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Setd6 SET domain containing 6 [ Mus musculus (house mouse) ]

Gene ID: 66083, updated on 4-May-2024

Summary

Official Symbol
Setd6provided by MGI
Official Full Name
SET domain containing 6provided by MGI
Primary source
MGI:MGI:1913333
See related
Ensembl:ENSMUSG00000031671 AllianceGenome:MGI:1913333
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
0610039J04Rik; 3110004G14Rik
Summary
Predicted to enable NF-kappaB binding activity; S-adenosyl-L-methionine binding activity; and protein-lysine N-methyltransferase activity. Involved in stem cell differentiation and stem cell population maintenance. Predicted to be located in chromosome; cytosol; and nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and neural retina. Orthologous to several human genes including SETD6 (SET domain containing 6, protein lysine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in adrenal adult (RPKM 5.9), CNS E11.5 (RPKM 5.6) and 28 other tissues See more
Orthologs
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Genomic context

See Setd6 in Genome Data Viewer
Location:
8 D1; 8 47.17 cM
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (96442211..96448135)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (95715634..95721507)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene gem (nuclear organelle) associated protein 8 pseudogene Neighboring gene N-myc downstream regulated gene 4 Neighboring gene predicted gene, 51585 Neighboring gene CCR4-NOT transcription complex, subunit 1 Neighboring gene predicted gene, 26493 Neighboring gene microRNA 7073

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (2) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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 methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of NF-kappaB transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in peptidyl-lysine methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in peptidyl-lysine monomethylation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in peptidyl-lysine monomethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of inflammatory response ISO
Inferred from Sequence Orthology
more info
 
involved_in stem cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in stem cell population maintenance IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in cytosol ISO
Inferred from Sequence Orthology
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

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)

  1. NM_001035123.4NP_001030295.1  N-lysine methyltransferase SETD6 isoform 1

    See identical proteins and their annotated locations for NP_001030295.1

    Status: VALIDATED

    Source sequence(s)
    AC113951
    Consensus CDS
    CCDS22566.1
    UniProtKB/Swiss-Prot
    B2RTA7, Q8C6I1, Q9CWY3
    Related
    ENSMUSP00000034096.5, ENSMUST00000034096.6
    Conserved Domains (2) summary
    pfam00856
    Location:247286
    SET; SET domain
    pfam09273
    Location:338465
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  2. NM_001368354.1NP_001355283.1  N-lysine methyltransferase SETD6 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC113951

RNA

  1. NR_160790.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC113951
  2. NR_160791.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC113951
  3. NR_160792.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC113951

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    96442211..96448135
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030243711.2XP_030099571.1  N-lysine methyltransferase SETD6 isoform X1

    Conserved Domains (2) summary
    pfam09273
    Location:337460
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19178
    Location:58302
    SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins
  2. XM_036154228.1XP_036010121.1  N-lysine methyltransferase SETD6 isoform X2

    Conserved Domains (2) summary
    cd19178
    Location:58281
    SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins
    pfam09273
    Location:316439
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  3. XM_030243712.2XP_030099572.1  N-lysine methyltransferase SETD6 isoform X4

    Conserved Domains (2) summary
    pfam09273
    Location:181304
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19178
    Location:1146
    SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins
  4. XM_036154230.1XP_036010123.1  N-lysine methyltransferase SETD6 isoform X5

    Conserved Domains (2) summary
    cl40432
    Location:1125
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam09273
    Location:160283
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  5. XM_036154229.1XP_036010122.1  N-lysine methyltransferase SETD6 isoform X3

    Conserved Domains (2) summary
    cd19178
    Location:58281
    SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins
    pfam09273
    Location:316444
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  6. XM_036154231.1XP_036010124.1  N-lysine methyltransferase SETD6 isoform X6

    Conserved Domains (2) summary
    cl40432
    Location:134
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    pfam09273
    Location:69192
    Rubis-subs-bind; Rubisco LSMT substrate-binding