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

Gene ID: 9869, updated on 6-Sep-2021

Summary

Official Symbol
SETDB1provided by HGNC
Official Full Name
SET domain bifurcated histone lysine methyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:10761
See related
Ensembl:ENSG00000143379 MIM:604396
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]
Expression
Ubiquitous expression in testis (RPKM 14.6), spleen (RPKM 8.9) and 25 other tissues See more
Orthologs
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Genomic context

See SETDB1 in Genome Data Viewer
Location:
1q21.3
Exon count:
23
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (150926263..150964737)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150898739..150937213)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RPS27A pseudogene 6 Neighboring gene cortexin domain containing 2 Neighboring gene uncharacterized LOC107985204 Neighboring gene CYCS pseudogene 51 Neighboring gene ceramide synthase 2 Neighboring gene CRISPRi-validated cis-regulatory element chr1.8492

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?

Phenotypes

Associated conditions

Description Tests
Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3.
GeneReviews: Not available
New loci associated with kidney function and chronic kidney disease.
GeneReviews: Not available

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0067

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
enables promoter-specific chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in intracellular membrane-bounded organelle 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 IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETDB1
Names
ERG-associated protein with a SET domain, ESET
SET domain bifurcated 1
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_001353346.1
NP_001353347.1
NP_001380887.1
NP_001380888.1
NP_001380889.1
NP_001380890.1
NP_001380893.1
NP_001380894.1
NP_001380895.1
NP_001380896.1
NP_001380897.1
NP_036564.3

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_001145415.2NP_001138887.1  histone-lysine N-methyltransferase SETDB1 isoform 1

    See identical proteins and their annotated locations for NP_001138887.1

    Status: REVIEWED

    Source sequence(s)
    AI582266, D31891, DA418593
    Consensus CDS
    CCDS44217.1
    UniProtKB/Swiss-Prot
    Q15047
    Related
    ENSP00000271640.5, ENST00000271640.9
    Conserved Domains (6) summary
    smart00391
    Location:597672
    MBD; Methyl-CpG binding domain
    cd10517
    Location:674875
    SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl40432
    Location:12021291
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cd21181
    Location:348401
    Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
  2. NM_001243491.2NP_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. Variants 3 and 10-12 all encode the same isoform (3).
    Source sequence(s)
    BC009362, DA418593
    Consensus CDS
    CCDS58026.1
    UniProtKB/Swiss-Prot
    Q15047
    Related
    ENSP00000357958.2, ENST00000368962.6
    Conserved Domains (3) summary
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl02573
    Location:348380
    Tudor_SF; Tudor domain superfamily
  3. NM_001366417.1NP_001353346.1  histone-lysine N-methyltransferase SETDB1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (6) summary
    smart00391
    Location:598673
    MBD; Methyl-CpG binding domain
    cd10517
    Location:675876
    SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl40432
    Location:12031292
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cd21181
    Location:348401
    Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
  4. NM_001366418.1NP_001353347.1  histone-lysine N-methyltransferase SETDB1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (6) summary
    smart00391
    Location:598673
    MBD; Methyl-CpG binding domain
    cd10517
    Location:675876
    SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl40432
    Location:12031292
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cd21181
    Location:348401
    Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
  5. NM_001393958.1NP_001380887.1  histone-lysine N-methyltransferase SETDB1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (6) summary
    smart00391
    Location:598673
    MBD; Methyl-CpG binding domain
    cd10517
    Location:675876
    SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl40432
    Location:12031292
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cd21181
    Location:348401
    Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
  6. NM_001393959.1NP_001380888.1  histone-lysine N-methyltransferase SETDB1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (6) summary
    smart00391
    Location:598673
    MBD; Methyl-CpG binding domain
    cd10517
    Location:675876
    SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl40432
    Location:12031292
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cd21181
    Location:348401
    Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
  7. NM_001393960.1NP_001380889.1  histone-lysine N-methyltransferase SETDB1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (6) summary
    smart00391
    Location:597672
    MBD; Methyl-CpG binding domain
    cd10517
    Location:674875
    SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl40432
    Location:12021291
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cd21181
    Location:348401
    Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
  8. NM_001393961.1NP_001380890.1  histone-lysine N-methyltransferase SETDB1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (4) summary
    smart00391
    Location:598673
    MBD; Methyl-CpG binding domain
    smart00333
    Location:348400
    TUDOR; Tudor domain
    cd10517
    Location:675876
    SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl40432
    Location:12031291
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  9. NM_001393964.1NP_001380893.1  histone-lysine N-methyltransferase SETDB1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (3) summary
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl02573
    Location:348380
    Tudor_SF; Tudor domain superfamily
  10. NM_001393965.1NP_001380894.1  histone-lysine N-methyltransferase SETDB1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (3) summary
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl02573
    Location:348380
    Tudor_SF; Tudor domain superfamily
  11. NM_001393966.1NP_001380895.1  histone-lysine N-methyltransferase SETDB1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (3) summary
    pfam18300
    Location:193250
    DUF5604; Domain of unknown function (DUF5604)
    cd20382
    Location:260341
    Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    cl02573
    Location:348380
    Tudor_SF; Tudor domain superfamily
  12. NM_001393967.1NP_001380896.1  histone-lysine N-methyltransferase SETDB1 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (1) summary
    pfam18300
    Location:193225
    DUF5604; Domain of unknown function (DUF5604)
  13. NM_001393968.1NP_001380897.1  histone-lysine N-methyltransferase SETDB1 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL590133
    Conserved Domains (1) summary
    pfam18300
    Location:193225
    DUF5604; Domain of unknown function (DUF5604)
  14. NM_012432.4NP_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)
    BC028671, D31891, DA418593
    Consensus CDS
    CCDS972.1
    UniProtKB/Swiss-Prot
    Q15047
    Related
    ENSP00000357965.4, ENST00000368969.8
    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

RNA

  1. NR_172060.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL590133

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_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    150926263..150964737
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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