Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	9682
Gene name Gene Name - the full gene name approved by the HGNC.	Lysine demethylase 4A
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	KDM4A
Synonyms (NCBI Gene) Gene synonyms aliases	JHDM3A, JMJD2, JMJD2A, TDRD14A
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p34.2-p34.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demeth

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miRTarBase ID	miRNA	Experiments	Reference
MIRT029498	hsa-miR-26b-5p	Microarray	19088304
MIRT052257	hsa-let-7b-5p	CLASH	23622248
MIRT050862	hsa-miR-17-5p	CLASH	23622248
MIRT041060	hsa-miR-505-3p	CLASH	23622248
MIRT053771	hsa-miR-34a-5p	Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	24802408
MIRT734856	hsa-miR-137	Luciferase reporter assay, qRT-PCR, Western blot	26461474
MIRT734856	hsa-miR-137	Luciferase reporter assay, Western blotting, Immunoprecipitaion (IP), Immunohistochemistry (IHC), qRT-PCR, Flow cytometry, ELISA	33499717
MIRT1084452	hsa-miR-1206	CLIP-seq
MIRT1084453	hsa-miR-1305	CLIP-seq
MIRT1084454	hsa-miR-2115	CLIP-seq
MIRT1084455	hsa-miR-299-5p	CLIP-seq
MIRT1084456	hsa-miR-3155	CLIP-seq
MIRT1084457	hsa-miR-3155b	CLIP-seq
MIRT1084458	hsa-miR-3190	CLIP-seq
MIRT1084459	hsa-miR-3194-3p	CLIP-seq
MIRT1084460	hsa-miR-346	CLIP-seq
MIRT1084461	hsa-miR-3613-3p	CLIP-seq
MIRT1084462	hsa-miR-4255	CLIP-seq
MIRT1084463	hsa-miR-4271	CLIP-seq
MIRT1084464	hsa-miR-4288	CLIP-seq
MIRT1084465	hsa-miR-4328	CLIP-seq
MIRT1084466	hsa-miR-4521	CLIP-seq
MIRT1084467	hsa-miR-4639-5p	CLIP-seq
MIRT1084468	hsa-miR-4698	CLIP-seq
MIRT1084469	hsa-miR-4716-5p	CLIP-seq
MIRT1084470	hsa-miR-4725-3p	CLIP-seq
MIRT1084471	hsa-miR-4733-3p	CLIP-seq
MIRT1084472	hsa-miR-4761-5p	CLIP-seq
MIRT1084473	hsa-miR-4763-5p	CLIP-seq
MIRT1084474	hsa-miR-4789-3p	CLIP-seq
MIRT1084475	hsa-miR-484	CLIP-seq
MIRT1084476	hsa-miR-485-3p	CLIP-seq
MIRT1084477	hsa-miR-495	CLIP-seq
MIRT1084478	hsa-miR-501-3p	CLIP-seq
MIRT1084479	hsa-miR-502-3p	CLIP-seq
MIRT1084480	hsa-miR-516a-3p	CLIP-seq
MIRT1084481	hsa-miR-607	CLIP-seq
MIRT1084482	hsa-miR-624	CLIP-seq
MIRT1084483	hsa-miR-632	CLIP-seq
MIRT1084484	hsa-miR-654-3p	CLIP-seq
MIRT1084485	hsa-miR-659	CLIP-seq
MIRT1084486	hsa-miR-760	CLIP-seq
MIRT1084487	hsa-miR-767-5p	CLIP-seq
MIRT2021418	hsa-miR-1207-3p	CLIP-seq
MIRT2021419	hsa-miR-1250	CLIP-seq
MIRT2021420	hsa-miR-125a-3p	CLIP-seq
MIRT2021421	hsa-miR-1260	CLIP-seq
MIRT2021422	hsa-miR-1260b	CLIP-seq
MIRT2021423	hsa-miR-1343	CLIP-seq
MIRT2021424	hsa-miR-1825	CLIP-seq
MIRT2021425	hsa-miR-200b	CLIP-seq
MIRT2021426	hsa-miR-200c	CLIP-seq
MIRT2021427	hsa-miR-296-5p	CLIP-seq
MIRT2021428	hsa-miR-3064-3p	CLIP-seq
MIRT2021429	hsa-miR-3065-3p	CLIP-seq
MIRT1084460	hsa-miR-346	CLIP-seq
MIRT2021430	hsa-miR-3665	CLIP-seq
MIRT2021431	hsa-miR-3690	CLIP-seq
MIRT2021432	hsa-miR-3919	CLIP-seq
MIRT2021433	hsa-miR-3942-3p	CLIP-seq
MIRT1084464	hsa-miR-4288	CLIP-seq
MIRT2021434	hsa-miR-429	CLIP-seq
MIRT2021435	hsa-miR-4290	CLIP-seq
MIRT2021436	hsa-miR-4470	CLIP-seq
MIRT2021437	hsa-miR-4520a-3p	CLIP-seq
MIRT2021438	hsa-miR-4638-3p	CLIP-seq
MIRT2021439	hsa-miR-4645-5p	CLIP-seq
MIRT2021440	hsa-miR-4673	CLIP-seq
MIRT2021441	hsa-miR-4687-5p	CLIP-seq
MIRT1084469	hsa-miR-4716-5p	CLIP-seq
