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

Gene Gene information from NCBI Gene database. Gene miRNA Transcription factors Gene ontology Other IDs Protein Pathways
Entrez ID	9869
Gene name	SET domain bifurcated histone lysine methyltransferase 1
Gene symbol	SETDB1
Synonyms (NCBI Gene)	ESETH3-K9-HMTase4KG1TKMT1ETDRD21
Chromosome	1
Chromosome location	1q21.3
Summary	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

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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-seqImmunohistochemistryLuciferase reporter assayNext Generation Sequencing (NGS)qRT-PCRWestern blot	26481868
MIRT059476	hsa-miR-29a-3p	ChIP-seqImmunohistochemistryLuciferase reporter assayNext Generation Sequencing (NGS)qRT-PCRWestern 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

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

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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

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

SETDB1 (SET domain bifurcated histone lysine methyltransferase 1)