setdb2 SET domain bifurcated histone lysine methyltransferase 2 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: setdb2provided by ZNC
Official Full Name: SET domain bifurcated histone lysine methyltransferase 2provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-7093
See related: AllianceGenome:ZFIN:ZDB-GENE-030131-7093
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:77298; wu:fk80d09
Summary: Enables histone H3K9 methyltransferase activity. Involved in heart looping; left/right axis specification; and negative regulation of DNA-templated transcription. Acts upstream of or within convergent extension involved in gastrulation and determination of left/right symmetry. Predicted to be located in chromosome. Predicted to be active in nucleus. Orthologous to human SETDB2 (SET domain bifurcated histone lysine methyltransferase 2). [provided by Alliance of Genome Resources, Jan 2025]
Annotation information: Annotation category: partial on reference assembly
Orthologs: all
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Genomic context

Location:: chromosome: Un

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	Unplaced Scaffold	NW_003334027.1 (8472..12634)
105	previous assembly	GRCz10 (GCF_000002035.5)	Unplaced Scaffold	NW_003334027.1 (8472..12634)

NW_003334027.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Setdb2 controls convergence and extension movements during zebrafish gastrulation by transcriptional regulation of dvr1.
Title: Setdb2 controls convergence and extension movements during zebrafish gastrulation by transcriptional regulation of dvr1.
essential role for Setdb2-Fgf8 signaling in restricting dorsal organizer territory and regulating left-right asymmetry
Title: Setdb2 restricts dorsal organizer territory and regulates left-right asymmetry through suppressing fgf8 activity.
Setdb2 restricts dorsal organizer territory and regulates left-right asymmetry through suppressing fgf8 activity.
Title: Setdb2 restricts dorsal organizer territory and regulates left-right asymmetry through suppressing fgf8 activity.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables histone H3K9 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9me2 methyltransferase activity	IEA Inferred from Electronic Annotation 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 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 cell division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromosome segregation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within convergent extension involved in gastrulation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within convergent extension involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in left/right axis specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
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
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETDB2

Names: SET domain, bifurcated 2

NP_996941.1

EC 2.1.1.366

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)

NM_207058.1 → NP_996941.1 histone-lysine N-methyltransferase SETDB2

See identical proteins and their annotated locations for NP_996941.1

Status: PROVISIONAL

Source sequence(s)

BC066376

UniProtKB/Swiss-Prot

Q06ZW3, Q6NZ23

Conserved Domains (3) summary

smart00317
Location:332 → 535

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

pfam05033
Location:225 → 324

Pre-SET; Pre-SET motif

cl00110
Location:151 → 205

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...