Kdm4d (lysine demethylase 4D) - Rat Genome Database

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Pathways
Gene: Kdm4d (lysine demethylase 4D) Rattus norvegicus
Analyze
Symbol: Kdm4d
Name: lysine 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 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 pericentric heterochromatin and site of double-strand break. Predicted to be active in chromatin and nucleus. Orthologous to several human genes including 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8819,561,253 - 19,586,412 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl819,548,676 - 19,587,331 (-)EnsemblGRCr8
mRatBN7.2811,279,756 - 11,304,920 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx815,271,854 - 15,297,256 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0813,569,605 - 13,595,007 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0811,558,890 - 11,584,068 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0812,968,192 - 12,993,651 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl813,511,805 - 13,513,337 (-)Ensemblrn6Rnor6.0
Rnor_5.0813,454,239 - 13,456,523 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4811,222,556 - 11,247,715 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera812,774,633 - 12,798,709 (-)NCBICelera
Cytogenetic Map8q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl819,548,676 - 19,587,331 (-)EnsemblGRCr8
mRatBN7.2811,279,756 - 11,304,920 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx815,271,854 - 15,297,256 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0813,569,605 - 13,595,007 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0811,558,890 - 11,584,068 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0812,968,192 - 12,993,651 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl813,511,805 - 13,513,337 (-)Ensemblrn6Rnor6.0
Rnor_5.0813,454,239 - 13,456,523 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4811,222,556 - 11,247,715 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
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 (+)Ensemblhg38GRCh38
GRCh371194,706,873 - 94,732,683 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361194,346,493 - 94,372,326 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38914,462,548 - 14,500,522 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl914,462,548 - 14,500,482 (-)Ensemblmm10GRCm38
MGSCv37914,267,025 - 14,304,926 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha216,013,480 - 6,048,512 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0216,183,585 - 6,218,049 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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
KDM4D
(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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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 1.0HetGla 1.0hetGla2
Kdm4d
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1810,256,450 - 10,280,650 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Kdm4d
117 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

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

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 5 30 168 95 85 50 58 50 11 257 125 9 137 63 109 35 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000033932   ⟹   ENSRNOP00000059913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl819,549,565 - 19,587,331 (-)Ensembl
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000071532   ⟹   ENSRNOP00000067344
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl819,549,565 - 19,587,331 (-)Ensembl
mRatBN7.2 Ensembl811,268,859 - 11,305,290 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000124622   ⟹   ENSRNOP00000105224
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl819,548,676 - 19,586,752 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000127250   ⟹   ENSRNOP00000099256
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl819,549,565 - 19,587,331 (-)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:
Protein Sequences
Protein RefSeqs NP_001073180 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A1A5Q5 (Get FASTA)   NCBI Sequence Viewer  
  AAI28761 (Get FASTA)   NCBI Sequence Viewer  
  EDL78474 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059913.1
  ENSRNOP00000067344.1
  ENSRNOP00000099256
RefSeq Acc Id: NP_001073180   ⟸   NM_001079712
- UniProtKB: A1A5Q5 (UniProtKB/Swiss-Prot),   A6JN92 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000059913   ⟸   ENSRNOT00000033932
Ensembl Acc Id: ENSRNOP00000067344   ⟸   ENSRNOT00000071532
Ensembl Acc Id: ENSRNOP00000105224   ⟸   ENSRNOT00000124622
Ensembl Acc Id: ENSRNOP00000099256   ⟸   ENSRNOT00000127250
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
Ensembl Transcript ENSRNOT00000033932.6 UniProtKB/Swiss-Prot
  ENSRNOT00000071532.2 UniProtKB/Swiss-Prot
  ENSRNOT00000127250 ENTREZGENE
Gene3D-CATH Cupin UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7112650 IMAGE-MGC_LOAD
InterPro JmjC_dom UniProtKB/Swiss-Prot
  JmjN UniProtKB/Swiss-Prot
KEGG Report rno:689582 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156756 IMAGE-MGC_LOAD
NCBI Gene 689582 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/Swiss-Prot
  LYSINE-SPECIFIC DEMETHYLASE 4D UniProtKB/Swiss-Prot
Pfam JmjC UniProtKB/Swiss-Prot
  JmjN UniProtKB/Swiss-Prot
PhenoGen Kdm4d PhenoGen
PROSITE JMJC UniProtKB/Swiss-Prot
  JMJN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000045905 RatGTEx
SMART JmjC UniProtKB/Swiss-Prot
  JmjN UniProtKB/Swiss-Prot
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot
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