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SETD1B SET domain containing 1B, histone lysine methyltransferase [ Homo sapiens (human) ]

Gene ID: 23067, updated on 5-Dec-2021

Summary

Official Symbol
SETD1Bprovided by HGNC
Official Full Name
SET domain containing 1B, histone lysine methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:29187
See related
Ensembl:ENSG00000139718 MIM:611055
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KMT2G; Set1B; IDDSELD
Summary
SET1B is a component of a histone methyltransferase complex that produces trimethylated histone H3 at Lys4 (Lee et al., 2007 [PubMed 17355966]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in endometrium (RPKM 7.9), spleen (RPKM 6.1) and 25 other tissues See more
Orthologs
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Genomic context

See SETD1B in Genome Data Viewer
Location:
12q24.31
Exon count:
19
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (121803665..121832656)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122241915..122270562)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984442 Neighboring gene ras homolog family member F, filopodia associated Neighboring gene long intergenic non-protein coding RNA 1089 Neighboring gene uncharacterized LOC105370035 Neighboring gene 4-hydroxyphenylpyruvate dioxygenase Neighboring gene proteasome 26S subunit, non-ATPase 9 Neighboring gene RNA, U7 small nuclear 170 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
GeneReviews: Not available
Intellectual developmental disorder with seizures and language delay
MedGen: C5436574 OMIM: 619000 GeneReviews: Not available
Compare labs

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of SET domain containing 1B (SETD1B) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20803, KIAA1076

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to histone methyltransferase activity (H3-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
enables histone-lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in histone H3-K4 dimethylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in histone H3-K4 methylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in histone H3-K4 monomethylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in histone H3-K4 trimethylation IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
part_of Set1C/COMPASS complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of Set1C/COMPASS complex IPI
Inferred from Physical Interaction
more info
PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETD1B
Names
SET domain-containing protein 1B
lysine N-methyltransferase 2G
NP_001340274.1
XP_006719359.1
XP_024304666.1

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_001353345.2NP_001340274.1  histone-lysine N-methyltransferase SETD1B

    Status: REVIEWED

    Source sequence(s)
    AC079360, AC084018
    Consensus CDS
    CCDS86338.1
    Related
    ENSP00000474253.1, ENST00000604567.6
    Conserved Domains (5) summary
    smart00317
    Location:18341949
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:19501966
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12549
    Location:101193
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:16791821
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl25865
    Location:12371308
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    121803665..121832656
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719296.3XP_006719359.1  histone-lysine N-methyltransferase SETD1B isoform X1

    See identical proteins and their annotated locations for XP_006719359.1

    UniProtKB/Swiss-Prot
    Q9UPS6
    Related
    ENSP00000481531.1, ENST00000619791.1
    Conserved Domains (5) summary
    smart00317
    Location:18341949
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:19501966
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12549
    Location:101193
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:16791821
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl25865
    Location:12371308
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)
  2. XM_024448898.1XP_024304666.1  histone-lysine N-methyltransferase SETD1B isoform X1

    Conserved Domains (5) summary
    smart00317
    Location:18341949
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:19501966
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12549
    Location:101193
    RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)
    pfam11764
    Location:16791821
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl25865
    Location:12371308
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_015048.1: Suppressed sequence

    Description
    NM_015048.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
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