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

    Gene ID: 9869, updated on 20-Feb-2017
    Official Symbol
    SETDB1provided by HGNC
    Official Full Name
    SET domain bifurcated 1provided by HGNC
    Primary source
    HGNC:HGNC:10761
    See related
    Ensembl:ENSG00000143379 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]
    Orthologs
    Location:
    1q21.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 1 NC_000001.11 (150926246..150964744)
    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 ribosomal protein S27a pseudogene 6 Neighboring gene uncharacterized LOC100996521 Neighboring gene uncharacterized LOC107985204 Neighboring gene cytochrome c, somatic pseudogene 51 Neighboring gene ceramide synthase 2 Neighboring gene uncharacterized LOC105371438

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    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 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 Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA0067

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone-lysine N-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    Ras protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone lysine methylation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of methylation-dependent chromatin silencing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to ethanol IEA
    Inferred from Electronic Annotation
    more info
     
    response to vitamin IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    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
    ERG-associated protein with SET domain
    ERG-associated protein with a SET domain, ESET
    H3-K9-HMTase 4
    histone H3-K9 methyltransferase 4
    histone-lysine N-methyltransferase, H3lysine-9 specific 4
    lysine N-methyltransferase 1E
    tudor domain containing 21
    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 identical proteins and their annotated locations for 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
      smart00391
      Location:597672
      MBD; Methyl-CpG binding domain
      smart00468
      Location:679786
      PreSET; N-terminal to some SET domains
      smart00333
      Location:348400
      TUDOR; Tudor domain
      smart00317
      Location:12061268
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    2. NM_001243491.1NP_001230420.1  histone-lysine N-methyltransferase SETDB1 isoform 3

      See identical proteins and their annotated locations for 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
      TUDOR; Tudor domain
    3. NM_012432.3NP_036564.3  histone-lysine N-methyltransferase SETDB1 isoform 2

      See identical proteins and their annotated locations for 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
      smart00391
      Location:597672
      MBD; Methyl-CpG binding domain
      smart00468
      Location:679786
      PreSET; N-terminal to some SET domains
      smart00333
      Location:348400
      TUDOR; Tudor domain
      smart00317
      Location:12061267
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p7 Primary Assembly

      Range
      150926246..150964744
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002953.1XP_016858442.1  histone-lysine N-methyltransferase SETDB1 isoform X1

      Conserved Domains (4) summary
      smart00391
      Location:598673
      MBD; Methyl-CpG binding domain
      smart00468
      Location:680787
      PreSET; N-terminal to some SET domains
      smart00333
      Location:348400
      TUDOR; Tudor domain
      smart00317
      Location:12071269
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    2. XM_005245641.3XP_005245698.1  histone-lysine N-methyltransferase SETDB1 isoform X1

      See identical proteins and their annotated locations for XP_005245698.1

      Conserved Domains (4) summary
      smart00391
      Location:598673
      MBD; Methyl-CpG binding domain
      smart00468
      Location:680787
      PreSET; N-terminal to some SET domains
      smart00333
      Location:348400
      TUDOR; Tudor domain
      smart00317
      Location:12071269
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    3. XM_017002954.1XP_016858443.1  histone-lysine N-methyltransferase SETDB1 isoform X2

      Related
      ENSP00000436148, OTTHUMP00000234729, ENST00000534805, OTTHUMT00000392376
    4. XM_017002955.1XP_016858444.1  histone-lysine N-methyltransferase SETDB1 isoform X3

      UniProtKB/Swiss-Prot
      Q15047
      Conserved Domains (1) summary
      smart00333
      Location:257317
      TUDOR; Tudor domain

    Alternate CHM1_1.1

    Genomic

    1. NC_018912.2 Alternate CHM1_1.1

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