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Setdb2 SET domain, bifurcated 2 [ Mus musculus (house mouse) ]

Gene ID: 239122, updated on 2-Apr-2024

Summary

Official Symbol
Setdb2provided by MGI
Official Full Name
SET domain, bifurcated 2provided by MGI
Primary source
MGI:MGI:2685139
See related
Ensembl:ENSMUSG00000071350 AllianceGenome:MGI:2685139
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
Clld8; Gm293; KMT1F
Summary
Predicted to enable histone methyltransferase activity (H3-K9 specific). Predicted to be involved in several processes, including heterochromatin organization; histone H3-K9 methylation; and regulation of gene expression. Predicted to act upstream of or within cell division; chromatin organization; and methylation. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including gonad; nervous system; and nose. Orthologous to human SETDB2 (SET domain bifurcated histone lysine methyltransferase 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver E14 (RPKM 2.7), liver E18 (RPKM 2.2) and 28 other tissues See more
Orthologs
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Genomic context

See Setdb2 in Genome Data Viewer
Location:
14 C3; 14 31.48 cM
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (59639458..59678329, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (59402009..59440880, complement)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_36838 Neighboring gene STARR-seq mESC enhancer starr_36839 Neighboring gene PHD finger protein 11D Neighboring gene predicted gene, 45935 Neighboring gene PHD finger protein 11C Neighboring gene STARR-positive B cell enhancer ABC_E4112 Neighboring gene calcium binding protein 39-like Neighboring gene cytidine and dCMP deaminase domain containing 1 Neighboring gene aldo-keto reductase family 1, member B8 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)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (3) 

General gene information

Markers

Readthrough Gm45935

Readthrough gene: Gm45935, Included gene: Phf11d, Included gene: Phf11c

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K9 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H3K9 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K9me2 methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
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
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell division IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in chromosome segregation ISO
Inferred from Sequence Orthology
more info
 
involved_in heterochromatin organization IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in mitotic cell cycle ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of DNA methylation-dependent heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol 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
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETDB2
NP_001307649.1
NP_001307650.1

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_001320720.1NP_001307649.1  histone-lysine N-methyltransferase SETDB2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC114007, AI428348, BC172021
    Consensus CDS
    CCDS84142.1
    UniProtKB/TrEMBL
    B2RXP3, B4XVN8, B4XVN9
    Related
    ENSMUSP00000124696.2, ENSMUST00000161459.8
    Conserved Domains (3) summary
    smart00317
    Location:612674
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd01395
    Location:152212
    HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...
    pfam05033
    Location:234346
    Pre-SET; Pre-SET motif
  2. NM_001320721.1NP_001307650.1  histone-lysine N-methyltransferase SETDB2 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC114007, AI428348, BC172021
    UniProtKB/TrEMBL
    B4XVP0
    Conserved Domains (3) summary
    smart00317
    Location:590652
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cd01395
    Location:130190
    HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...
    pfam05033
    Location:212324
    Pre-SET; Pre-SET motif

RNA

  1. NR_135463.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC114007, AI428348, BC172021

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_000080.7 Reference GRCm39 C57BL/6J

    Range
    59639458..59678329 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001081024.1: Suppressed sequence

    Description
    NM_001081024.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.