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

    Gene ID: 66083, updated on 27-Nov-2024

    Summary

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    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 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 human SETD6 (SET domain containing 6, protein lysine methyltransferase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 5.9), CNS E11.5 (RPKM 5.6) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    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. The nuclear localization pattern and interaction partners of GTF2IRD1 demonstrate a role in chromatin regulation. Carmona-Mora P, et al. Hum Genet, 2015 Oct. PMID 26275350
    3. The Epigenetic Factor Landscape of Developing Neocortex Is Regulated by Transcription Factors Pax6→ Tbr2→ Tbr1. Elsen GE, et al. Front Neurosci, 2018. PMID 30186101, Free PMC Article
    4. Genomic analysis of mouse retinal development. Blackshaw S, et al. PLoS Biol, 2004 Sep. PMID 15226823, Free PMC Article
    5. High-throughput discovery of novel developmental phenotypes. Dickinson ME, et al. Nature, 2016 Sep 22. PMID 27626380, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal.
      Title: SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables NF-kappaB binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 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 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 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)

    1. NM_001035123.4 → NP_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:247 → 286
      SET; SET domain
      pfam09273
      Location:338 → 465
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    2. NM_001368354.1 → NP_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_030243711.2 → XP_030099571.1  N-lysine methyltransferase SETD6 isoform X1

      Conserved Domains (2) summary
      pfam09273
      Location:337 → 460
      Rubis-subs-bind; Rubisco LSMT substrate-binding
      cd19178
      Location:58 → 302
      SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins

    2. XM_036154228.1 → XP_036010121.1  N-lysine methyltransferase SETD6 isoform X2

      Conserved Domains (2) summary
      cd19178
      Location:58 → 281
      SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins
      pfam09273
      Location:316 → 439
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    3. XM_030243712.2 → XP_030099572.1  N-lysine methyltransferase SETD6 isoform X4

      Conserved Domains (2) summary
      pfam09273
      Location:181 → 304
      Rubis-subs-bind; Rubisco LSMT substrate-binding
      cd19178
      Location:1 → 146
      SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins

    4. XM_036154230.1 → XP_036010123.1  N-lysine methyltransferase SETD6 isoform X5

      Conserved Domains (2) summary
      cl40432
      Location:1 → 125
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
      pfam09273
      Location:160 → 283
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    5. XM_036154229.1 → XP_036010122.1  N-lysine methyltransferase SETD6 isoform X3

      Conserved Domains (2) summary
      cd19178
      Location:58 → 281
      SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins
      pfam09273
      Location:316 → 444
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    6. XM_036154231.1 → XP_036010124.1  N-lysine methyltransferase SETD6 isoform X6

      Conserved Domains (2) summary
      cl40432
      Location:1 → 34
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
      pfam09273
      Location:69 → 192
      Rubis-subs-bind; Rubisco LSMT substrate-binding
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9CWY3.1 GenPept UniProtKB/Swiss-Prot:Q9CWY3

    Gene LinkOut

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