MIRT2021442	hsa-miR-4742-5p	CLIP-seq
MIRT2021443	hsa-miR-4756-3p	CLIP-seq
MIRT2021444	hsa-miR-526b	CLIP-seq
MIRT1084483	hsa-miR-632	CLIP-seq
MIRT2021445	hsa-miR-634	CLIP-seq
MIRT1084484	hsa-miR-654-3p	CLIP-seq
MIRT2021446	hsa-miR-657	CLIP-seq
MIRT2252935	hsa-miR-1179	CLIP-seq
MIRT2021418	hsa-miR-1207-3p	CLIP-seq
MIRT2252936	hsa-miR-1253	CLIP-seq
MIRT2252937	hsa-miR-1262	CLIP-seq
MIRT2252938	hsa-miR-127-5p	CLIP-seq
MIRT2252939	hsa-miR-146b-3p	CLIP-seq
MIRT2252940	hsa-miR-148a	CLIP-seq
MIRT2252941	hsa-miR-148b	CLIP-seq
MIRT2252942	hsa-miR-152	CLIP-seq
MIRT2252943	hsa-miR-153	CLIP-seq
MIRT2021424	hsa-miR-1825	CLIP-seq
MIRT2252944	hsa-miR-198	CLIP-seq
MIRT2021425	hsa-miR-200b	CLIP-seq
MIRT2021426	hsa-miR-200c	CLIP-seq
MIRT2252945	hsa-miR-23a	CLIP-seq
MIRT2252946	hsa-miR-23b	CLIP-seq
MIRT2252947	hsa-miR-23c	CLIP-seq
MIRT2252948	hsa-miR-298	CLIP-seq
MIRT2252949	hsa-miR-3157-3p	CLIP-seq
MIRT2252950	hsa-miR-3173-5p	CLIP-seq
MIRT2252951	hsa-miR-320e	CLIP-seq
MIRT2252952	hsa-miR-338-3p	CLIP-seq
MIRT1084461	hsa-miR-3613-3p	CLIP-seq
MIRT2252953	hsa-miR-3616-3p	CLIP-seq
MIRT2252954	hsa-miR-3714	CLIP-seq
MIRT2021432	hsa-miR-3919	CLIP-seq
MIRT2021433	hsa-miR-3942-3p	CLIP-seq
MIRT2252955	hsa-miR-3944-5p	CLIP-seq
MIRT1084463	hsa-miR-4271	CLIP-seq
MIRT2021434	hsa-miR-429	CLIP-seq
MIRT2021435	hsa-miR-4290	CLIP-seq
MIRT2252956	hsa-miR-4310	CLIP-seq
MIRT1084465	hsa-miR-4328	CLIP-seq
MIRT2252957	hsa-miR-4436b-3p	CLIP-seq
MIRT2252958	hsa-miR-4492	CLIP-seq
MIRT2252959	hsa-miR-4498	CLIP-seq
MIRT2252960	hsa-miR-455-3p	CLIP-seq
MIRT2252961	hsa-miR-4640-5p	CLIP-seq
MIRT2021439	hsa-miR-4645-5p	CLIP-seq
MIRT2252962	hsa-miR-4652-3p	CLIP-seq
MIRT2021440	hsa-miR-4673	CLIP-seq
MIRT2252963	hsa-miR-4676-5p	CLIP-seq
MIRT2252964	hsa-miR-4691-3p	CLIP-seq
MIRT2252965	hsa-miR-4701-3p	CLIP-seq
MIRT1084469	hsa-miR-4716-5p	CLIP-seq
MIRT2252966	hsa-miR-4721	CLIP-seq
MIRT1084470	hsa-miR-4725-3p	CLIP-seq
MIRT2252967	hsa-miR-4726-5p	CLIP-seq
MIRT2021443	hsa-miR-4756-3p	CLIP-seq
MIRT1084474	hsa-miR-4789-3p	CLIP-seq
MIRT1084476	hsa-miR-485-3p	CLIP-seq
MIRT1084477	hsa-miR-495	CLIP-seq
MIRT2252968	hsa-miR-575	CLIP-seq
MIRT1084484	hsa-miR-654-3p	CLIP-seq
MIRT2252969	hsa-miR-762	CLIP-seq
MIRT2252970	hsa-miR-874	CLIP-seq
MIRT2252935	hsa-miR-1179	CLIP-seq
MIRT2252936	hsa-miR-1253	CLIP-seq
MIRT2252937	hsa-miR-1262	CLIP-seq
MIRT2555914	hsa-miR-1269	CLIP-seq
MIRT2555915	hsa-miR-1269b	CLIP-seq
MIRT2555916	hsa-miR-1288	CLIP-seq
MIRT2555917	hsa-miR-1298	CLIP-seq
MIRT2555918	hsa-miR-145	CLIP-seq
MIRT2252940	hsa-miR-148a	CLIP-seq
MIRT2252941	hsa-miR-148b	CLIP-seq
MIRT2252942	hsa-miR-152	CLIP-seq
MIRT2021424	hsa-miR-1825	CLIP-seq
MIRT2555919	hsa-miR-199a-5p	CLIP-seq
MIRT2555920	hsa-miR-199b-5p	CLIP-seq
MIRT1084454	hsa-miR-2115	CLIP-seq
MIRT1084456	hsa-miR-3155	CLIP-seq
MIRT1084457	hsa-miR-3155b	CLIP-seq
MIRT1084459	hsa-miR-3194-3p	CLIP-seq
MIRT2252955	hsa-miR-3944-5p	CLIP-seq
MIRT2252956	hsa-miR-4310	CLIP-seq
MIRT2555921	hsa-miR-4515	CLIP-seq
MIRT2252961	hsa-miR-4640-5p	CLIP-seq
MIRT2252964	hsa-miR-4691-3p	CLIP-seq
MIRT2252965	hsa-miR-4701-3p	CLIP-seq
MIRT2252967	hsa-miR-4726-5p	CLIP-seq
MIRT1084471	hsa-miR-4733-3p	CLIP-seq
MIRT2555922	hsa-miR-4740-5p	CLIP-seq
