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setdb1a SET domain bifurcated histone lysine methyltransferase 1a [ Danio rerio (zebrafish) ]

Gene ID: 553292, updated on 9-Dec-2024

Summary

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Official Symbol
setdb1aprovided by ZNC
Official Full Name
SET domain bifurcated histone lysine methyltransferase 1aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-2421
See related
Ensembl:ENSDARG00000041243 AllianceGenome:ZFIN:ZDB-GENE-030131-2421
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
SETDB1; fc07d03; wu:fc07d03; si:ch211-81a5.6
Summary
Predicted to enable histone H3K9 methyltransferase activity and promoter-specific chromatin binding activity. Predicted to be involved in heterochromatin organization; negative regulation of gene expression; and positive regulation of DNA methylation-dependent heterochromatin formation. Predicted to act upstream of or within chromatin organization and methylation. Predicted to be located in chromosome. Predicted to be active in nucleus. Is expressed in telencephalon. Human ortholog(s) of this gene implicated in autistic disorder and lung cancer. Orthologous to human SETDB1 (SET domain bifurcated histone lysine methyltransferase 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs
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Genomic context

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See setdb1a in Genome Data Viewer
Location:
chromosome: 19
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (9111548..9144392)
105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (9192623..9225467)

Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene ash1 (absent, small, or homeotic)-like (Drosophila) Neighboring gene leucine rich repeat containing 71 Neighboring gene CDC-like kinase 2a Neighboring gene si:ch211-81a5.8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. m(6)A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Zhao BS, et al. Nature, 2017 Feb 23. PMID 28192787, Free PMC Article
  2. Ythdf m(6)A Readers Function Redundantly during Zebrafish Development. Kontur C, et al. Cell Rep, 2020 Dec 29. PMID 33378672, Free PMC Article
  3. In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish. Xiong Z, et al. Elife, 2021 Feb 16. PMID 33591275, Free PMC Article
  4. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. Sun XJ, et al. PLoS One, 2008 Jan 30. PMID 18231586, Free PMC Article
  5. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K9 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables promoter-specific chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in heterochromatin organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
histone-lysine N-methyltransferase SETDB1-A
Names
SET domain, bifurcated 1a
NP_001038232.1

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_001044767.2 → NP_001038232.1  histone-lysine N-methyltransferase SETDB1-A

    See identical proteins and their annotated locations for NP_001038232.1

    Status: VALIDATED

    Source sequence(s)
    CR626935
    UniProtKB/Swiss-Prot
    Q1L8U8
    Related
    ENSDARP00000082769.5, ENSDART00000088336.6
    Conserved Domains (4) summary
    smart00317
    Location:1348 → 1413
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd01395
    Location:943 → 1003
    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:1030 → 1143
    Pre-SET; Pre-SET motif
    pfam15323
    Location:394 → 525
    Ashwin; Developmental protein

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007130.7 Reference GRCz11 Primary Assembly

    Range
    9111548..9144392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q1L8U8.1 GenPept UniProtKB/Swiss-Prot:Q1L8U8

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