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

    Gene ID: 84505, updated on 6-Sep-2021

    Summary

    Official Symbol
    Setdb1provided by MGI
    Official Full Name
    SET domain, bifurcated 1provided by MGI
    Primary source
    MGI:MGI:1934229
    See related
    Ensembl:ENSMUSG00000015697
    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
    ESE; 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
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    Genomic context

    See Setdb1 in Genome Data Viewer
    Location:
    3; 3 F2.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (95230836..95264513, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 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_000069.7Genomic Context describing neighboring genes Neighboring gene prune exopolyphosphatase Neighboring gene MINDY lysine 48 deubiquitinase 1 Neighboring gene annexin A9 Neighboring gene predicted gene, 53243 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 Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    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
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone methyltransferase activity (H3-K9 specific) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables histone methyltransferase activity (H3-K9 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone methyltransferase activity (H3-K9 specific) ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone-lysine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone-lysine N-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in Ras protein signal transduction ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within bone development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heterochromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in histone H3-K9 methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within histone H3-K9 trimethylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in histone lysine methylation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within inner cell mass cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA methylation-dependent heterochromatin assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in positive regulation of DNA methylation-dependent heterochromatin assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA methylation-dependent heterochromatin assembly ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in intracellular membrane-bounded organelle 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
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus 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
    XP_036019318.1

    NCBI Reference Sequences (RefSeq)

    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_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
      ENSMUSP00000015841.6, ENSMUST00000015841.12
      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
      ENSMUSP00000102789.4, ENSMUST00000107171.10
      Conserved Domains (6) summary
      smart00391
      Location:614689
      MBD; Methyl-CpG binding domain
      cd10517
      Location:691911
      SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
      cl40432
      Location:12181307
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
      pfam18300
      Location:193250
      DUF5604; Domain of unknown function (DUF5604)
      cd20382
      Location:260341
      Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
      cd21181
      Location:348401
      Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
    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
      ENSMUSP00000102788.3, ENSMUST00000107170.3
      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 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      95230836..95264513 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036163425.1XP_036019318.1  histone-lysine N-methyltransferase SETDB1 isoform X1

      Conserved Domains (6) summary
      smart00391
      Location:614689
      MBD; Methyl-CpG binding domain
      cd10517
      Location:691911
      SET_SETDB1; SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins
      cl40432
      Location:12181307
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
      pfam18300
      Location:193250
      DUF5604; Domain of unknown function (DUF5604)
      cd20382
      Location:260341
      Tudor_SETDB1_rpt1; first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
      cd21181
      Location:348401
      Tudor_SETDB1_rpt2; second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins
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