• Gene id: 55693

Gene Summary

• Gene Symbol: KDM4D   Gene   UCSC   Ensembl
• Aliases: JMJD2D
• Gene name: lysine demethylase 4D
• Alternate names: lysine-specific demethylase 4D, jmjC domain-containing histone demethylation protein 3D, jumonji domain containing 2D, jumonji domain-containing protein 2D, lysine (K)-specific demethylase 4D,
• Gene location: 11q21 (94973708: 94999518)     Exons: 3     NC_000011.10
• OMIM: 609766

Protein Summary

• Protein general information: Q6B0I6  
  • Name: Lysine specific demethylase 4D (EC 1.14.11. ) (JmjC domain containing histone demethylation protein 3D) (Jumonji domain containing protein 2D)
  • Length: 523  
  • Mass: 58603
• Sequence:

  METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPL
  QQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTK
  QWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLER
  LARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRW
  IDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDRAVVDHMEPRVPASQELSTQKEVQLPRRAALGLR
  QLPSHWARHSPWPMAARSGTRCHTLVCSSLPRRSAVSGTATQPRAAAVHSSKKPSSTPSSTPGPSAQIIHPSNGR
  RGRGRPPQKLRAQELTLQTPAKRPLLAGTTCTASGPEPEPLPEDGALMDKPVPLSPGLQHPVKASGCSWAPVP

• Structural information:
  • Protein Domains: (18..6-)
    (/note="JmjN-)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00537-)
    (146..31-)
    (/note="JmjC-)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00538"-)
  • Interpro: IPR003347  IPR003349  
  • Prosite: PS51184 PS51183
  • PDB: 3DXT 3DXU 4D6Q 4D6R 4D6S 4HON 4HOO 5F5A 5F5C 5FP4 5FP7 5FP8 5FP9 5FPA 5FPB 5PH0 5PH1 5PH2 5PH3 5PH4 5PH5 5PH6 5PH7 5PH8 5PH9 5PHA 5PHB 5PHC 5PHD 5PHE 5PHF 5PHG 5PHH 5PHI 5PHJ 5PHK 5PHL 5PHM 5PHN 5PHO 5PHP 5PHQ 5PHR 5PHS 5PHT 5PHU 5PHV 5PHW 5PHX 5PHY 5PHZ 5PI0 5PI1 5PI2 5PI3 5PI4 5PI5 5PI6 5PI7 5PI8 5PI9 5PIA 5PIB 5PI
  • PDBsum: 3DXT 3DXU 4D6Q 4D6R 4D6S 4HON 4HOO 5F5A 5F5C 5FP4 5FP7 5FP8 5FP9 5FPA 5FPB 5PH0 5PH1 5PH2 5PH3 5PH4 5PH5 5PH6 5PH7 5PH8 5PH9 5PHA 5PHB 5PHC 5PHD 5PHE 5PHF 5PHG 5PHH 5PHI 5PHJ 5PHK 5PHL 5PHM 5PHN 5PHO 5PHP 5PHQ 5PHR 5PHS 5PHT 5PHU 5PHV 5PHW 5PHX 5PHY 5PHZ 5PI0 5PI1 5PI2 5PI3 5PI4 5PI5 5PI6 5PI7 5PI8 5PI9 5PIA 5PIB 5PI
  • DIP: 29606
  • STRING: ENSP00000334181
• Other Databases: GeneCards:  KDM4D  Malacards:  KDM4D

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0032454	histone demethylase activity (H3-K9 specific)	IBA	molecular function
GO:0035097	histone methyltransferase complex	IBA	cellular component
GO:0005634	nucleus	IBA	cellular component
GO:0006338	chromatin remodeling	IBA	biological process
GO:0032452	histone demethylase activity	IBA	molecular function
GO:0006325	chromatin organization	IEA	biological process
GO:0046872	metal ion binding	IEA	molecular function
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0016491	oxidoreductase activity	IEA	molecular function
GO:0005634	nucleus	IEA	cellular component
GO:0051213	dioxygenase activity	IEA	molecular function
GO:0032454	histone demethylase activity (H3-K9 specific)	IEA	molecular function
GO:0035861	site of double-strand break	IDA	cellular component
GO:2001034	positive regulation of double-strand break repair via nonhomologous end joining	IMP	biological process
GO:0071479	cellular response to ionizing radiation	IMP	biological process
GO:0035563	positive regulation of chromatin binding	IMP	biological process
GO:0001932	regulation of protein phosphorylation	IMP	biological process
GO:0000724	double-strand break repair via homologous recombination	IMP	biological process
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:0032454	histone demethylase activity (H3-K9 specific)	IDA	molecular function
GO:0033169	histone H3-K9 demethylation	IDA	biological process
GO:0033169	histone H3-K9 demethylation	IEA	biological process
GO:0032454	histone demethylase activity (H3-K9 specific)	IEA	molecular function
GO:0005721	pericentric heterochromatin	IEA	cellular component
GO:1900113	negative regulation of histone H3-K9 trimethylation	IEA	biological process
GO:0035861	site of double-strand break	IEA	cellular component
GO:0032452	histone demethylase activity	IEA	molecular function
GO:0031490	chromatin DNA binding	IEA	molecular function
GO:0006974	cellular response to DNA damage stimulus	IEA	biological process
GO:0005634	nucleus	IEA	cellular component
GO:0003684	damaged DNA binding	IEA	molecular function
GO:0005634	nucleus	IEA	cellular component
GO:0032454	histone demethylase activity (H3-K9 specific)	IDA	molecular function
GO:0033169	histone H3-K9 demethylation	IDA	biological process
GO:0072562	blood microparticle	HDA	cellular component

Diseases

Associated diseases	References
nephroblastoma	PMID:24219278
Non obstructive azoospermia	MIK: 23869807
Sertoli cell only syndrome	MIK: 23869807
Spermatogenic defects	MIK: 31037746
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17327269	Teratozoospermia			19 (6 controls, 13 cases)	Male infertility	GSE6872 analyzed by GEO2R (cutoff 1.5 fold)
23869807	Non obstructive azoospermia, Sertoli cell only syndrome			20 (4 controls, 16 cases)	Male infertility	GSE45887 analyzed by GEO2R (cutoff 1.5 fold)
31037746	Spermatogenic defects			28 men with azoospermia	Male infertility	Microarray