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

Gene Gene miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	9869
Gene name Gene Name - the full gene name approved by the HGNC.	SET domain bifurcated histone lysine methyltransferase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SETDB1
Synonyms (NCBI Gene) Gene synonyms aliases	ESET, H3-K9-HMTase4, KG1T, KMT1E, TDRD21
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q21.3
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a histone methyltransferase which regulates histone methylation, gene silencing, and transcriptional repression. This gene has been identified as a target for treatment in Huntington Disease, given that gene silencing and transcription d

Show/Hide all(49)

miRTarBase ID	miRNA	Experiments	Reference
MIRT048947	hsa-miR-92a-3p	CLASH	23622248
MIRT045818	hsa-miR-152-3p	CLASH	23622248
MIRT043011	hsa-miR-324-3p	CLASH	23622248
MIRT038516	hsa-miR-296-3p	CLASH	23622248
MIRT052718	hsa-miR-1260b	CLASH	23622248
MIRT439145	hsa-let-7c-5p	3'LIFE	25074381
MIRT439145	hsa-let-7c-5p	3'LIFE	25074381
MIRT059476	hsa-miR-29a-3p	ChIP-seq, Immunohistochemistry, Luciferase reporter assay, Next Generation Sequencing (NGS), qRT-PCR, Western blot	26481868
MIRT059476	hsa-miR-29a-3p	ChIP-seq, Immunohistochemistry, Luciferase reporter assay, Next Generation Sequencing (NGS), qRT-PCR, Western blot	26481868
MIRT1340761	hsa-miR-1972	CLIP-seq
MIRT1340762	hsa-miR-29a	CLIP-seq
MIRT1340763	hsa-miR-29b	CLIP-seq
MIRT1340764	hsa-miR-29c	CLIP-seq
MIRT1340765	hsa-miR-3689a-3p	CLIP-seq
MIRT1340766	hsa-miR-3689c	CLIP-seq
MIRT1340767	hsa-miR-4650-5p	CLIP-seq
MIRT1340768	hsa-miR-4722-3p	CLIP-seq
MIRT1340769	hsa-miR-4728-5p	CLIP-seq
MIRT1340770	hsa-miR-4763-5p	CLIP-seq
MIRT1340771	hsa-miR-621	CLIP-seq
MIRT1340772	hsa-miR-1296	CLIP-seq
MIRT1340761	hsa-miR-1972	CLIP-seq
MIRT1340773	hsa-miR-198	CLIP-seq
MIRT1340762	hsa-miR-29a	CLIP-seq
MIRT1340763	hsa-miR-29b	CLIP-seq
MIRT1340764	hsa-miR-29c	CLIP-seq
MIRT1340774	hsa-miR-3154	CLIP-seq
MIRT1340775	hsa-miR-3202	CLIP-seq
MIRT1340776	hsa-miR-3663-5p	CLIP-seq
MIRT1340777	hsa-miR-4533	CLIP-seq
MIRT1340767	hsa-miR-4650-5p	CLIP-seq
MIRT1340778	hsa-miR-4713-3p	CLIP-seq
MIRT1340768	hsa-miR-4722-3p	CLIP-seq
MIRT1340770	hsa-miR-4763-5p	CLIP-seq
MIRT1340771	hsa-miR-621	CLIP-seq
MIRT2100812	hsa-miR-1200	CLIP-seq
MIRT2100813	hsa-miR-3065-5p	CLIP-seq
MIRT2100814	hsa-miR-3130-5p	CLIP-seq
MIRT2100815	hsa-miR-3667-5p	CLIP-seq
MIRT2100816	hsa-miR-421	CLIP-seq
MIRT2100817	hsa-miR-4324	CLIP-seq
MIRT2100818	hsa-miR-4482	CLIP-seq
MIRT2100819	hsa-miR-544b	CLIP-seq
MIRT2100820	hsa-miR-7	CLIP-seq
MIRT2100821	hsa-miR-873	CLIP-seq
MIRT2325356	hsa-miR-4723-5p	CLIP-seq
MIRT2100821	hsa-miR-873	CLIP-seq
MIRT1340772	hsa-miR-1296	CLIP-seq
MIRT2459173	hsa-miR-4695-3p	CLIP-seq

Transcription factors

Show/Hide all(3)

Transcription factor	Regulation	Reference
DNMT3A	Unknown	16682412
MBD1	Repression	17066076
MBD1	Unknown	15327775

