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] See more...

Aliases for SETD1B Gene

Aliases for SETD1B Gene

  • SET Domain Containing 1B, Histone Lysine Methyltransferase 2 3 5
  • KMT2G 2 3 4
  • Histone-Lysine N-Methyltransferase SETD1B 3 4
  • SET Domain-Containing Protein 1B 3 4
  • Lysine N-Methyltransferase 2G 3 4
  • KIAA1076 2 4
  • Set1B 2 3
  • SET Domain Containing 1B 2
  • EC 2.1.1.354 4
  • EC 2.1.1.43 51
  • EC 2.1.1 51
  • IDDSELD 3
  • SETD1B 5
  • HSET1B 4
  • SET1B 4

External Ids for SETD1B Gene

Previous GeneCards Identifiers for SETD1B Gene

  • GC12P120726
  • GC12P122243
  • GC12P119254
  • GC12P121865
  • GC12P121868
  • GC12P122341
  • GC12P122421
  • GC12P122447
  • GC12P122640
  • GC12P121871
  • GC12P121875
  • GC12P121878
  • GC12P122003
  • GC12P122057
  • GC12P122108
  • GC12P122183
  • GC12P122263
  • GC12P122842

Summaries for SETD1B Gene

Entrez Gene Summary for SETD1B Gene

  • 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]

GeneCards Summary for SETD1B Gene

SETD1B (SET Domain Containing 1B, Histone Lysine Methyltransferase) is a Protein Coding gene. Diseases associated with SETD1B include Intellectual Developmental Disorder With Seizures And Language Delay and Epilepsy. Among its related pathways are Chromatin Regulation / Acetylation and Chromatin organization. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SETD1A.

UniProtKB/Swiss-Prot Summary for SETD1B Gene

  • Histone methyltransferase that specifically methylates 'Lys-4' of histone H3, when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. The non-overlapping localization with SETD1A suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. Specifically tri-methylates 'Lys-4' of histone H3 in vitro.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SETD1B Gene

Genomics for SETD1B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SETD1B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SETD1B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SETD1B

Top Transcription factor binding sites by QIAGEN in the SETD1B gene promoter:
  • AhR
  • AREB6
  • HOXA5
  • Ik-3
  • Lmo2
  • MyoD
  • Olf-1
  • USF-1
  • USF1

Genomic Locations for SETD1B Gene

Latest Assembly
chr12:121,803,665-121,832,656
(GRCh38/hg38)
Size:
28,992 bases
Orientation:
Plus strand

Previous Assembly
chr12:122,241,915-122,270,562
(GRCh37/hg19 by Entrez Gene)
Size:
28,648 bases
Orientation:
Plus strand

chr12:122,242,086-122,270,562
(GRCh37/hg19 by Ensembl)
Size:
28,477 bases
Orientation:
Plus strand

Genomic View for SETD1B Gene

Genes around SETD1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD1B Gene

Proteins for SETD1B Gene

  • Protein details for SETD1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPS6-SET1B_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SETD1B
    Protein Accession:
    Q9UPS6
    Secondary Accessions:
    • F6MFW1

    Protein attributes for SETD1B Gene

    Size:
    1966 amino acids
    Molecular mass:
    212803 Da
    Quaternary structure:
    • Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. Interacts with HCFC1 and ASH2L/ASH2. Interacts (via the RRM domain) with WDR82. Interacts (via the RRM domain) with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A) only in the presence of WDR82. Binds specifically to CTD heptad repeats phosphorylated on 'Ser-5' of each heptad. Interacts with RBM15. Interacts (via WIN motif) with WDR5 (PubMed:22665483, PubMed:22266653).

