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    Setd1b SET domain containing 1B, histone lysine methyltransferase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 100359816, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Setd1bprovided by RGD
    Official Full Name
    SET domain containing 1B, histone lysine methyltransferaseprovided by RGD
    Primary source
    RGD:2323325
    See related
    EnsemblRapid:ENSRNOG00000001337 AllianceGenome:RGD:2323325
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable histone H3K4 methyltransferase activity. Predicted to be involved in chromatin remodeling and methylation. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of Set1C/COMPASS complex. Orthologous to human SETD1B (SET domain containing 1B, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 28.0), Thymus (RPKM 21.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Setd1b in Genome Data Viewer
    Location:
    12q16
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (39056809..39082399, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (33395963..33421671, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (38843167..38869180, complement)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, non-ATPase 9 Neighboring gene uncharacterized LOC102547495 Neighboring gene 4-hydroxyphenylpyruvate dioxygenase Neighboring gene ras homolog family member F, filopodia associated Neighboring gene transmembrane protein 120B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation. Bledau AS, et al. Development, 2014 Mar. PMID 24550110
    2. Biochemical reconstitution and phylogenetic comparison of human SET1 family core complexes involved in histone methylation. Shinsky SA, et al. J Biol Chem, 2015 Mar 6. PMID 25561738, Free PMC Article
    3. Identification and characterization of the human Set1B histone H3-Lys4 methyltransferase complex. Lee JH, et al. J Biol Chem, 2007 May 4. PMID 17355966
    4. Wdr82 is a C-terminal domain-binding protein that recruits the Setd1A Histone H3-Lys4 methyltransferase complex to transcription start sites of transcribed human genes. Lee JH, et al. Mol Cell Biol, 2008 Jan. PMID 17998332, Free PMC Article
    5. Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. Wu M, et al. Mol Cell Biol, 2008 Dec. PMID 18838538, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to histone H3K4 methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K4 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Set1C/COMPASS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Set1C/COMPASS complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of histone methyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase SETD1B
    Names
    rCG21620-like

    NCBI Reference Sequences (RefSeq)

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    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_086030.1 Reference GRCr8

      Range
      39056809..39082399 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063271884.1 → XP_063127954.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/TrEMBL
      A0A8I6ANV4, F1LWJ1
      Related
      ENSRNOP00000001807.9, ENSRNOT00000001807.10

    2. XM_039090130.1 → XP_038946058.1  histone-lysine N-methyltransferase SETD1B isoform X2

      UniProtKB/TrEMBL
      A0A8I6ABT2, F1LWJ1
      Related
      ENSRNOP00000089465.1, ENSRNOT00000116702.2
      Conserved Domains (3) summary
      cd19169
      Location:1840 → 1987
      SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins
      pfam11764
      Location:1704 → 1846
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      cd12549
      Location:100 → 192
      RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

    3. XM_039090129.1 → XP_038946057.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/TrEMBL
      A0A8I6ANV4, F1LWJ1
      Related
      ENSRNOP00000094115.1, ENSRNOT00000105357.2
      Conserved Domains (3) summary
      cd19169
      Location:1841 → 1988
      SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins
      pfam11764
      Location:1704 → 1847
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      cd12549
      Location:100 → 192
      RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

    4. XM_063271885.1 → XP_063127955.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/TrEMBL
      A0A8I6ANV4, F1LWJ1
    Nucleotide Protein Strain
    Heading Accession and Version

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