MIRT1084473	hsa-miR-4763-5p	CLIP-seq
MIRT1084475	hsa-miR-484	CLIP-seq
MIRT1084480	hsa-miR-516a-3p	CLIP-seq
MIRT1084486	hsa-miR-760	CLIP-seq
MIRT2252935	hsa-miR-1179	CLIP-seq
MIRT2252936	hsa-miR-1253	CLIP-seq
MIRT2252937	hsa-miR-1262	CLIP-seq
MIRT2555914	hsa-miR-1269	CLIP-seq
MIRT2555915	hsa-miR-1269b	CLIP-seq
MIRT2555916	hsa-miR-1288	CLIP-seq
MIRT2555918	hsa-miR-145	CLIP-seq
MIRT2252940	hsa-miR-148a	CLIP-seq
MIRT2252941	hsa-miR-148b	CLIP-seq
MIRT2252942	hsa-miR-152	CLIP-seq
MIRT2021424	hsa-miR-1825	CLIP-seq
MIRT2555919	hsa-miR-199a-5p	CLIP-seq
MIRT2555920	hsa-miR-199b-5p	CLIP-seq
MIRT1084454	hsa-miR-2115	CLIP-seq
MIRT2683270	hsa-miR-3127-5p	CLIP-seq
MIRT1084456	hsa-miR-3155	CLIP-seq
MIRT1084457	hsa-miR-3155b	CLIP-seq
MIRT1084459	hsa-miR-3194-3p	CLIP-seq
MIRT2252955	hsa-miR-3944-5p	CLIP-seq
MIRT2252956	hsa-miR-4310	CLIP-seq
MIRT2555921	hsa-miR-4515	CLIP-seq
MIRT2252961	hsa-miR-4640-5p	CLIP-seq
MIRT2683271	hsa-miR-4668-3p	CLIP-seq
MIRT2683272	hsa-miR-4690-3p	CLIP-seq
MIRT2252964	hsa-miR-4691-3p	CLIP-seq
MIRT2252965	hsa-miR-4701-3p	CLIP-seq
MIRT2252967	hsa-miR-4726-5p	CLIP-seq
MIRT1084471	hsa-miR-4733-3p	CLIP-seq
MIRT2555922	hsa-miR-4740-5p	CLIP-seq
MIRT2683273	hsa-miR-4749-3p	CLIP-seq
MIRT1084473	hsa-miR-4763-5p	CLIP-seq
MIRT1084475	hsa-miR-484	CLIP-seq
MIRT1084480	hsa-miR-516a-3p	CLIP-seq
MIRT2683274	hsa-miR-605	CLIP-seq
MIRT1084486	hsa-miR-760	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IBA
GO:0001650	Component	Fibrillar center	IDA
GO:0005515	Function	Protein binding	IPI	16415788, 16603238, 17567753, 22373579, 27109047, 37179361
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	16024779
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	IMP	21914792
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005721	Component	Pericentric heterochromatin	IEA
GO:0005829	Component	Cytosol	IDA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IBA
GO:0008270	Function	Zinc ion binding	IDA	27214403
GO:0008270	Function	Zinc ion binding	IEA
GO:0010468	Process	Regulation of gene expression	IBA
GO:0010507	Process	Negative regulation of autophagy	IMP	25660547
GO:0010629	Process	Negative regulation of gene expression	IMP	25660547
GO:0014898	Process	Cardiac muscle hypertrophy in response to stress	IEA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0031625	Function	Ubiquitin protein ligase binding	IPI	22373579
GO:0032452	Function	Histone demethylase activity	IEA
GO:0032452	Function	Histone demethylase activity	TAS
GO:0032454	Function	Histone H3K9 demethylase activity	IBA
GO:0032454	Function	Histone H3K9 demethylase activity	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IDA	16024779
GO:0046872	Function	Metal ion binding	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:0051864	Function	Histone H3K36 demethylase activity	IBA
GO:0051864	Function	Histone H3K36 demethylase activity	IDA	16024779, 21914792
GO:0051864	Function	Histone H3K36 demethylase activity	IEA
GO:0140005	Function	Histone H4K20me2 reader activity	IDA	22373579
GO:0140681	Function	Histone H3K36me2/H3K36me3 demethylase activity	IEA
GO:0140684	Function	Histone H3K9me2/H3K9me3 demethylase activity	IEA
GO:0140684	Function	Histone H3K9me2/H3K9me3 demethylase activity	IMP	21914792

