U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 291844, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
Setd6provided by RGD
Official Full Name
SET domain containing 6, protein lysine methyltransferaseprovided by RGD
Primary source
RGD:1560538
See related
Ensembl: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 methylation; 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, Apr 2022]
Expression
Biased expression in Kidney (RPKM 46.9), Heart (RPKM 37.0) and 9 other tissues See more
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See Setd6 in Genome Data Viewer
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_086037.1Genomic Context describing neighboring genes Neighboring gene CCR4-NOT transcription complex, subunit 1 Neighboring gene small nucleolar RNA SNORA50 Neighboring gene small nucleolar RNA, H/ACA box 46 Neighboring gene uncharacterized LOC120098501 Neighboring gene NDRG family member 4 Neighboring gene gem (nuclear organelle) associated protein 8, pseudogene 10

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal. Binda O, et al. Epigenetics, 2013 Feb. PMID 23324626, Free PMC Article
  2. Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Levy D, et al. Nat Immunol, 2011 Jan. PMID 21131967, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

Pathways from PubChem

Go to the top of the page

General gene information

Go to the top of the page Help

Markers

Homology

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 peptidyl-lysine monomethylation IBA
Inferred from Biological aspect of Ancestor
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

Go to the top of the page Help
Preferred Names
N-lysine methyltransferase SETD6
Names
SET domain-containing protein 6

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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)

  1. 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
    ENSRNOP00000016626.4, ENSRNOT00000016626.6
    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

  1. NC_086037.1 Reference GRCr8

    Range
    9349011..9356515 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    pfam00856
    Location:248 → 311
    SET; SET domain

  2. 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

  3. XM_039097550.2 → XP_038953478.1  N-lysine methyltransferase SETD6 isoform X1

    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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
D3ZSK5.1 GenPept UniProtKB/Swiss-Prot:D3ZSK5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous