWD0 (UniProtKB/TrEMBL),   A6HKZ4 (UniProtKB/TrEMBL)
Protein Domains
JmjC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYK2-F1-model_v2 AlphaFold Q6AYK2 1-403 view protein structure

Transcriptome

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

Promoters
RGD ID:13697924
Promoter ID:EPDNEW_R8449
Type:initiation region
Name:Jmjd6_2
Description:arginine demethylase and lysine hydroxylase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8450  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.010105,787,562 - 105,787,622EPDNEW
RGD ID:13697925
Promoter ID:EPDNEW_R8450
Type:single initiation site
Name:Jmjd6_1
Description:arginine demethylase and lysine hydroxylase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8449  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.010105,787,807 - 105,787,867EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305395 AgrOrtholog
BioCyc Gene G2FUF-22581 BioCyc
BioCyc Pathway PWY-7894 [procollagen hydroxylation and glycosylation] BioCyc
BioCyc Pathway Image PWY-7894 BioCyc
Ensembl Genes ENSRNOG00000000250 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000064671 ENTREZGENE
  ENSRNOT00000116096 ENTREZGENE
Gene3D-CATH 1.20.1280.270 UniProtKB/Swiss-Prot
  Cupin UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7113380 IMAGE-MGC_LOAD
InterPro JmjC_dom UniProtKB/Swiss-Prot
  JMJD6_ArgDemeth/LysHydrox UniProtKB/Swiss-Prot
KEGG Report rno:360665 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93932 IMAGE-MGC_LOAD
NCBI Gene 360665 ENTREZGENE
PANTHER ARGININE DEMETHYLASE AND LYSYL-HYDROXYLASE JMJD UniProtKB/Swiss-Prot
  BIFUNCTIONAL ARGININE DEMETHYLASE AND LYSYL-HYDROXYLASE JMJD6 UniProtKB/Swiss-Prot
Pfam JmjC UniProtKB/Swiss-Prot
PhenoGen Jmjd6 PhenoGen
PROSITE JMJC UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000000250 RatGTEx
SMART JmjC UniProtKB/Swiss-Prot
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot
UniProt A0A8I5Y5A5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AJV5 ENTREZGENE
  A0A8L2QWD0 ENTREZGENE, UniProtKB/TrEMBL
  A6HKZ2 ENTREZGENE, UniProtKB/TrEMBL
  A6HKZ3 ENTREZGENE, UniProtKB/TrEMBL
  A6HKZ4 ENTREZGENE, UniProtKB/TrEMBL
  JMJD6_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-07-20 Jmjd6  jumonji domain containing 6, arginine demethylase and lysine hydroxylase  Jmjd6  arginine demethylase and lysine hydroxylase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-04-18 Jmjd6  arginine demethylase and lysine hydroxylase  Jmjd6  jumonji domain containing 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-09-25 Jmjd6  jumonji domain containing 6  Ptdsr  phosphatidylserine receptor  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2005-12-06 Ptdsr  phosphatidylserine receptor  Ptdsr_predicted  phosphatidylserine receptor (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ptdsr_predicted  phosphatidylserine receptor (predicted)      Symbol and Name status set to approved 70820 APPROVED