Smyd1 SET and MYND domain containing 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smyd1provided by RGD
Official Full Name: SET and MYND domain containing 1provided by RGD
Primary source: RGD:1305105
See related: EnsemblRapid:ENSRNOG00000006776 AllianceGenome:RGD:1305105
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable transcription corepressor activity. Predicted to be involved in positive regulation of myoblast differentiation and positive regulation of myotube differentiation. Predicted to act upstream of or within several processes, including chromatin remodeling; negative regulation of DNA-templated transcription; and skeletal muscle cell differentiation. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human SMYD1 (SET and MYND domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Muscle (RPKM 734.3) and Heart (RPKM 704.2) See more
Orthologs: human mouse all
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Genomic context

Location:: 4q32

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (104757281..104811307, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (103195330..103252989, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (99071122..99125143, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Role of Muscle-Specific Histone Methyltransferase (Smyd1) in Exercise-Induced Cardioprotection against Pathological Remodeling after Myocardial Infarction.
Title: Role of Muscle-Specific Histone Methyltransferase (Smyd1) in Exercise-Induced Cardioprotection against Pathological Remodeling after Myocardial Infarction.
Smyd1 is responsible for restricting growth in the adult heart, with its absence leading to cellular hypertrophy, organ remodeling, and fulminate heart failure. Molecular studies reveal Smyd1 to be a muscle-specific regulator of gene expression and indicate that Smyd1 modulates expression of gene isoforms whose expression is associated with cardiac pathology. Activation of Smyd1 can prevent pathological cell growth.
Title: The chromatin-binding protein Smyd1 restricts adult mammalian heart growth.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables histone H3K4 methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within chromatin remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of myoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal muscle cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SMYD1

Names: SET and MYND domain-containing protein 1

NP_001100065.1

EC 2.1.1.354

XP_006236694.1

EC 2.1.1.354

XP_017448024.1

EC 2.1.1.354

XP_038963241.1

EC 2.1.1.354

XP_063141845.1

EC 2.1.1.354

XP_063141846.1

EC 2.1.1.354

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_001106595.1 → NP_001100065.1 histone-lysine N-methyltransferase SMYD1

See identical proteins and their annotated locations for NP_001100065.1

Status: PROVISIONAL

Source sequence(s)

CH473957

UniProtKB/TrEMBL

A0A8I6AQZ0, A6IA68, D4A3D2

Related

ENSRNOP00000009184.5, ENSRNOT00000009184.7

Conserved Domains (2) summary

smart00317
Location:194 → 257

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

pfam01753
Location:52 → 90

zf-MYND; MYND finger

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

104757281..104811307 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063285776.1 → XP_063141846.1 histone-lysine N-methyltransferase SMYD1 isoform X5
XM_039107313.2 → XP_038963241.1 histone-lysine N-methyltransferase SMYD1 isoform X4

UniProtKB/TrEMBL

A0A8I5YCG5, A0A8I6AQZ0

Conserved Domains (1) summary

cd10526
Location:7 → 222

SET_SMYD1; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 1 (SMYD1) and similar proteins
XM_006236632.5 → XP_006236694.1 histone-lysine N-methyltransferase SMYD1 isoform X1

See identical proteins and their annotated locations for XP_006236694.1

UniProtKB/TrEMBL

A0A8I6AKQ9, A0A8I6AQZ0, A6IA67

Conserved Domains (2) summary

smart00317
Location:194 → 244

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

pfam01753
Location:52 → 90

zf-MYND; MYND finger
XM_063285775.1 → XP_063141845.1 histone-lysine N-methyltransferase SMYD1 isoform X3

UniProtKB/TrEMBL

A0A8I6A681
XM_017592535.3 → XP_017448024.1 histone-lysine N-methyltransferase SMYD1 isoform X2

UniProtKB/TrEMBL

A0A8I6AQZ0

Related

ENSRNOP00000086450.2, ENSRNOT00000119454.2