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    SETDB2 SET domain bifurcated 2 [ Homo sapiens (human) ]

    Gene ID: 83852, updated on 8-Jul-2018
    Official Symbol
    SETDB2provided by HGNC
    Official Full Name
    SET domain bifurcated 2provided by HGNC
    Primary source
    HGNC:HGNC:20263
    See related
    Ensembl:ENSG00000136169 MIM:607865; Vega:OTTHUMG00000016918
    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
    CLLD8; CLLL8; KMT1F; C13orf4
    Summary
    This gene encodes a member of a family of proteins that contain a methyl-CpG-binding domain (MBD) and a SET domain and function as histone methyltransferases. This protein is recruited to heterochromatin and plays a role in the regulation of chromosome segregation. This region is commonly deleted in chronic lymphocytic leukemia. Naturally-occuring readthrough transcription occurs from this gene to the downstream PHF11 (PHD finger protein 11) gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in testis (RPKM 6.5), lymph node (RPKM 5.5) and 25 other tissues See more
    Orthologs
    See SETDB2 in Genome Data Viewer
    Location:
    13q14.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 13 NC_000013.11 (49444293..49495003)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50018429..50069139)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370203 Neighboring gene cytidine and dCMP deaminase domain containing 1 Neighboring gene calcium binding protein 39 like Neighboring gene SETDB2-PHF11 readthrough Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 14 Neighboring gene PHD finger protein 11 Neighboring gene RCC1 and BTB domain containing protein 1

    • 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?

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat associates with SETDB2 in vitro PubMed

    Go to the HIV-1, Human Interaction Database

    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • Histone Modifications, organism-specific biosystem (from WikiPathways)
      Histone Modifications, organism-specific biosystemHistones can undergo many post-translational modifications that are involved in transcription regulation. This pathway provides an overview of various modifications for histones H3 and H4 and the en...
    • Lysine degradation, organism-specific biosystem (from KEGG)
      Lysine degradation, organism-specific biosystem
      Lysine degradation
    • Lysine degradation, conserved biosystem (from KEGG)
      Lysine degradation, conserved biosystem
      Lysine degradation
    • PKMTs methylate histone lysines, organism-specific biosystem (from REACTOME)
      PKMTs methylate histone lysines, organism-specific biosystemLysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM),...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Readthrough SETDB2-PHF11

    Readthrough gene: SETDB2-PHF11, Included gene: PHF11

    Homology

    Clone Names

    • DKFZp586I0123, DKFZp761J1217

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    histone methyltransferase activity (H3-K9 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone-lysine N-methyltransferase activity TAS
    Traceable Author Statement
    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
    cell division IEA
    Inferred from Electronic Annotation
    more info
     
    chromosome segregation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heart looping ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    histone H3-K9 methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    left/right axis specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol 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
    PubMed 
    Preferred Names
    histone-lysine N-methyltransferase SETDB2
    Names
    chronic lymphocytic leukemia deletion region gene 8 protein
    lysine N-methyltransferase 1F
    NP_001153780.1
    NP_001307628.1
    NP_114121.2

    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_001160308.2NP_001153780.1  histone-lysine N-methyltransferase SETDB2 isoform b

      See identical proteins and their annotated locations for NP_001153780.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AL139321, AW297242, BC028202, BC047434, DB164537
      Consensus CDS
      CCDS53868.1
      UniProtKB/Swiss-Prot
      Q96T68
      Related
      ENSP00000326477.9, ENST00000317257.12
      Conserved Domains (3) summary
      smart00317
      Location:618684
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cd01395
      Location:152212
      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:234347
      Pre-SET; Pre-SET motif
    2. NM_001320699.1NP_001307628.1  histone-lysine N-methyltransferase SETDB2 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' region and initiates translation at downstream start codon compared to variant 1. The encoded isoform (c) has a shorter N-terminus than isoform a.
      Source sequence(s)
      AL136218, AL139321
      Related
      ENSP00000482240.1, ENST00000611815.1
      Conserved Domains (3) summary
      smart00317
      Location:618684
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cd01395
      Location:152212
      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:234347
      Pre-SET; Pre-SET motif
    3. NM_031915.2NP_114121.2  histone-lysine N-methyltransferase SETDB2 isoform a

      See identical proteins and their annotated locations for NP_114121.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AF334407, AL139321, AW297242, BC028202, DB164537
      Consensus CDS
      CCDS9417.1
      UniProtKB/Swiss-Prot
      Q96T68
      Related
      ENSP00000346175.5, OTTHUMP00000018417, ENST00000354234.8, OTTHUMT00000044925
      Conserved Domains (3) summary
      smart00317
      Location:630696
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      cd01395
      Location:164224
      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:246359
      Pre-SET; Pre-SET motif

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p12 Primary Assembly

      Range
      49444293..49495003
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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