Show/Hide all(36)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IDA	27029610
GO:0005515	Function	Protein binding	IPI	16682412, 17577629, 20871592, 21170338, 23034801, 24705354, 26022416, 27029610, 27732843, 29774127, 32051553, 32296183, 32814053, 33961781, 35512704, 37179361
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	27732843
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	IMP	27732843
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	IMP	27732843
GO:0006325	Process	Chromatin organization	IEA
GO:0006346	Process	DNA methylation-dependent constitutive heterochromatin formation	IEA
GO:0006346	Process	DNA methylation-dependent constitutive heterochromatin formation	IMP	24623306, 27732843
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0010629	Process	Negative regulation of gene expression	IBA
GO:0010629	Process	Negative regulation of gene expression	IDA	39096901
GO:0016740	Function	Transferase activity	IEA
GO:0032259	Process	Methylation	IEA
GO:0042054	Function	Histone methyltransferase activity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0046974	Function	Histone H3K9 methyltransferase activity	IBA
GO:0046974	Function	Histone H3K9 methyltransferase activity	IDA	14536086
GO:0046974	Function	Histone H3K9 methyltransferase activity	IEA
GO:0070828	Process	Heterochromatin organization	IBA
GO:0140938	Function	Histone H3 methyltransferase activity	TAS
GO:0140947	Function	Histone H3K9me2 methyltransferase activity	IEA
GO:0140948	Function	Histone H3K9 monomethyltransferase activity	IEA
GO:0140949	Function	Histone H3K9 trimethyltransferase activity	IDA	14536086
GO:0141005	Process	Transposable element silencing by heterochromatin formation	IDA	37938770
GO:0141005	Process	Transposable element silencing by heterochromatin formation	ISS
GO:0141005	Process	Transposable element silencing by heterochromatin formation	TAS
GO:1990841	Function	Promoter-specific chromatin binding	IDA	24623306
GO:1990841	Function	Promoter-specific chromatin binding	IEA

MIM	HGNC	e!Ensembl
604396	10761	ENSG00000143379

Protein

UniProt ID

Q15047

Protein name

Histone-lysine N-methyltransferase SETDB1 (EC 2.1.1.366) (ERG-associated protein with SET domain) (ESET) (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (Lysine N-methyltransferase 1E) (SET domain bifurcated 1)

Protein function

Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated hist

PDB

3DLM , 4X3S , 5KCH , 5KCO , 5KE2 , 5KE3 , 5KH6 , 5QT1 , 5QT2 , 6AU2 , 6AU3 , 6BHD , 6BHE , 6BHG , 6BHH , 6BHI , 6BPI , 7C9N , 7CAJ , 7CD9 , 7CJT , 8G5E , 8IYA , 8UWP , 9CUW , 9CUX

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF18300	DUF5604	193 → 250	Domain of unknown function (DUF5604)	Domain
PF18359	TUDOR_5	258 → 309	Histone methyltransferase Tudor domain 1	Domain
PF18358	Tudor_4	348 → 397	Histone methyltransferase Tudor domain	Domain
PF01429	MBD	594 → 668	Methyl-CpG binding domain	Domain
PF05033	Pre-SET	682 → 795	Pre-SET motif	Family
PF00856	SET	814 → 1266	SET domain	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. High expression in testis.

