The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a... See more...

Aliases for SETD1A Gene

Aliases for SETD1A Gene

  • SET Domain Containing 1A, Histone Lysine Methyltransferase 2 3 5
  • KMT2F 2 3 4
  • Set1/Ash2 Histone Methyltransferase Complex Subunit SET1 3 4
  • Histone-Lysine N-Methyltransferase SETD1A 3 4
  • SET Domain-Containing Protein 1A 3 4
  • Lysine N-Methyltransferase 2F 3 4
  • SET Domain Containing 1A 2 3
  • KIAA0339 2 4
  • HSET1A 3 4
  • Set1 2 3
  • EC 2.1.1.354 4
  • EC 2.1.1.43 51
  • SETD1A 5
  • EPEDD 3
  • Set1A 3
  • SET1A 4
  • SET1 4

External Ids for SETD1A Gene

Previous GeneCards Identifiers for SETD1A Gene

  • GC16P030877
  • GC16P030878
  • GC16P030968
  • GC16P028531
  • GC16P030948

Summaries for SETD1A Gene

Entrez Gene Summary for SETD1A Gene

  • The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily. [provided by RefSeq, Dec 2016]

GeneCards Summary for SETD1A Gene

SETD1A (SET Domain Containing 1A, Histone Lysine Methyltransferase) is a Protein Coding gene. Diseases associated with SETD1A include Epilepsy, Early-Onset, With Or Without Developmental Delay and Schizophrenia. Among its related pathways are Lysine degradation and PKMTs methylate histone lysines. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SETD1B.

UniProtKB/Swiss-Prot Summary for SETD1A 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 SETD1B suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SETD1A Gene

Genomics for SETD1A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SETD1A 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 SETD1A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SETD1A

Top Transcription factor binding sites by QIAGEN in the SETD1A gene promoter:
  • CUTL1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • HTF
  • MZF-1
  • SEF-1 (1)

Genomic Locations for SETD1A Gene

Genomic Locations for SETD1A Gene
chr16:30,956,618-30,984,664
(GRCh38/hg38)
Size:
28,047 bases
Orientation:
Plus strand
chr16:30,968,615-30,996,437
(GRCh37/hg19)
Size:
27,823 bases
Orientation:
Plus strand

Genomic View for SETD1A Gene

Genes around SETD1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD1A Gene

Proteins for SETD1A Gene

  • Protein details for SETD1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15047-SET1A_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SETD1A
    Protein Accession:
    O15047
    Secondary Accessions:
    • A6NP62
    • Q6PIF3
    • Q8TAJ6

    Protein attributes for SETD1A Gene

    Size:
    1707 amino acids
    Molecular mass:
    186034 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. Interacts with ASH2/ASH2L, CXXC1/CFP1 and RBBP5. 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 ZNF335. Interacts with SUPT6H. Interacts with NAP1L1 (By similarity). Interacts (via WIN motif) with WDR5 (PubMed:17998332, PubMed:22665483, PubMed:22266653).
    SequenceCaution:
    • Sequence=AAH35795.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA20797.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SETD1A Gene

neXtProt entry for SETD1A Gene

Selected DME Specific Peptides for SETD1A Gene

O15047:
  • IGSSYLF
  • KYGEVEEVEIL
  • CGTESCR
  • TSVMGNIIH
  • ARFINHCC
  • MTILYDIWN
  • FRVDHDTIIDATKCGN
  • SLDSRIEMLLK
  • PNCYAKV
  • SERRSEQRRLLS

Post-translational modifications for SETD1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SETD1A Gene

Domains & Families for SETD1A Gene

Gene Families for SETD1A Gene

Protein Domains for SETD1A Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
  • Nuclear protein SET
ProtoNet:

Suggested Antigen Peptide Sequences for SETD1A Gene

GenScript: Design optimal peptide antigens:
  • Set1/Ash2 histone methyltransferase complex subunit SET1 (SET1A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15047

UniProtKB/Swiss-Prot:

SET1A_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 SETD1A: view

Function for SETD1A Gene

Molecular function for SETD1A 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 SETD1B suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression.
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:0000250|UniProtKB:Q9UPS6};.

