Setd2 SET domain containing 2, histone lysine methyltransferase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Setd2provided by RGD
Official Full Name: SET domain containing 2, histone lysine methyltransferaseprovided by RGD
Primary source: RGD:1305576
See related: EnsemblRapid:ENSRNOG00000020915 AllianceGenome:RGD:1305576
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable alpha-tubulin binding activity and histone methyltransferase activity (H3-K36 specific). Predicted to be involved in several processes, including defense response to other organism; nucleic acid metabolic process; and peptidyl-lysine methylation. Predicted to act upstream of or within several processes, including animal organ development; histone H3-K36 trimethylation; and tube morphogenesis. Predicted to be located in chromosome and nucleus. Human ortholog(s) of this gene implicated in carcinoma (multiple); gastrointestinal system cancer (multiple); idiopathic pulmonary fibrosis; and malignant mesothelioma. Orthologous to human SETD2 (SET domain containing 2, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 333.0), Spleen (RPKM 295.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q32

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (119390207..119475863)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (110511808..110597475)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (118802478..118888224)

Chromosome 8 - NC_086026.1 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 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?

N6-methyladenosine modification in trophoblasts promotes circSETD2 expression, inhibits miR-181a-5p, and elevates MCL1 transcription to reduce apoptosis of trophoblasts.
Title: N6-methyladenosine modification in trophoblasts promotes circSETD2 expression, inhibits miR-181a-5p, and elevates MCL1 transcription to reduce apoptosis of trophoblasts.
The significance of this study lies in reporting the significantly reduced expression of two proteins: histone-lysine N-methyltransferase (SETD2) and sorting nexin-9 (SNX9) at very early stage (13 weeks) of tumorigenesis, while the full-fledged tumors developed after 6 months.
Title: Reduced expression of SETD2 and SNX9 proteins in chemically induced mammary tumorigenesis in Wistar rats: a prognostic histological and proteomic study.

Submit: New GeneRIF Correction

General gene information

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Markers

RH132638 (e-PCR)
- UniSTS:215921

D8Rat90 (e-PCR), detects polymorphism
- UniSTS:228311

BE118240 (e-PCR)
- UniSTS:248802

UniSTS:236262 (e-PCR)
- UniSTS:236262

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables alpha-tubulin binding	ISO Inferred from Sequence Orthology more info
enables histone H3K36 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein-lysine N-methyltransferase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within angiogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell migration involved in vasculogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within coronary vasculature morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in defense response to virus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic organ development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic placenta morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in endodermal cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mesoderm morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in microtubule cytoskeleton organization involved in mitosis	ISO Inferred from Sequence Orthology more info
involved_in mismatch repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within morphogenesis of a branching structure	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
involved_in nucleosome organization	ISO Inferred from Sequence Orthology more info
involved_in peptidyl-lysine trimethylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within peptidyl-lysine trimethylation	ISO Inferred from Sequence Orthology more info
involved_in peptidyl-lysine trimethylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pericardium development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interferon-alpha production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ossification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of cytokinesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of mRNA export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to chromatin	ISO Inferred from Sequence Orthology more info
involved_in response to alkaloid	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to metal ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to type I interferon	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell development	ISO Inferred from Sequence Orthology more info
involved_in stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within vasculogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in chromosome	IBA Inferred from Biological aspect of Ancestor more info
located_in chromosome	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 SETD2

NP_001388092.1

EC 2.1.1.354

XP_038937538.1

EC 2.1.1.354

XP_063121702.1

EC 2.1.1.354

XP_063121703.1

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_001401163.1 → NP_001388092.1 histone-lysine N-methyltransferase SETD2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

Related

ENSRNOP00000097369.2, ENSRNOT00000113014.2

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_086026.1 Reference GRCr8

Range

119390207..119475863

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063265632.1 → XP_063121702.1 histone-lysine N-methyltransferase SETD2 isoform X2
XM_063265633.1 → XP_063121703.1 histone-lysine N-methyltransferase SETD2 isoform X3

UniProtKB/TrEMBL

A0A8I6AUV5

Related

ENSRNOP00000078840.2, ENSRNOT00000114303.2
XM_039081610.2 → XP_038937538.1 histone-lysine N-methyltransferase SETD2 isoform X1

UniProtKB/TrEMBL

A0A0G2KB10, A0A8I6A709

Related

ENSRNOP00000075606.1, ENSRNOT00000087154.3

Conserved Domains (4) summary

smart00570
Location:1455 → 1509

AWS; associated with SET domains

cd19172
Location:1509 → 1650

SET_SETD2; SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins

pfam00397
Location:2350 → 2379

WW; WW domain

pfam08236
Location:2426 → 2514

SRI; SRI (Set2 Rpb1 interacting) domain