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SETDB1 SET domain, bifurcated 1 [ Homo sapiens (human) ]

Gene ID: 9869, updated on 6-Jul-2014
Official Symbol
SETDB1provided by HGNC
Official Full Name
SET domain, bifurcated 1provided by HGNC
Primary source
HGNC:10761
Locus tag
RP11-316M1.1
See related
Ensembl:ENSG00000143379; HPRD:06828; MIM:604396; Vega:OTTHUMG00000035003
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ESET; KG1T; KMT1E; TDRD21; H3-K9-HMTase4
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 dysfunction likely play a role in the disease pathogenesis. Alternatively spliced transcript variants of this gene have been described.[provided by RefSeq, Jun 2011]
See SETDB1 in Epigenomics, MapViewer
Location:
1q21
Exon count :
22
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 1 NC_000001.11 (150926339..150964913)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150898815..150937389)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100996521 Neighboring gene ribosomal protein S27a pseudogene 6 Neighboring gene cytochrome c, somatic pseudogene 51 Neighboring gene ceramide synthase 2 Neighboring gene annexin A9

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3.
NHGRI GWA Catalog
New loci associated with kidney function and chronic kidney disease.
NHGRI GWA Catalog

Replication interactions

Interaction Pubs
Knockdown of SET domain, bifurcated 1 (SETDB1) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat, p14 tat HIV-1 Tat associates with and is methylated at lysine's 50 and 51 by SETDB1. SETDB1 knockdown increases the transactivation of the HIV-1 LTR PubMed

Go to the HIV-1, Human Protein Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
histone-lysine N-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
bone development IEA
Inferred from Electronic Annotation
more info
 
histone lysine methylation IEA
Inferred from Electronic Annotation
more info
 
inner cell mass cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
chromosome IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 
Preferred Names
histone-lysine N-methyltransferase SETDB1
Names
histone-lysine N-methyltransferase SETDB1
H3-K9-HMTase 4
tudor domain containing 21
lysine N-methyltransferase 1E
histone H3-K9 methyltransferase 4
ERG-associated protein with SET domain
ERG-associated protein with a SET domain, ESET
histone-lysine N-methyltransferase, H3lysine-9 specific 4
NP_001138887.1
NP_001230420.1
NP_036564.3

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001145415.1NP_001138887.1  histone-lysine N-methyltransferase SETDB1 isoform 1

    See proteins identical to NP_001138887.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AI582266, D31891, DA418593
    Consensus CDS
    CCDS44217.1
    UniProtKB/Swiss-Prot
    Q15047
    Related
    ENSP00000271640, OTTHUMP00000032929, ENST00000271640, OTTHUMT00000084717
    Conserved Domains (4) summary
    smart00333
    Location:348400
    Blast Score: 109
    TUDOR; Tudor domain
    smart00317
    Location:12061268
    Blast Score: 208
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd01395
    Location:599660
    Blast Score: 253
    HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...
    pfam05033
    Location:681795
    Blast Score: 316
    Pre-SET; Pre-SET motif
  2. NM_001243491.1NP_001230420.1  histone-lysine N-methyltransferase SETDB1 isoform 3

    See proteins identical to NP_001230420.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, differs in the 3' UTR and lacks a large portion of the coding region, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus and lacks the histone methyltransferase and SET domains, compared to isoform 1.
    Source sequence(s)
    BC009362, DA418593
    Consensus CDS
    CCDS58026.1
    UniProtKB/Swiss-Prot
    Q15047
    Related
    ENSP00000357958, OTTHUMP00000032930, ENST00000368962, OTTHUMT00000084718
    Conserved Domains (1) summary
    smart00333
    Location:257317
    Blast Score: 102
    TUDOR; Tudor domain
  3. NM_012432.3NP_036564.3  histone-lysine N-methyltransferase SETDB1 isoform 2

    See proteins identical to NP_036564.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter protein (isoform 2) compared to isoform 1.
    Source sequence(s)
    AI582266, BC028671, D31891, DA418593
    Consensus CDS
    CCDS972.1
    UniProtKB/Swiss-Prot
    Q15047
    Related
    ENSP00000357965, OTTHUMP00000234730, ENST00000368969, OTTHUMT00000392377
    Conserved Domains (4) summary
    smart00333
    Location:348400
    Blast Score: 109
    TUDOR; Tudor domain
    smart00317
    Location:12061267
    Blast Score: 196
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd01395
    Location:599660
    Blast Score: 253
    HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...
    pfam05033
    Location:681795
    Blast Score: 316
    Pre-SET; Pre-SET motif

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000001.11 

    Range
    150926339..150964913
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005245641.1XP_005245698.1  

    See proteins identical to XP_005245698.1

    Conserved Domains (4) summary
    smart00333
    Location:348400
    Blast Score: 109
    TUDOR; Tudor domain
    smart00317
    Location:12071269
    Blast Score: 208
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd01395
    Location:600661
    Blast Score: 253
    HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...
    pfam05033
    Location:682796
    Blast Score: 316
    Pre-SET; Pre-SET motif
  2. XM_006711672.1XP_006711735.1  

    Conserved Domains (3) summary
    smart00333
    Location:348400
    Blast Score: 107
    TUDOR; Tudor domain
    cd01395
    Location:600661
    Blast Score: 251
    HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...
    cl02622
    Location:680739
    Blast Score: 200
    Pre-SET; Pre-SET motif

Alternate HuRef

Genomic

  1. AC_000133.1 

    Range
    122275918..122314348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 

    Range
    152294142..152332540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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