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 histone 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210102,041,131 - 102,047,182 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10102,041,120 - 102,047,182 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10107,145,069 - 107,151,158 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.010106,608,158 - 106,614,247 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.010101,961,962 - 101,968,013 (-)NCBIRnor_WKY
Rnor_6.010105,781,752 - 105,787,803 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10105,781,753 - 105,787,803 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010105,440,305 - 105,446,356 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410106,942,942 - 106,948,652 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110106,957,446 - 106,963,156 (-)NCBI
Celera10100,609,595 - 100,615,642 (-)NCBICelera
Cytogenetic Map10q32.2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
acrolein  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
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)
bisphenol A  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (EXP,ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dieldrin  (EXP)
dioxygen  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
fenpyroximate  (ISO)
flusilazole  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
Heptachlor epoxide  (ISO)
hexaconazole  (ISO)
hexadecanoic acid  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
Licochalcone B  (ISO)
methamphetamine  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nicotine  (ISO)
ochratoxin A  (EXP,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)
triadimefon  (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
cellular_component  (ND)
cytoplasm  (IBA,ISO,ISS)
cytosol  (ISO)
nucleolus  (ISO,ISS)
nucleoplasm  (ISO,ISS)
nucleus  (IBA,ISO,ISS)
plasma membrane  (ISO)
ribonucleoprotein complex  (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
mRatBN7.210102,041,131 - 102,047,182 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10102,041,120 - 102,047,182 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10107,145,069 - 107,151,158 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.010106,608,158 - 106,614,247 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.010101,961,962 - 101,968,013 (-)NCBIRnor_WKY
Rnor_6.010105,781,752 - 105,787,803 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10105,781,753 - 105,787,803 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010105,440,305 - 105,446,356 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410106,942,942 - 106,948,652 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110106,957,446 - 106,963,156 (-)NCBI
Celera10100,609,595 - 100,615,642 (-)NCBICelera
Cytogenetic Map10q32.2NCBI
JMJD6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381776,712,836 - 76,726,606 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1776,712,832 - 76,726,799 (-)EnsemblGRCh38hg38GRCh38
GRCh371774,708,918 - 74,722,688 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361772,220,509 - 72,234,476 (-)NCBINCBI36Build 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 Ensembl
GRCm3811116,837,432 - 116,843,767 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11116,837,432 - 116,843,449 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711116,698,746 - 116,704,763 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555065,577,735 - 5,588,307 (+)NCBIChiLan1.0ChiLan1.0
JMJD6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11776,356,142 - 76,370,117 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1776,356,142 - 76,370,117 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01770,789,922 - 70,803,791 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha94,718,621 - 4,729,606 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.094,712,963 - 4,722,109 (+)NCBIROS_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_1.0
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
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248016,560,746 - 6,571,190 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Jmjd6
11 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
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)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)1096703043107057807Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1097010147104670812Rat

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
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 35 26 19 18 19 2 66 29 40 10
Low 8 31 22 1 22 8 9 8 6 1 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064671   ⟹   ENSRNOP00000062806
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10102,041,120 - 102,047,182 (-)Ensembl
Rnor_6.0 Ensembl10105,781,753 - 105,787,803 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109361   ⟹   ENSRNOP00000093570
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10102,042,040 - 102,047,182 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116096   ⟹   ENSRNOP00000077039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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: XR_005489892
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210102,041,131 - 102,047,015 (-)NCBI
RefSeq Acc Id: XR_358006
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
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: XR_358007
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
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: XR_358008
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
Protein Sequences
Protein RefSeqs NP_001012143 (Get FASTA)   NCBI Sequence Viewer  
  XP_006247868 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79012 (Get FASTA)   NCBI Sequence Viewer  
  EDM06697 (Get FASTA)   NCBI Sequence Viewer  
  EDM06699 (Get FASTA)   NCBI Sequence Viewer  
  Q6AYK2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001012143   ⟸   NM_001012143
- UniProtKB: Q6AYK2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006247868   ⟸   XM_006247806
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000062806   ⟸   ENSRNOT00000064671
RefSeq Acc Id: ENSRNOP00000077039   ⟸   ENSRNOT00000116096
RefSeq Acc Id: ENSRNOP00000093570   ⟸   ENSRNOT00000109361
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
Ensembl Genes ENSRNOG00000000250 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062806.3 UniProtKB/TrEMBL
  ENSRNOP00000077039 ENTREZGENE
  ENSRNOP00000077039.1 UniProtKB/TrEMBL
  ENSRNOP00000093570.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064671 ENTREZGENE
  ENSRNOT00000064671.3 UniProtKB/TrEMBL
  ENSRNOT00000109361.1 UniProtKB/TrEMBL
  ENSRNOT00000116096 ENTREZGENE
  ENSRNOT00000116096.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7113380 IMAGE-MGC_LOAD
InterPro JmjC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:360665 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93932 IMAGE-MGC_LOAD
NCBI Gene 360665 ENTREZGENE
Pfam JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Jmjd6 PhenoGen
PROSITE JMJC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5Y5A5_RAT UniProtKB/TrEMBL
  A0A8I6AJV5_RAT UniProtKB/TrEMBL
  A0A8L2QWD0_RAT 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