Kdm4d (lysine demethylase 4D) - Rat Genome Database

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Gene: Kdm4d (lysine demethylase 4D) Rattus norvegicus
Analyze
Symbol: Kdm4d (Ensembl: LOC108348070)
Name: lysine demethylase 4D (Ensembl:lysine-specific demethylase 4D)
RGD ID: 1591045
Description: Predicted to enable chromatin DNA binding activity; damaged DNA binding activity; and histone H3K9me2/H3K9me3 demethylase activity. Predicted to be involved in chromatin remodeling; inflammatory response; and regulation of gene expression. Predicted to act upstream of or within several processes, including cellular response to ionizing radiation; double-strand break repair via homologous recombination; and positive regulation of double-strand break repair via nonhomologous end joining. Predicted to be located in site of double-strand break. Predicted to be part of pericentric heterochromatin. Predicted to be active in nucleus. Orthologous to human KDM4D (lysine demethylase 4D); PARTICIPATES IN histone modification pathway; INTERACTS WITH bisphenol A; decabromodiphenyl ether; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: [histone H3]-trimethyl-L-lysine(9) demethylase 4D; jmjC domain-containing histone demethylation protein 3D; jumonji domain-containing protein 2D; LOC689582; lysine (K)-specific demethylase 4D; lysine-specific demethylase 4D; MGC156756; similar to jumonji domain containing 2D
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
GRCr8819,561,253 - 19,586,412 (-)NCBIGRCr8
mRatBN7.2811,279,756 - 11,304,920 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx815,271,854 - 15,297,256 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0813,569,605 - 13,595,007 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0811,558,890 - 11,584,068 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0812,968,192 - 12,993,651 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl813,511,805 - 13,513,337 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0813,454,239 - 13,456,523 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4811,222,556 - 11,247,715 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera812,774,633 - 12,798,709 (-)NCBICelera
Cytogenetic Map8q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Comprehensive gene review and curation RGD comprehensive gene curation
4. The oncogenic potential of Jumonji D2 (JMJD2/KDM4) histone demethylase overexpression. Young LC and Hendzel MJ, Biochem Cell Biol. 2013 Dec;91(6):369-77. doi: 10.1139/bcb-2012-0054. Epub 2012 Dec 5.
Additional References at PubMed
PMID:6953429   PMID:12477932   PMID:16738407   PMID:19144645   PMID:21293030   PMID:21914792   PMID:22516433   PMID:24550317   PMID:25124442  


Genomics

Comparative Map Data
Kdm4d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8819,561,253 - 19,586,412 (-)NCBIGRCr8
mRatBN7.2811,279,756 - 11,304,920 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx815,271,854 - 15,297,256 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0813,569,605 - 13,595,007 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0811,558,890 - 11,584,068 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0812,968,192 - 12,993,651 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl813,511,805 - 13,513,337 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0813,454,239 - 13,456,523 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4811,222,556 - 11,247,715 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera812,774,633 - 12,798,709 (-)NCBICelera
Cytogenetic Map8q12NCBI
KDM4D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381194,973,709 - 94,999,519 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1194,973,709 - 94,999,519 (+)EnsemblGRCh38hg38GRCh38
GRCh371194,706,873 - 94,732,683 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361194,346,493 - 94,372,326 (+)NCBINCBI36Build 36hg18NCBI36
Build 341194,346,492 - 94,372,322NCBI
Celera1191,994,632 - 92,020,465 (+)NCBICelera
Cytogenetic Map11q21NCBI
HuRef1190,771,786 - 90,797,622 (+)NCBIHuRef
CHM1_11194,589,894 - 94,615,685 (+)NCBICHM1_1
T2T-CHM13v2.01194,980,727 - 95,006,531 (+)NCBIT2T-CHM13v2.0
Kdm4d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39914,373,844 - 14,411,818 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl914,373,844 - 14,411,778 (-)EnsemblGRCm39 Ensembl
GRCm38914,462,548 - 14,500,522 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl914,462,548 - 14,500,482 (-)EnsemblGRCm38mm10GRCm38
MGSCv37914,267,025 - 14,304,926 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36914,212,978 - 14,250,879 (-)NCBIMGSCv36mm8
Celera911,743,297 - 11,781,220 (-)NCBICelera
Cytogenetic Map9A1- A2NCBI
cM Map94.05NCBI
Kdm4d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049556058,977 - 10,539 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049556057,585 - 32,650 (-)NCBIChiLan1.0ChiLan1.0
KDM4D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2995,827,863 - 95,853,819 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11196,919,287 - 96,945,255 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01189,987,537 - 90,013,421 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11193,509,937 - 93,535,825 (+)NCBIpanpan1.1PanPan1.1panPan2
LOC485121
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1216,002,292 - 6,037,344 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl215,987,723 - 6,004,783 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,013,480 - 6,048,512 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0216,183,585 - 6,218,049 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1215,970,707 - 6,005,729 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0216,033,623 - 6,068,647 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0216,081,461 - 6,116,493 (-)NCBIUU_Cfam_GSD_1.0
LOC101967900
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494779,836,345 - 79,838,225 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493667453,200 - 73,042 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100627380
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1927,083,348 - 27,085,693 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2930,996,547 - 30,998,411 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103248265
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1186,190,515 - 86,215,061 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl186,212,761 - 86,214,490 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604339,576,496 - 39,600,714 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm4d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473539,640,090 - 39,695,833 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Kdm4d
72 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:241
Count of miRNA genes:152
Interacting mature miRNAs:169
Transcripts:ENSRNOT00000033932
Prediction methods:Microtar, 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
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat

