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

    Gene ID: 23067, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:29187
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SETD1B in Genome Data Viewer
    Location:
    12q24.31
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (121790155..121832656)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (121800295..121829318)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122241915..122270562)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122101860-122102399 Neighboring gene uncharacterized LOC105370034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122109697-122110623 Neighboring gene MORN repeat containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122124874-122125860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4986 Neighboring gene transmembrane protein 120B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122165743-122166363 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122194907-122195407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122204395-122204898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122207988-122208500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4987 Neighboring gene Sharpr-MPRA regulatory region 8824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122216872-122217390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122217391-122217909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122227166-122227882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122230665-122231496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122231502-122232042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122232583-122233123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122236367-122236906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122235825-122236366 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122236907-122237446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122237447-122237986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4997 Neighboring gene long intergenic non-protein coding RNA 1089 Neighboring gene ras homolog family member F, filopodia associated Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122248237-122249046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122249091-122249703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122252006-122252512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122276754-122277424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122278096-122278765 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:122293687-122294886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122297907-122298424 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122298425-122298941 Neighboring gene Sharpr-MPRA regulatory region 2080 Neighboring gene 4-hydroxyphenylpyruvate dioxygenase Neighboring gene Sharpr-MPRA regulatory region 2229 Neighboring gene transcript inducer of AURKA lysosomal degradation Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326353-122326966 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326967-122327580 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
    Intellectual developmental disorder with seizures and language delay not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2024-08-28)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2024-08-28)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
    EBI GWAS Catalog

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ20803, KIAA1076

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3 methyltransferase activity TAS
    Traceable Author Statement
    more info
     
    contributes_to histone H3K4 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K4 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K4 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 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
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    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
    lysine N-methyltransferase 2G
    NP_001340274.1
    XP_024304666.1
    XP_047284508.1
    XP_047284509.1
    XP_054227457.1
    XP_054227458.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      UniProtKB/Swiss-Prot
      F6MFW1, Q9UPS6
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      121790155..121832656
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428553.1XP_047284509.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/Swiss-Prot
      F6MFW1, Q9UPS6
    2. XM_024448898.2XP_024304666.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/Swiss-Prot
      F6MFW1, Q9UPS6
      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)
    3. XM_047428552.1XP_047284508.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/Swiss-Prot
      F6MFW1, Q9UPS6
      Related
      ENSP00000481531.1, ENST00000619791.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      121800295..121829318
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371482.1XP_054227457.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/Swiss-Prot
      F6MFW1, Q9UPS6
    2. XM_054371483.1XP_054227458.1  histone-lysine N-methyltransferase SETD1B isoform X1

      UniProtKB/Swiss-Prot
      F6MFW1, Q9UPS6

    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.