    Three dimensional structures from OCA and Proteopedia for SETD1B Gene

    Alternative splice isoforms for SETD1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETD1B Gene

Selected DME Specific Peptides for SETD1B Gene

Q9UPS6:
  • FDEWWDK
  • KYGEVEEVEIL
  • ISSSSSQ
  • SCDSDLLKFNQLKFRKKK
  • VTVPPPPLPAPPGVPP
  • KKKKRDDG
  • TPTSEKMDE
  • DLNRKMVEVVAFR
  • TGCARSE
  • KLYRYDG
  • GTPFSQD
  • VPKFKIDE
  • PRTPGRD
  • SERRSEQRRLLS
  • YTPQTLPVG
  • ADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVD
  • FCKSHIHDWGLFAMEPI
  • EEITYDYKFPIEDVKIPCLC
  • TSVMGNIIH
  • SSGEDMEISDDE
  • MTILYDIWN
  • SRPSSTGLEDISPTPLPDS
  • FRVDHDTIIDATKCGN
  • SLDSRIEMLLK
  • PNCYAKV
  • NHSCNPN

Post-translational modifications for SETD1B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SETD1B Gene

Domains & Families for SETD1B Gene

Gene Families for SETD1B Gene

Protein Domains for SETD1B Gene

Suggested Antigen Peptide Sequences for SETD1B Gene

GenScript: Design optimal peptide antigens:
  • Histone-lysine N-methyltransferase (F6MFW1_HUMAN)
  • SET domain-containing protein 1B (SET1B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UPS6

UniProtKB/Swiss-Prot:

SET1B_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with SETD1B: view

Function for SETD1B Gene

Molecular function for SETD1B Gene

UniProtKB/Swiss-Prot Function:
Histone methyltransferase that specifically methylates 'Lys-4' of histone H3, when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. The non-overlapping localization with SETD1A suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. Specifically tri-methylates 'Lys-4' of histone H3 in vitro.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60260, Rhea:RHEA-COMP:15537, Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.354; Evidence={ECO:0000269|PubMed:17355966};.

Enzyme Numbers (IUBMB) for SETD1B Gene

Phenotypes From GWAS Catalog for SETD1B Gene

Gene Ontology (GO) - Molecular Function for SETD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IEA,IPI 17998332
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SETD1B: view
genes like me logo Genes that share phenotypes with SETD1B: view

Human Phenotype Ontology for SETD1B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for SETD1B Gene

miRTarBase miRNAs that target SETD1B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD1B

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for SETD1B Gene

Localization for SETD1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETD1B Gene

Nucleus speckle. Chromosome. Note=Localizes to a largely non-overlapping set of euchromatic nuclear speckles with SETD1A, suggesting that SETD1A and SET1B each bind to a unique set of target genes.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SETD1B gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SETD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005694 chromosome IEA --
GO:0016607 nuclear speck IEA --
GO:0035097 histone methyltransferase complex IDA 17355966
genes like me logo Genes that share ontologies with SETD1B: view

Pathways & Interactions for SETD1B Gene

genes like me logo Genes that share pathways with SETD1B: view

Pathways by source for SETD1B Gene

1 BioSystems pathway for SETD1B Gene
2 KEGG pathways for SETD1B Gene
1 Cell Signaling Technology pathway for SETD1B Gene
1 GeneTex pathway for SETD1B Gene

Gene Ontology (GO) - Biological Process for SETD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0032259 methylation IEA --
GO:0044648 histone H3-K4 dimethylation IDA 25561738
GO:0051568 histone H3-K4 methylation IEA,IDA 17355966
GO:0080182 histone H3-K4 trimethylation IDA 25561738
genes like me logo Genes that share ontologies with SETD1B: view

No data available for SIGNOR curated interactions for SETD1B Gene

Drugs & Compounds for SETD1B Gene

(1) Drugs for SETD1B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for SETD1B Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-Amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with SETD1B: view

Transcripts for SETD1B Gene

mRNA/cDNA for SETD1B Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD1B

Alternative Splicing Database (ASD) splice patterns (SP) for SETD1B Gene

No ASD Table

Relevant External Links for SETD1B Gene

GeneLoc Exon Structure for
SETD1B

Expression for SETD1B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SETD1B Gene