MIM	HGNC	e!Ensembl
609764	22978	ENSG00000066135

Protein

UniProt ID

O75164

Protein name

Lysine-specific demethylase 4A (EC 1.14.11.66) (EC 1.14.11.69) (JmjC domain-containing histone demethylation protein 3A) (Jumonji domain-containing protein 2A) ([histone H3]-trimethyl-L-lysine(36) demethylase 4A) ([histone H3]-trimethyl-L-lysine(9) demeth

Protein function

Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code (PubMed:26741168, PubMed:21768309). Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-2

PDB

2GF7 , 2GFA , 2GP3 , 2GP5 , 2OQ6 , 2OQ7 , 2OS2 , 2OT7 , 2OX0 , 2P5B , 2PXJ , 2Q8C , 2Q8D , 2Q8E , 2QQR , 2QQS , 2VD7 , 2WWJ , 2YBK , 2YBP , 2YBS , 3NJY , 3PDQ , 3RVH , 3U4S , 4AI9 , 4BIS , 4GD4 , 4URA , 4V2V , 4V2W , 5A7N , 5A7O , 5A7P , 5A7Q , 5A7S , 5A7W , 5A80 , 5ANQ , 5D6W , 5D6X , 5D6Y , 5F2S , 5F2W , 5F32 , 5F37 , 5F39 , 5F3C , 5F3E , 5F3G , 5F3I

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02375	JmjN	15 → 49	jmjN domain	Family
PF02373	JmjC	175 → 291	JmjC domain, hydroxylase	Domain
PF13831	PHD_2	732 → 767		Family
PF13832	zf-HC5HC2H_2	773 → 884		Domain
PF18104	Tudor_2	902 → 936	Jumonji domain-containing protein 2A Tudor domain	Domain
PF18104	Tudor_2	960 → 994	Jumonji domain-containing protein 2A Tudor domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:15927959}.