Sequence

MSSLPGCIGLDAATATVESEEIAELQQAVVEELGISMEELRHFIDEELEKMDCVQQRKKQ
LAELETWVIQKESEVAHVDQLFDDASRAVTNCESLVKDFYSKLGLQYRDSSSEDESSRPT
EIIEIPDEDDDVLSIDSGDAGSRTPKDQKLREAMAALRKSAQDVQKFMDAVNKKSSSQDL
HKGTLSQMSGELSKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKS
LLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDG
YASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEG
TWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMKTSSASALEKKQGQLRTRP
NMGAVRSKGPVVQYTQDLTGTGTQFKPVEPPQPTAPPAPPFPPAPPLSPQAGDSDLESQL
AQSRKQVAKKSTSFRPGSVGSGHSSPTSPALSENVSGGKPGINQTYRSPLGSTASAPAPS
ALPAPPAPPVFHGMLERAPAEPSYRAPMEKLFYLPHVCSYTCLSRVRPMRNEQYRGKNPL
LVPLLYDFRRMTARRRVNRKMGFHVIYKTPCGLCLRTMQEIERYLFETGCDFLFLEMFCL
DPYVLVDRKFQPYKPFYYILDITYGKEDVPLSCVNEIDTTPPPQVAYSKERIPGKGVFIN
TGPEFLVGCDCKDGCRDKSKCACHQLTIQATACTPGGQINPNSGYQYKRLEECLPTGVYE
CNKRCKCDPNMCTNRLVQHGLQVRLQLFKTQNKGWGIRCLDDIAKGSFVCIYAGKILTDD
FADKEGLEMGDEYFANLDHIESVENFKEGYESDAPCSSDSSGVDLKDQEDGNSGTEDPEE
SNDDSSDDNFCKDEDFSTSSVWRSYATRRQTRGQKENGLSETTSKDSHPPDLGPPHIPVP
PSIPVGGCNPPSSEETPKNKVASWLSCNSVSEGGFADSDSHSSFKTNEGGEGRAGGSRME
AEKASTSGLGIKDEGDIKQAKKEDTDDRNKMSVVTESSRNYGYNPSPVKPEGLRRPPSKT
SMHQSRRLMASAQSNPDDVLTLSSSTESEGESGTSRKPTAGQTSATAVDSDDIQTISSGS
EGDDFEDKKNMTGPMKRQVAVKSTRGFALKSTHGIAIKSTNMASVDKGESAPVRKNTRQF
YDGEESCYIIDAKLEGNLGRYLNHSCSPNLFVQNVFVDTHDLRFPWVAFFASKRIRAGTE
LTWDYNYEVGSVEGKELLCCCGAIECRGRLL

Sequence length

1291

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Metabolic pathways Signaling pathways regulating pluripotency of stem cells		PKMTs methylate histone lysines

Show/Hide Unknown Diseases (2)

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.
Alzheimer disease	Alzheimer's disease or family history of Alzheimer's disease	N/A	N/A	GWAS
Myocardial Infarction	Myocardial infarction	N/A	N/A	GWAS

Show/Hide Text Mining Associations (50)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	35474385
Asthma	Associate	37569643
Astrocytoma	Associate	34296393
Autism Spectrum Disorder	Associate	27119313
Autism Spectrum Disorder	Stimulate	35682642
Autistic Disorder	Associate	23055267
Breast Neoplasms	Associate	26840455, 30545440, 31735020, 35395812
Breast Neoplasms	Stimulate	32305991
Carcinogenesis	Associate	27164857
Carcinoma Hepatocellular	Stimulate	27164857
Carcinoma Hepatocellular	Associate	31811111, 33355042, 34843122
Carcinoma Non Small Cell Lung	Associate	26536195, 30054425
Cholangiocarcinoma	Associate	30983519
Cockayne Syndrome	Associate	31276581
Colorectal Neoplasms	Associate	31896605
COVID 19	Associate	34299101
Encephalitis	Associate	35682642
Epilepsy	Associate	23055267
Fibrosis	Associate	31811111
Glioblastoma	Associate	36077559
Glioma	Associate	25602259
Hereditary Breast and Ovarian Cancer Syndrome	Associate	26840455
Hypoxia	Associate	25961932, 37850636
Hypoxia Brain	Associate	37850636
Inflammation	Associate	37850636
Interferon gamma receptor 1 deficiency	Associate	34299101
Leukemia Myeloid Acute	Associate	28887438, 29066607
Lung Neoplasms	Associate	35474385
Lymphatic Metastasis	Associate	32305991
Lymphatic Metastasis	Stimulate	36436682
Melanoma	Associate	21983785, 31630191, 34906316
Mesothelioma	Associate	37369845
Mesothelioma Malignant	Associate	26824986, 34648949, 38630790
Mitochondrial Diseases	Associate	31276581
Multiple Myeloma	Stimulate	35372573
Multiple Sclerosis	Associate	36992419
Neoplasm Metastasis	Stimulate	27164857
Neoplasm Metastasis	Associate	36436682
Neoplasms	Stimulate	25602259, 28887438
Neoplasms	Associate	29066607, 32305991, 33676569, 34162889, 34843122, 34906316, 35372573, 35864175
Neoplasms	Inhibit	37369845
Neuroinflammatory Diseases	Associate	36992419
Prader Willi Syndrome	Associate	24760766
Prostatic Neoplasms	Stimulate	24556744
Prostatitis	Associate	24556744
Purpura Thrombocytopenic Idiopathic	Stimulate	37628621
Stomach Neoplasms	Associate	34108525
Triple Negative Breast Neoplasms	Associate	37970920
Urinary Bladder Neoplasms	Associate	36436682
von Hippel Lindau Disease	Associate	37850636

SETDB1 (SET domain bifurcated histone lysine methyltransferase 1)