Smyd3 SET and MYND domain containing 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smyd3provided by RGD
Official Full Name: SET and MYND domain containing 3provided by RGD
Primary source: RGD:1562635
See related: EnsemblRapid:ENSRNOG00000066304 AllianceGenome:RGD:1562635
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 RNA polymerase II complex binding activity; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and histone methyltransferase activity. Predicted to be involved in methylation. Predicted to act upstream of or within several processes, including cellular response to dexamethasone stimulus; nucleosome assembly; and regulation of protein phosphorylation. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human SMYD3 (SET and MYND domain containing 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 59.6), Kidney (RPKM 40.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q26

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (93241274..93798221, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (90709263..91266209, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (97330120..97807813, complement)

Chromosome 13 - NC_086031.1 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?

Smyd3-PARP16 axis accelerates unfolded protein response and vascular aging.
Title: Smyd3-PARP16 axis accelerates unfolded protein response and vascular aging.

Submit: New GeneRIF Correction

General gene information

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Markers

BE118607 (e-PCR)
- UniSTS:248855

D13Got81 (e-PCR)
- UniSTS:113713

BE102203 (e-PCR)
- UniSTS:244096

D13Got79 (e-PCR)
- UniSTS:115353

BE117945 (e-PCR)
- UniSTS:248734

BE107361 (e-PCR)
- UniSTS:261542

AU047954 (e-PCR)
- UniSTS:110016

RH141956 (e-PCR)
- UniSTS:223947

RH132992 (e-PCR)
- UniSTS:216275

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II complex binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables histone H3K36 dimethyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H4 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within cellular response to dexamethasone stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of protein localization	ISO Inferred from Sequence Orthology more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within myotube cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of protein kinase activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nucleosome assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of peptidyl-serine phosphorylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	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 SMYD3

Names: SET and MYND domain-containing protein 3

NP_001020933.1

EC 2.1.1.354

XP_038946915.1

EC 2.1.1.354

XP_038946916.1

EC 2.1.1.354

XP_038946917.1

EC 2.1.1.354

XP_063128617.1

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_001025762.1 → NP_001020933.1 histone-lysine N-methyltransferase SMYD3

See identical proteins and their annotated locations for NP_001020933.1

Status: PROVISIONAL

Source sequence(s)

BC097455

UniProtKB/TrEMBL

A6JGF2, Q4V8B9

Related

ENSRNOP00000084109.1, ENSRNOT00000105406.2

Conserved Domains (2) summary

pfam00856
Location:201 → 239

SET; SET domain

pfam01753
Location:49 → 87

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_086031.1 Reference GRCr8

Range

93241274..93798221 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039090987.2 → XP_038946915.1 histone-lysine N-methyltransferase SMYD3 isoform X1

UniProtKB/TrEMBL

A6JGF2

Conserved Domains (2) summary

cd19203
Location:47 → 217

SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins

pfam01753
Location:2 → 36

zf-MYND; MYND finger
XM_039090988.2 → XP_038946916.1 histone-lysine N-methyltransferase SMYD3 isoform X2

UniProtKB/TrEMBL

A6JGF2

Conserved Domains (2) summary

cd19203
Location:44 → 214

SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins

pfam01753
Location:3 → 33

zf-MYND; MYND finger
XM_039090989.2 → XP_038946917.1 histone-lysine N-methyltransferase SMYD3 isoform X3

UniProtKB/TrEMBL

A6JGF3

Conserved Domains (1) summary

cl40432
Location:1 → 120

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
XM_063272547.1 → XP_063128617.1 histone-lysine N-methyltransferase SMYD3 isoform X4

UniProtKB/TrEMBL

A0A8I6ANX2

Related

ENSRNOP00000095032.1, ENSRNOT00000102694.2