Protein differential expression in normal tissues from HIPED for SETD1B Gene

This gene is overexpressed in NK cells (21.2), Peripheral blood mononuclear cells (14.3), Islet of Langerhans (13.2), Ovary (9.0), and CD8 Tcells (7.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SETD1B Gene



Protein tissue co-expression partners for SETD1B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SETD1B

SOURCE GeneReport for Unigene cluster for SETD1B Gene:

Hs.507122

Evidence on tissue expression from TISSUES for SETD1B Gene

  • Nervous system(4.4)
  • Liver(4.4)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with SETD1B: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SETD1B Gene

Orthologs for SETD1B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SETD1B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SETD1B 31
  • 99 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SETD1B 31
  • 90 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Setd1b 31
  • 87 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SETD1B 30 31
  • 86.56 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SETD1B 31
  • 64 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SETD1B 31
  • 64 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SETD1B 31
  • 60 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SETD1B 31
  • 58 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.6802 30
Zebrafish
(Danio rerio)
Actinopterygii setd1ba 31
  • 51 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Set1 31
  • 25 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea set-2 31
  • 21 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET1 31
  • 21 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.7781 31
  • 42 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4378 30
Species where no ortholog for SETD1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SETD1B Gene

ENSEMBL:
Gene Tree for SETD1B (if available)
TreeFam:
Gene Tree for SETD1B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SETD1B: view image

Paralogs for SETD1B Gene

genes like me logo Genes that share paralogs with SETD1B: view

Variants for SETD1B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SETD1B Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
976775 Likely Pathogenic: SETD1B-associated disorder 121,830,166(+) A/G
NM_001353345.2(SETD1B):c.5828A>G (p.Tyr1943Cys)
MISSENSE
977429 Uncertain Significance: Global developmental delay; Seizures 121,822,547(+) C/T
NM_001353345.2(SETD1B):c.3968C>T (p.Pro1323Leu)
MISSENSE
977478 Pathogenic: Intellectual developmental disorder with seizures and language delay 121,830,108(+) AAGAT/A
NM_001353345.2(SETD1B):c.5773_5776del (p.Ile1925fs)
FRAMESHIFT
977480 Pathogenic: Intellectual developmental disorder with seizures and language delay 121,817,249(+) C/T
NM_001353345.2(SETD1B):c.2932C>T (p.Gln978Ter)
NONSENSE
977481 Pathogenic: Intellectual developmental disorder with seizures and language delay 121,822,543(+) C/T
NM_001353345.2(SETD1B):c.3964C>T (p.Gln1322Ter)
NONSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SETD1B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SETD1B Gene

Variant ID Type Subtype PubMed ID
esv3892268 CNV loss 25118596
nsv1160065 CNV deletion 26073780
nsv520973 CNV loss 19592680
nsv911 CNV deletion 18451855

Variation tolerance for SETD1B Gene

Gene Damage Index Score: 3.84; 58.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETD1B Gene

Human Gene Mutation Database (HGMD)
SETD1B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETD1B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD1B Gene

Disorders for SETD1B Gene

MalaCards: The human disease database

(5) MalaCards diseases for SETD1B Gene - From: OMI, CVR, GTR, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SETD1B

genes like me logo Genes that share disorders with SETD1B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SETD1B Gene

Publications for SETD1B Gene

  1. Identification and characterization of the human Set1B histone H3-Lys4 methyltransferase complex. (PMID: 17355966) Lee JH … Skalnik DG (The Journal of biological chemistry 2007) 2 3 4
  2. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  3. A novel de novo frameshift variant in SETD1B causes epilepsy. (PMID: 31110234) Den K … Matsumoto N (Journal of human genetics 2019) 3 74
  4. The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases. (PMID: 22266653) Zhang P … Couture JF (Nucleic acids research 2012) 3 4
  5. Structural basis for WDR5 interaction (Win) motif recognition in human SET1 family histone methyltransferases. (PMID: 22665483) Dharmarajan V … Cosgrove MS (The Journal of biological chemistry 2012) 3 4

Products for SETD1B Gene

Sources for SETD1B Gene