Kdm4d (lysine (K)-specific demethylase 4D) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Kdm4d (lysine (K)-specific demethylase 4D) Mus musculus
Analyze
Symbol: Kdm4d
Name: lysine (K)-specific demethylase 4D
RGD ID: 1622025
MGI Page MGI
Description: Enables chromatin DNA binding activity; damaged DNA binding activity; and histone H3K9 demethylase activity. Acts upstream of or within DNA damage response. Located in nucleus and site of double-strand break. Part of pericentric heterochromatin. Orthologous to human KDM4D (lysine demethylase 4D).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 4932416A15; [histone H3]-trimethyl-L-lysine(9) demethylase 4D; jmjC domain-containing histone demethylation protein 3D; Jmjd2d; jumonji domain containing 2D; jumonji domain-containing protein 2D; lysine-specific demethylase 4D
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm9361   Kdm4dl  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
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 Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. Mouse MP Annotation Import Pipeline RGD automated import pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:15489334   PMID:15618518   PMID:16141072   PMID:16141073  
PMID:16738407   PMID:18022353   PMID:18287559   PMID:19144645   PMID:21267068   PMID:21293030   PMID:21555854   PMID:21677750   PMID:21873635   PMID:24550317   PMID:25417163   PMID:27626377  
PMID:29800554   PMID:30472235   PMID:30973865   PMID:32080306   PMID:32094404   PMID:32325033   PMID:34368113   PMID:35027670   PMID:35145029  


Genomics

Comparative Map Data
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
(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
(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
(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
1267 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:356
Count of miRNA genes:281
Interacting mature miRNAs:305
Transcripts:ENSMUST00000058796, ENSMUST00000115647
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142326Tgq19_mtriglyceride QTL 19 (mouse)Not determined121060750Mouse
1300899Chol6_mcholesterol 6 (mouse)Not determined9129902913Mouse
13434920Dcollq1_mdifferential colonization level QTL 1 (mouse)9130341840Mouse
35673312Ari7_mantibody response to influenza 7, day 45, IgG3 (mouse)9780000122211296Mouse
1300849Sles4_msystemic lupus erythmatosus suppressor 4 (mouse)Not determined9910756237306370Mouse
13504833Bglu19_mblood glucose level 19 (mouse)9991076843910768Mouse
1300532Tbs2_mtuberculosis severity 2 (mouse)Not determined91236997046370114Mouse
10043917Obq37_mobesity QTL 37 (mouse)Not determined91339117547391175Mouse

Markers in Region
UniSTS:487758  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38914,462,760 - 14,464,245UniSTSGRCm38
MGSCv37914,267,204 - 14,268,689UniSTSGRCm37
Celera911,743,476 - 11,744,979UniSTS
Cytogenetic Map9A1UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000058796   ⟹   ENSMUSP00000061632
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl914,373,844 - 14,411,778 (-)Ensembl
GRCm38.p6 Ensembl914,462,548 - 14,500,482 (-)Ensembl
RefSeq Acc Id: ENSMUST00000115647   ⟹   ENSMUSP00000111311
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl914,374,506 - 14,411,696 (-)Ensembl
GRCm38.p6 Ensembl914,463,210 - 14,500,400 (-)Ensembl
RefSeq Acc Id: NM_001410506   ⟹   NP_001397435
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39914,373,844 - 14,411,730 (-)NCBI
RefSeq Acc Id: NM_173433   ⟹   NP_775609
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39914,373,844 - 14,411,730 (-)NCBI
GRCm38914,462,581 - 14,500,482 (-)NCBI
MGSCv37914,267,025 - 14,304,926 (-)RGD
Celera911,743,297 - 11,781,220 (-)NCBI
cM Map9 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006510270   ⟹   XP_006510333
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39914,373,844 - 14,411,818 (-)NCBI
GRCm38914,462,548 - 14,500,522 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_775609   ⟸   NM_173433
- UniProtKB: Q2M1G7 (UniProtKB/Swiss-Prot),   B8JK34 (UniProtKB/Swiss-Prot),   A2CGB5 (UniProtKB/Swiss-Prot),   Q8BI19 (UniProtKB/Swiss-Prot),   Q3U2K5 (UniProtKB/Swiss-Prot),   Z4YLE9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006510333   ⟸   XM_006510270
- Peptide Label: isoform X1
- UniProtKB: Q2M1G7 (UniProtKB/Swiss-Prot),   B8JK34 (UniProtKB/Swiss-Prot),   A2CGB5 (UniProtKB/Swiss-Prot),   Q8BI19 (UniProtKB/Swiss-Prot),   Q3U2K5 (UniProtKB/Swiss-Prot),   Z4YLE9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000111311   ⟸   ENSMUST00000115647
RefSeq Acc Id: ENSMUSP00000061632   ⟸   ENSMUST00000058796
RefSeq Acc Id: NP_001397435   ⟸   NM_001410506
- UniProtKB: Q3U2K5 (UniProtKB/Swiss-Prot),   Q2M1G7 (UniProtKB/Swiss-Prot),   B8JK34 (UniProtKB/Swiss-Prot),   A2CGB5 (UniProtKB/Swiss-Prot),   Q8BI19 (UniProtKB/Swiss-Prot)
Protein Domains
JmjC   JmjN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3U2K5-F1-model_v2 AlphaFold Q3U2K5 1-510 view protein structure

Promoters
RGD ID:6844390
Promoter ID:MM_KWN:56387
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000115647,   NM_023153,   OTTMUST00000049839
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36914,304,869 - 14,305,369 (+)MPROMDB
RGD ID:8668806
Promoter ID:EPDNEW_M12434
Type:initiation region
Name:Kdm4d_1
Description:Mus musculus lysine -specific demethylase 4D , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38914,500,554 - 14,500,614EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3606484 AgrOrtholog
Ensembl Genes ENSMUSG00000053914 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000058796 ENTREZGENE
  ENSMUST00000058796.7 UniProtKB/Swiss-Prot
  ENSMUST00000115647 ENTREZGENE
  ENSMUST00000115647.3 UniProtKB/TrEMBL
Gene3D-CATH Cupin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro JmjC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:244694 UniProtKB/Swiss-Prot
MGD MGI:3606484 ENTREZGENE
NCBI Gene 244694 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
SMART JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A2CGB5 ENTREZGENE
  B8JK34 ENTREZGENE
  KDM4D_MOUSE UniProtKB/Swiss-Prot
  Q2M1G7 ENTREZGENE
  Q3U2K5 ENTREZGENE
  Q8BI19 ENTREZGENE
  Z4YLE9 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A2CGB5 UniProtKB/Swiss-Prot
  B8JK34 UniProtKB/Swiss-Prot
  Q2M1G7 UniProtKB/Swiss-Prot
  Q8BI19 UniProtKB/Swiss-Prot