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

Gene ID: 83852, updated on 19-Sep-2021

Summary

Official Symbol
SETDB2provided by HGNC
Official Full Name
SET domain bifurcated histone lysine methyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:20263
See related
Ensembl:ENSG00000136169 MIM:607865
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
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Genomic context

See SETDB2 in Genome Data Viewer
Location:
13q14.2
Exon count:
16
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (49444274..49495003)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50018410..50069139)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene cytidine and dCMP deaminase domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 13963 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

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables histone methyltransferase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone methyltransferase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
enables histone-lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cell division IEA
Inferred from Electronic Annotation
more info
 
involved_in chromosome segregation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in heart looping ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in heterochromatin organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H3-K9 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H3-K9 methylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in left/right axis specification ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of DNA methylation-dependent heterochromatin assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETDB2
Names
SET domain bifurcated 2
chronic lymphocytic leukemia deletion region gene 8 protein
lysine N-methyltransferase 1F
NP_001153780.1
NP_001307628.1
NP_001380904.1
NP_001380905.1
NP_001380906.1
NP_001380907.1
NP_001380908.1
NP_001380909.1
NP_114121.2

NCBI Reference Sequences (RefSeq)

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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_001160308.3NP_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)
    AL136218, 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_001320699.2NP_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_001393975.1NP_001380904.1  histone-lysine N-methyltransferase SETDB2 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL136218, AL139321
    Conserved Domains (2) summary
    cd01395
    Location:140200
    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 ...
    cd10523
    Location:198694
    SET_SETDB2; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins
  4. NM_001393976.1NP_001380905.1  histone-lysine N-methyltransferase SETDB2 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL136218, AL139321
    Conserved Domains (2) summary
    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 ...
    cd10523
    Location:210561
    SET_SETDB2; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins
  5. NM_001393977.1NP_001380906.1  histone-lysine N-methyltransferase SETDB2 isoform f

    Status: REVIEWED

    Source sequence(s)
    AL136218
    Conserved Domains (2) summary
    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 ...
    cl40432
    Location:222433
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  6. NM_001393978.1NP_001380907.1  histone-lysine N-methyltransferase SETDB2 isoform g

    Status: REVIEWED

    Source sequence(s)
    AL136218, AL139321
    Conserved Domains (2) summary
    cd01395
    Location:140200
    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 ...
    cd10523
    Location:198549
    SET_SETDB2; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins
  7. NM_001393979.1NP_001380908.1  histone-lysine N-methyltransferase SETDB2 isoform h

    Status: REVIEWED

    Source sequence(s)
    AL136218
    Conserved Domains (2) summary
    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 ...
    cl40432
    Location:210421
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  8. NM_001393980.1NP_001380909.1  histone-lysine N-methyltransferase SETDB2 isoform i

    Status: REVIEWED

    Source sequence(s)
    AL136218
    Conserved Domains (2) summary
    cd01395
    Location:140200
    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 ...
    cl40432
    Location:198409
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  9. NM_031915.3NP_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) encodes the longest isoform (a).
    Source sequence(s)
    AF334407, AL136218, AL139321, AW297242, BC028202, DB164537
    Consensus CDS
    CCDS9417.1
    UniProtKB/Swiss-Prot
    Q96T68
    Related
    ENSP00000346175.5, ENST00000354234.8
    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

RNA

  1. NR_172062.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL136218, AL139321

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    49444274..49495003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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