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Aliases for SETD1B Gene

Aliases for SETD1B Gene

  • SET Domain Containing 1B 2 3 5
  • SET Domain-Containing Protein 1B 3 4
  • Lysine N-Methyltransferase 2G 3 4
  • EC 2.1.1.43 4 56
  • HSET1B 3 4
  • Set1B 3 4
  • KMT2G 3 4
  • Histone-Lysine N-Methyltransferase SETD1B 3
  • KIAA1076 4
  • EC 2.1.1 56

External Ids for SETD1B Gene

Previous GeneCards Identifiers for SETD1B Gene

  • GC12P120726
  • GC12P122243
  • GC12P119254
  • GC12P121865
  • GC12P121868
  • GC12P121871
  • GC12P121875
  • GC12P121878
  • GC12P122003
  • GC12P122057

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) is a Protein Coding gene. Diseases associated with SETD1B include Syndromic Intellectual Disability. Among its related pathways are PKMTs methylate histone lysines 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 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.

Additional gene information for SETD1B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETD1B Gene

Genomics for SETD1B Gene

GeneHancer (GH) Regulatory Elements for SETD1B Gene

Promoters and enhancers for SETD1B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I121783 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 606.2 -7.5 -7538 24.5 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ENSG00000272849 SETD1B RHOF ZCCHC8 RSRC2 PSMD9 ANAPC5 KNTC1 LINC01089 HPD
GH12I121398 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 57.7 -403.2 -403204 3.3 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B ANAPC5 RNF34 SETD1B ENSG00000272849 KDM2B PSMD9 ENSG00000258435 LINC01089 MLXIP RPL31P52
GH12I121351 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 30.5 -451.1 -451145 2.7 MLX DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 NFYC MEF2D ZNF610 ANAPC5 SETD1B PSMD9 CAMKK2 RNF34 SRSF9 MLXIP ENSG00000272849 ENSG00000258435
GH12I122523 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 23.4 +722.4 722441 5.6 YBX1 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC RSRC2 KNTC1 ZCCHC8 ENSG00000235423 PSMD9 SETD1B C12orf65 ENSG00000252192 MLXIP ENSG00000272849
GH12I122265 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.4 +462.8 462833 2.6 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ENSG00000256861 VPS33A RSRC2 C12orf65 ZCCHC8 ENSG00000235423 ANAPC5 ENSG00000272849 SETD1B LINC01089
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SETD1B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SETD1B gene promoter:

Genomic Locations for SETD1B Gene

Genomic Locations for SETD1B Gene
chr12:121,803,530-121,832,656
(GRCh38/hg38)
Size:
29,127 bases
Orientation:
Plus strand
chr12:122,242,086-122,270,562
(GRCh37/hg19)

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.

    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

Suggested Antigen Peptide Sequences for SETD1B Gene

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 CatalyticActivity:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
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.

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:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 17998332
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0018024 histone-lysine N-methyltransferase activity TAS --
genes like me logo Genes that share ontologies with SETD1B: view
genes like me logo Genes that share phenotypes with SETD1B: view

miRNA for SETD1B Gene

miRTarBase miRNAs that target SETD1B

Clone Products

No data available for Human Phenotype Ontology , 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 5

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 TAS --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
GO:0016607 nuclear speck IEA --
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 GeneTex pathway for SETD1B Gene
1 BioSystems pathway for SETD1B Gene
1 KEGG pathway for SETD1B Gene
1 Cell Signaling Technology pathway for SETD1B Gene

Gene Ontology (GO) - Biological Process for SETD1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0032259 methylation IEA --
GO:0051568 histone H3-K4 methylation IDA 17355966
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
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
genes like me logo Genes that share compounds with SETD1B: view

Transcripts for SETD1B Gene

Unigene Clusters for SETD1B Gene

SET domain containing 1B:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for SETD1B Gene

GeneLoc Exon Structure for
SETD1B
ECgene alternative splicing isoforms for
SETD1B

Expression for SETD1B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for SETD1B Gene



Protein tissue co-expression partners for SETD1B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SETD1B Gene:

SETD1B

SOURCE GeneReport for Unigene cluster for SETD1B Gene:

Hs.507122

Evidence on tissue expression from TISSUES for SETD1B Gene

  • Liver(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with SETD1B: view

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 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETD1B 34
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setd1b 34
  • 87 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SETD1B 33 34
  • 86.56 (n)
oppossum
(Monodelphis domestica)
Mammalia SETD1B 34
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETD1B 34
  • 64 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETD1B 34
  • 60 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETD1B 34
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.6802 33
zebrafish
(Danio rerio)
Actinopterygii setd1ba 34
  • 51 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Set1 34
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-2 34
  • 21 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET1 34
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7781 34
  • 42 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4378 33
Species where no ortholog for SETD1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for SETD1B Gene

Paralogs for SETD1B Gene

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

Variants for SETD1B Gene

Sequence variations from dbSNP and Humsavar for SETD1B Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000022042 -- 121,803,127(+) C/T upstream_transcript_variant
rs1000034067 -- 121,823,277(+) C/T coding_sequence_variant, synonymous_variant
rs1000136481 -- 121,802,911(+) T/C upstream_transcript_variant
rs1000250301 -- 121,823,670(+) G/A coding_sequence_variant, synonymous_variant
rs1000398805 -- 121,824,339(+) A/C intron_variant

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

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

Disorders for SETD1B Gene

MalaCards: The human disease database

(1) MalaCards diseases for SETD1B Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
syndromic intellectual disability
- 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 58
  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 58
  3. Rbm15-Mkl1 interacts with the Setd1b histone H3-Lys4 methyltransferase via a SPOC domain that is required for cytokine-independent proliferation. (PMID: 22927943) Lee JH … Skalnik DG (PloS one 2012) 3 4 58
  4. Wdr82 is a C-terminal domain-binding protein that recruits the Setd1A Histone H3-Lys4 methyltransferase complex to transcription start sites of transcribed human genes. (PMID: 17998332) Lee JH … Skalnik DG (Molecular and cellular biology 2008) 3 4 58
  5. Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. (PMID: 18838538) Wu M … Shilatifard A (Molecular and cellular biology 2008) 3 4 58

Products for SETD1B Gene

Sources for SETD1B Gene

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