Sequence

MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYD
DIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERK
YWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGM
WKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRH
KMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYG
KQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESELP
PRAGNEEECPEEDMEGVEDGEEGDLKTSLAKHRIGTKRHRVCLEIPQEVSQSELFPKEDL
SSEQYEMTECPAALAPVRPTHSSVRQVEDGLTFPDYSDSTEVKFEELKNVKLEEEDEEEE
QAAAALDLSVNPASVGGRLVFSGSKKKSSSSLGSGSSRDSISSDSETSEPLSCRAQGQTG
VLTVHSYAKGDGRVTVGEPCTRKKGSAARSFSERELAEVADEYMFSLEENKKSKGRRQPL
SKLPRHHPLVLQECVSDDETSEQLTPEEEAEETEAWAKPLSQLWQNRPPNFEAEKEFNET
MAQQAPHCAVCMIFQTYHQVEFGGFNQNCGNASDLAPQKQRTKPLIPEMCFTSTGCSTDI
NLSTPYLEEDGTSILVSCKKCSVRVHASCYGVPPAKASEDWMCSRCSANALEEDCCLCSL
RGGALQRANDDRWVHVSCAVAILEARFVNIAERSPVDVSKIPLPRFKLKCIFCKKRRKRT
AGCCVQCSHGRCPTAFHVSCAQAAGVMMQPDDWPFVVFITCFRHKIPNLERAKGALQSIT
AGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEG
EVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELPKRVKSRLSV
ASDMRFNEIFTEKEVKQEKKRQRVINSRYREDYIEPALYRAIME

Sequence length

1064

Interactions

View interactions

	Reactome
			HDMs demethylate histones Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Attention Deficit Hyperactivity Disorder	Attention deficit hyperactivity disorder	N/A	N/A	GWAS
Hypertension	Hypertension risk in short sleep duration	N/A	N/A	GWAS
Schizophrenia	Schizophrenia	N/A	N/A	GWAS

Show/Hide Text Mining Associations (28)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Attention Deficit Disorder with Hyperactivity	Associate	29413154
Breast Neoplasms	Associate	21962223, 35833065
Carcinogenesis	Associate	15927959, 28693517, 29393482, 34111227
Carcinoma Hepatocellular	Associate	32481346, 32883983, 36973424, 39210306
Carcinoma in Situ	Inhibit	21400613
Carcinoma Non Small Cell Lung	Associate	25564517, 26722485
Depressive Disorder	Associate	21962223
Endometrial Neoplasms	Stimulate	24815446
Esophageal Squamous Cell Carcinoma	Associate	36965032
Glioma	Associate	37873881
Hypoxia	Associate	25961932
Intervertebral Disc Degeneration	Associate	35340126
Lung Neoplasms	Associate	26722485
Lymphatic Metastasis	Associate	21400613, 26722485
Lymphoma Primary Effusion	Associate	35914074
Meningioma	Associate	26240495
Nasopharyngeal Carcinoma	Associate	28693517
Neoplasm Invasiveness	Inhibit	21400613
Neoplasm Metastasis	Associate	24815446, 28693517
Neoplasms	Associate	21400613, 21962223, 23871696, 24815446, 26755726, 28212444, 34111227, 37873881, 37988559
Neoplasms	Inhibit	26461474, 36965032
Neuroendocrine Tumors	Associate	29393482
Opioid Related Disorders	Associate	34728798
Prostatic Neoplasms	Associate	24971742, 25189356, 27109047, 29393482, 37165308, 37870957
Prostatic Neoplasms Castration Resistant	Associate	37165308
Prostatitis	Associate	27109047, 37870957
Sarcoma Kaposi	Associate	35914074
Urinary Bladder Neoplasms	Associate	21400613

KDM4A (lysine demethylase 4A)