Markers in Region
RH143162  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2811,296,850 - 11,296,966 (+)MAPPERmRatBN7.2
Rnor_6.0812,985,586 - 12,985,701NCBIRnor6.0
Rnor_5.0812,930,932 - 12,931,047UniSTSRnor5.0
RGSC_v3.4811,239,651 - 11,239,766UniSTSRGSC3.4
Celera812,791,040 - 12,791,155UniSTS
RH 3.4 Map856.88UniSTS
Cytogenetic Map8q11UniSTS
RH138188  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2811,279,775 - 11,280,007 (+)MAPPERmRatBN7.2
Rnor_6.0813,511,372 - 13,511,603NCBIRnor6.0
Rnor_6.0812,968,212 - 12,968,443NCBIRnor6.0
Rnor_5.0813,454,259 - 13,454,490UniSTSRnor5.0
Rnor_5.0812,913,558 - 12,913,789UniSTSRnor5.0
RGSC_v3.4811,222,576 - 11,222,807UniSTSRGSC3.4
Celera812,774,653 - 12,774,884UniSTS
RH 3.4 Map8108.0UniSTS
Cytogenetic Map8q11UniSTS


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 7
Low 42 14
Below cutoff 2 10 35 20 16 20 3 4 32 24 19 7 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000033932   ⟹   ENSRNOP00000059913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000071532   ⟹   ENSRNOP00000067344
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)Ensembl
RefSeq Acc Id: NM_001079712   ⟹   NP_001073180
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8819,561,253 - 19,586,412 (-)NCBI
mRatBN7.2811,279,756 - 11,304,920 (-)NCBI
Rnor_6.0812,968,192 - 12,993,651 (-)NCBI
Rnor_5.0813,454,239 - 13,456,523 (-)NCBI
RGSC_v3.4811,222,556 - 11,247,715 (-)RGD
Celera812,774,633 - 12,798,709 (-)RGD
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001073180   ⟸   NM_001079712
- UniProtKB: A1A5Q5 (UniProtKB/Swiss-Prot),   A6JN92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059913   ⟸   ENSRNOT00000033932
RefSeq Acc Id: ENSRNOP00000067344   ⟸   ENSRNOT00000071532
Protein Domains
JmjC   JmjN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A1A5Q5-F1-model_v2 AlphaFold A1A5Q5 1-510 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591045 AgrOrtholog
BioCyc Gene G2FUF-31692 BioCyc
Ensembl Genes ENSRNOG00000045905 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055007218 UniProtKB/Swiss-Prot
  ENSRNOG00060005823 UniProtKB/Swiss-Prot
  ENSRNOG00065011690 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000033932.6 UniProtKB/Swiss-Prot
  ENSRNOT00000071532 ENTREZGENE
  ENSRNOT00000071532.2 UniProtKB/Swiss-Prot
  ENSRNOT00055011992 UniProtKB/Swiss-Prot
  ENSRNOT00055011996 UniProtKB/Swiss-Prot
  ENSRNOT00060009645 UniProtKB/Swiss-Prot
  ENSRNOT00060009652 UniProtKB/Swiss-Prot
  ENSRNOT00060009658 UniProtKB/Swiss-Prot
  ENSRNOT00065019007 UniProtKB/Swiss-Prot
  ENSRNOT00065019009 UniProtKB/Swiss-Prot
Gene3D-CATH Cupin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7112650 IMAGE-MGC_LOAD
InterPro JmjC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:689582 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:156756 IMAGE-MGC_LOAD
NCBI Gene 689582 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 4D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Kdm4d PhenoGen
PROSITE JMJC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JMJN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000045905 RatGTEx
  ENSRNOG00055007218 RatGTEx
  ENSRNOG00060005823 RatGTEx
  ENSRNOG00065011690 RatGTEx
SMART JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A1A5Q5 ENTREZGENE
  A6JN92 ENTREZGENE, UniProtKB/TrEMBL
  KDM4D_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm4d  lysine demethylase 4D  Kdm4d  lysine (K)-specific demethylase 4D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-23 Kdm4d  lysine (K)-specific demethylase 4D  LOC689582  similar to jumonji domain containing 2D  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689582  similar to jumonji domain containing 2D  LOC684198  similar to jumonji domain containing 2D  Data merged from RGD:1593858 1643240 APPROVED
2006-11-20 LOC689582  similar to jumonji domain containing 2D      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC684198  similar to jumonji domain containing 2D      Symbol and Name status set to provisional 70820 PROVISIONAL