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

Gene ID: 100359816, updated on 18-Sep-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 RNA binding activity. Predicted to contribute to histone methyltransferase activity (H3-K4 specific). Predicted to be involved in histone H3-K4 dimethylation; histone H3-K4 monomethylation; and histone H3-K4 trimethylation. Predicted to be located in 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, Apr 2022]
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 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
  
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 ISO
Inferred from Sequence Orthology
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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