smyd4 SET and MYND domain containing 4 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: smyd4provided by ZNC
Official Full Name: SET and MYND domain containing 4provided by ZNC
Primary source: ZFIN:ZDB-GENE-060929-248
See related: Ensembl:ENSDARG00000060983 AllianceGenome:ZFIN:ZDB-GENE-060929-248
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: smynd4; zgc:153385
Summary: Enables histone H3K4 methyltransferase activity and histone deacetylase activity. Acts upstream of or within heart looping. Predicted to be active in cytoplasm and nucleus. Is expressed in blood vessel; cardiac ventricle; heart; heart tube; and polster. Used to study congenital heart disease. Orthologous to human SMYD4 (SET and MYND domain containing 4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 10

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (36092600..36104574)
105	previous assembly	GRCz10 (GCF_000002035.5)	10	NC_007121.6 (36148839..36160811)

Chromosome 10 - NC_007121.7 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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See details

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?

smyd4 functions as a histone methyltransferase and, by interacting with HDAC1 serves as a potential modulator for histone acetylation. Transcriptome and bioinformatics analyses of smyd4L544Efs*1 and wild-type developing hearts suggested that smyd4 is a key epigenetic regulator involved in regulating endoplasmic reticulum-mediated protein processing and several important metabolic pathways in developing zebrafish hearts.
Title: The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

fc06b05.x1 (e-PCR)
- UniSTS:192231

fc06b05.x1 (e-PCR)
- UniSTS:192232

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables histone H3K4 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone deacetylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone deacetylase binding	IBA Inferred from Biological aspect of Ancestor 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

Process	Evidence Code	Pubs
acts_upstream_of_or_within determination of heart left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity 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: SET and MYND domain-containing protein 4

NP_001070062.1

EC 2.1.1.-

XP_068079927.1

EC 2.1.1.-

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)

NM_001076594.1 → NP_001070062.1 SET and MYND domain-containing protein 4

See identical proteins and their annotated locations for NP_001070062.1

Status: PROVISIONAL

Source sequence(s)

BC124341

UniProtKB/Swiss-Prot

A5XCC8, Q08C84

UniProtKB/TrEMBL

A0A8M9PTN1

Related

ENSDARP00000080925.4, ENSDART00000086490.7

Conserved Domains (4) summary

sd00006
Location:68 → 96

TPR; TPR repeat [structural motif]

pfam13424
Location:621 → 683

TPR_12; Tetratricopeptide repeat

cd10536
Location:352 → 556

SET_SMYD4; SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins

pfam01753
Location:246 → 285

zf-MYND; MYND finger