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    Setdb1 SET domain, bifurcated 1 [ Mus musculus (house mouse) ]

    Gene ID: 84505, updated on 14-Oct-2018

    Summary

    Official Symbol
    Setdb1provided by MGI
    Official Full Name
    SET domain, bifurcated 1provided by MGI
    Primary source
    MGI:MGI:1934229
    See related
    Ensembl:ENSMUSG00000015697 Vega:OTTMUSG00000046460
    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
    ESET; KMT1E; AU022152; mKIAA0067
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 22.1), limb E14.5 (RPKM 18.8) and 28 other tissues See more
    Orthologs

    Genomic context

    See Setdb1 in Genome Data Viewer
    Location:
    3; 3 F2.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 3 NC_000069.6 (95323525..95357202, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (95127447..95161124, complement)

    Chromosome 3 - NC_000069.6Genomic Context describing neighboring genes Neighboring gene prune exopolyphosphatase Neighboring gene MINDY lysine 48 deubiquitinase 1 Neighboring gene annexin A9 Neighboring gene ceramide synthase 2 Neighboring gene predicted gene, 37500 Neighboring gene RIKEN cDNA 4930558C23 gene Neighboring gene ribosomal protein S2 pseudogene

    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

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC90670

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    histone-lysine N-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    Ras protein signal transduction ISO
    Inferred from Sequence Orthology
    more info
     
    bone development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-K9 trimethylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    histone lysine methylation IEA
    Inferred from Electronic Annotation
    more info
     
    inner cell mass cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    methylation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of methylation-dependent chromatin silencing ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    colocalizes_with nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase SETDB1
    Names
    ERG-associated protein with SET domain
    SET domain ERG-associated histone methyltransferase
    NP_001157113.1
    NP_001157114.1
    NP_061365.3

    NCBI Reference Sequences (RefSeq)

    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_001163641.1NP_001157113.1  histone-lysine N-methyltransferase SETDB1 isoform a

      See identical proteins and their annotated locations for NP_001157113.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AK132202, BC060173, BY074856
      Consensus CDS
      CCDS17613.1
      UniProtKB/TrEMBL
      D3YYC3
      Related
      ENSMUSP00000015841.5, OTTMUSP00000018601, ENSMUST00000015841.11, OTTMUST00000041445
      Conserved Domains (5) summary
      smart00391
      Location:615690
      MBD; Methyl-CpG binding domain
      smart00468
      Location:697804
      PreSET; N-terminal to some SET domains
      smart00333
      Location:348400
      TUDOR; Tudor domain
      smart00317
      Location:12231285
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam11068
      Location:2498
      YlqD; YlqD protein
    2. NM_001163642.1NP_001157114.1  histone-lysine N-methyltransferase SETDB1 isoform b

      See identical proteins and their annotated locations for NP_001157114.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is 1 aa shorter compared to isoform a.
      Source sequence(s)
      AK132202, BC060173, BY074856, CN461297
      Consensus CDS
      CCDS50991.1
      UniProtKB/TrEMBL
      G5E8N3
      Related
      ENSMUSP00000102789.3, OTTMUSP00000018600, ENSMUST00000107171.9, OTTMUST00000041443
      Conserved Domains (5) summary
      smart00391
      Location:614689
      MBD; Methyl-CpG binding domain
      smart00468
      Location:696803
      PreSET; N-terminal to some SET domains
      smart00333
      Location:348400
      TUDOR; Tudor domain
      smart00317
      Location:12221284
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam11068
      Location:2498
      YlqD; YlqD protein
    3. NM_018877.3NP_061365.3  histone-lysine N-methyltransferase SETDB1 isoform a

      See identical proteins and their annotated locations for NP_061365.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AK132202, BC060173, BY074856
      Consensus CDS
      CCDS17613.1
      UniProtKB/TrEMBL
      D3YYC3
      Related
      ENSMUSP00000102788.2, OTTMUSP00000018599, ENSMUST00000107170.2, OTTMUST00000041441
      Conserved Domains (5) summary
      smart00391
      Location:615690
      MBD; Methyl-CpG binding domain
      smart00468
      Location:697804
      PreSET; N-terminal to some SET domains
      smart00333
      Location:348400
      TUDOR; Tudor domain
      smart00317
      Location:12231285
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      pfam11068
      Location:2498
      YlqD; YlqD protein

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000069.6 Reference GRCm38.p4 C57BL/6J

      Range
      95323525..95357202 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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