SMYD5 SMYD family member 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMYD5provided by HGNC
Official Full Name: SMYD family member 5provided by HGNC
Primary source: HGNC:HGNC:16258
See related: Ensembl:ENSG00000135632 MIM:619114; AllianceGenome:HGNC:16258
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RRG1; RAI15; NN8-4AG; ZMYND23
Summary: Predicted to enable histone H4K20 methyltransferase activity. Involved in regulation of stem cell differentiation and retrotransposon silencing by heterochromatin formation. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in ovary (RPKM 8.4), testis (RPKM 6.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p13.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (73214245..73227221)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (73227234..73240210)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (73441373..73454349)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SMYD5 is a ribosomal methyltransferase that catalyzes RPL40 lysine methylation to enhance translation output and promote hepatocellular carcinoma.
Title: SMYD5 is a ribosomal methyltransferase that catalyzes RPL40 lysine methylation to enhance translation output and promote hepatocellular carcinoma.
SMYD5 methylation of rpL40 links ribosomal output to gastric cancer.
Title: SMYD5 methylation of rpL40 links ribosomal output to gastric cancer.
Negative regulation of SH2B3 by SMYD5 controls epithelial-mesenchymal transition in lung cancer.
Title: Negative regulation of SH2B3 by SMYD5 controls epithelial-mesenchymal transition in lung cancer.
The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11.
Title: The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11.
Sperm chromatin-condensing protamine enhances SMYD5 thermal stability.
Title: Sperm chromatin-condensing protamine enhances SMYD5 thermal stability.
depletion of SMYD5 in human colon and lung cancer cells results in increased tumor growth and upregulation of genes overexpressed in colon and lung cancers, respectively. The findings implicate an important role for SMYD5 in maintaining chromosome integrity by regulating heterochromatin and repressing endogenous repetitive DNA elements during differentiation.
Title: SMYD5 Controls Heterochromatin and Chromosome Integrity during Embryonic Stem Cell Differentiation.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H3K36 trimethyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H4K20 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H4K20 methyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H4K20 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-lysine N-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression, epigenetic	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of gene expression, epigenetic	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytoplasmic translational elongation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of stem cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of stem cell division	ISS Inferred from Sequence or Structural Similarity more info
involved_in transposable element silencing by heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-trimethyltransferase SMYD5

Names: SET and MYND domain-containing protein 5; [histone H4]-lysine20 N-trimethyltransferase SMYD5; retinoic acid induced 15; retinoic acid responsive; retinoic acid-induced protein 15

NP_006053.2

EC 2.1.1.372

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.