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Setd1b SET domain containing 1B [ Mus musculus (house mouse) ]

Gene ID: 208043, updated on 8-Dec-2022

Summary

Official Symbol
Setd1bprovided by MGI
Official Full Name
SET domain containing 1Bprovided by MGI
Primary source
MGI:MGI:2652820
See related
Ensembl:ENSMUSG00000038384 AllianceGenome:MGI:2652820
Gene type
protein coding
RefSeq status
INFERRED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
KMT2G; mKIAA1076
Summary
Predicted to enable RNA binding activity and histone-lysine N-methyltransferase 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 act upstream of or within chromatin organization and methylation. Located in nucleus. Is expressed in several structures, including brain; cranium; early conceptus; oocyte; and sensory organ. Orthologous to human SETD1B (SET domain containing 1B, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 17.1), adrenal adult (RPKM 12.0) and 28 other tissues See more
Orthologs
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Genomic context

See Setd1b in Genome Data Viewer
Location:
5; 5 F
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (123280109..123306693)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (123142040..123168630)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene 6444 Neighboring gene transmembrane protein 120B Neighboring gene ras homolog family member F (in filopodia) Neighboring gene predicted gene, 54284 Neighboring gene 4-hydroxyphenylpyruvic acid dioxygenase Neighboring gene proteasome (prosome, macropain) 26S subunit, non-ATPase, 9

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 (4)  1 citation
  • Endonuclease-mediated (1) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC39035

Gene Ontology Provided by MGI

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
PubMed 
contributes_to histone H3K4 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K4 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone lysine N-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in histone H3-K4 dimethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H3-K4 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H3-K4 monomethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H3-K4 trimethylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within 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
PubMed 
part_of Set1C/COMPASS complex ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
part_of histone methyltransferase complex ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETD1B
Names
SET domain-containing protein 1B
NP_001035488.2
XP_006530300.1
XP_006530301.1

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_001040398.2NP_001035488.2  histone-lysine N-methyltransferase SETD1B

    See identical proteins and their annotated locations for NP_001035488.2

    Status: INFERRED

    Source sequence(s)
    AC158114, AI463740, AK141316, BC038367, CF536496
    Consensus CDS
    CCDS59684.1
    UniProtKB/Swiss-Prot
    Q8CFT2, Q8CGD1
    UniProtKB/TrEMBL
    Q3URP1
    Related
    ENSMUSP00000133933.2, ENSMUST00000163030.9
    Conserved Domains (3) summary
    cd19169
    Location:18341981
    SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins
    cd12549
    Location:100192
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:16981840
    N-SET; COMPASS (Complex proteins associated with Set1p) component N

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_000071.7 Reference GRCm39 C57BL/6J

    Range
    123280109..123306693
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006530238.5XP_006530301.1  histone-lysine N-methyltransferase SETD1B isoform X1

    See identical proteins and their annotated locations for XP_006530301.1

    Conserved Domains (3) summary
    cd12549
    Location:100192
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:16981841
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cd19169
    Location:18351982
    SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins
  2. XM_006530237.4XP_006530300.1  histone-lysine N-methyltransferase SETD1B isoform X1

    See identical proteins and their annotated locations for XP_006530300.1

    Conserved Domains (3) summary
    cd12549
    Location:100192
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:16981841
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cd19169
    Location:18351982
    SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_177581.2: Suppressed sequence

    Description
    NM_177581.2: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.