Setd6 SET domain containing 6, protein lysine methyltransferase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Setd6provided by RGD
Official Full Name: SET domain containing 6, protein lysine methyltransferaseprovided by RGD
Primary source: RGD:1560538
See related: EnsemblRapid:ENSRNOG00000012447 AllianceGenome:RGD:1560538
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
Also known as: RGD1560538
Summary: Predicted to enable NF-kappaB binding activity; S-adenosyl-L-methionine binding activity; and protein-lysine N-methyltransferase activity. Predicted to be involved in several processes, including negative regulation of NF-kappaB transcription factor activity; peptidyl-lysine monomethylation; and stem cell population maintenance. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human SETD6 (SET domain containing 6, protein lysine methyltransferase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Kidney (RPKM 46.9), Heart (RPKM 37.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p13

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (9349011..9356515, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (9343309..9350477, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (9758613..9766333, complement)

Chromosome 19 - NC_086037.1 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: 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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables NF-kappaB binding	ISO Inferred from Sequence Orthology more info
enables S-adenosyl-L-methionine binding	ISO Inferred from Sequence Orthology more info
enables S-adenosyl-L-methionine binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein-lysine N-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein-lysine N-methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables protein-lysine N-methyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in negative regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of NF-kappaB transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in peptidyl-lysine monomethylation	ISO Inferred from Sequence Orthology more info
involved_in peptidyl-lysine monomethylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in stem cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in stem cell population maintenance	ISO Inferred from Sequence Orthology more info
involved_in stem cell population maintenance	ISS Inferred from Sequence or Structural Similarity 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
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: N-lysine methyltransferase SETD6

Names: SET domain-containing protein 6

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_001106167.1 → NP_001099637.1 N-lysine methyltransferase SETD6

See identical proteins and their annotated locations for NP_001099637.1

Status: PROVISIONAL

Source sequence(s)

CH474006

UniProtKB/Swiss-Prot

D3ZSK5

Related

ENSRNOP00000112070.1, ENSRNOT00000135878.1

Conserved Domains (2) summary

cd19178
Location:59 → 303

SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins

pfam09273
Location:338 → 466

Rubis-subs-bind; Rubisco LSMT substrate-binding

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_086037.1 Reference GRCr8

Range

9349011..9356515 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255070.5 → XP_006255132.1 N-lysine methyltransferase SETD6 isoform X2

Conserved Domains (1) summary

pfam00856
Location:248 → 311

SET; SET domain
XM_039097552.2 → XP_038953480.1 N-lysine methyltransferase SETD6 isoform X3

Conserved Domains (2) summary

cl40432
Location:59 → 124

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

pfam09273
Location:125 → 253

Rubis-subs-bind; Rubisco LSMT substrate-binding
XM_039097550.2 → XP_038953478.1 N-lysine methyltransferase SETD6 isoform X1

Related

ENSRNOP00000016626.5, ENSRNOT00000016626.7

Conserved Domains (2) summary

cd19178
Location:59 → 327

SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins

pfam09273
Location:362 → 490

Rubis-subs-bind; Rubisco LSMT substrate-binding