Enzyme Numbers (IUBMB) for SETD1A Gene

Phenotypes From GWAS Catalog for SETD1A Gene

Gene Ontology (GO) - Molecular Function for SETD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 12670868
GO:0008013 beta-catenin binding IDA 22723415
GO:0008134 transcription factor binding IPI 27141965
genes like me logo Genes that share ontologies with SETD1A: view
genes like me logo Genes that share phenotypes with SETD1A: view

Animal Models for SETD1A Gene

MGI Knock Outs for SETD1A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD1A

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SETD1A Gene

Localization for SETD1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETD1A Gene

Nucleus speckle. Chromosome. Note=Localizes to a largely non-overlapping set of euchromatic nuclear speckles with SETD1B, suggesting that SETD1A and SETD1B 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 SETD1A gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SETD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 27141965
GO:0005634 nucleus IDA,IMP 22723415
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with SETD1A: view

Pathways & Interactions for SETD1A Gene

genes like me logo Genes that share pathways with SETD1A: view

Pathways by source for SETD1A Gene

1 BioSystems pathway for SETD1A Gene
2 KEGG pathways for SETD1A Gene
1 Cell Signaling Technology pathway for SETD1A Gene
1 GeneTex pathway for SETD1A Gene

Gene Ontology (GO) - Biological Process for SETD1A 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:0045652 regulation of megakaryocyte differentiation TAS --
GO:0080182 histone H3-K4 trimethylation IDA 25561738
genes like me logo Genes that share ontologies with SETD1A: view

No data available for SIGNOR curated interactions for SETD1A Gene

Drugs & Compounds for SETD1A Gene

(1) Drugs for SETD1A Gene - From: HMDB

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

(1) Additional Compounds for SETD1A 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 SETD1A: view

Transcripts for SETD1A Gene

mRNA/cDNA for SETD1A Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD1A

Alternative Splicing Database (ASD) splice patterns (SP) for SETD1A Gene

No ASD Table

Relevant External Links for SETD1A Gene

GeneLoc Exon Structure for
SETD1A

Expression for SETD1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SETD1A Gene

Protein differential expression in normal tissues from HIPED for SETD1A Gene

This gene is overexpressed in Retina (13.0), Peripheral blood mononuclear cells (12.7), CD8 Tcells (12.0), and Testis (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SETD1A Gene



Protein tissue co-expression partners for SETD1A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SETD1A

SOURCE GeneReport for Unigene cluster for SETD1A Gene:

Hs.297483

Evidence on tissue expression from TISSUES for SETD1A Gene

  • Liver(4.5)
  • Skin(3.1)
  • Nervous system(3)
  • Muscle(2.9)
  • Blood(2.8)
  • Intestine(2.7)
  • Kidney(2.6)
  • Heart(2.5)
  • Bone marrow(2.4)
  • Lung(2.3)
  • Pancreas(2.2)
  • Lymph node(2.2)
  • Thyroid gland(2.2)
  • Stomach(2.2)
  • Spleen(2.2)
genes like me logo Genes that share expression patterns with SETD1A: 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 SETD1A Gene

Orthologs for SETD1A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SETD1A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SETD1A 30 31
  • 99.32 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SETD1A 30 31
  • 88.62 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SETD1A 30 31
  • 88.55 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Setd1a 30 17 31
  • 84.31 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SETD1A 31
  • 79 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SETD1A 31
  • 64 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SETD1A 31
  • 55 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii setd1a 31
  • 38 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Set1 31
  • 25 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea set-2 31
  • 20 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET1 31 33
  • 22 (a)
OneToMany
Rice
(Oryza sativa)
Liliopsida Os.8820 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.7781 31
  • 39 (a)
OneToMany
Species where no ortholog for SETD1A 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)
  • Chicken (Gallus gallus)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for SETD1A Gene

ENSEMBL:
Gene Tree for SETD1A (if available)
TreeFam:
Gene Tree for SETD1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SETD1A: view image

Paralogs for SETD1A Gene

(1) SIMAP similar genes for SETD1A Gene using alignment to 3 proteins:

  • SET1A_HUMAN
  • C9J2Z9_HUMAN
  • L0R6N9_HUMAN
genes like me logo Genes that share paralogs with SETD1A: view

Variants for SETD1A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SETD1A Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
681048 Likely Benign: not provided 30,969,465(+) G/A INTRON_VARIANT
709311 Likely Benign: not provided 30,966,149(+) C/T SYNONYMOUS_VARIANT
711164 Benign: not provided 30,980,612(+) C/T SYNONYMOUS_VARIANT
712178 Benign: not provided 30,966,144(+) G/A MISSENSE_VARIANT
719085 Likely Benign: not provided 30,965,804(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SETD1A Gene

Structural Variations from Database of Genomic Variants (DGV) for SETD1A Gene

Variant ID Type Subtype PubMed ID
dgv35n68 CNV loss 17160897
esv2673466 CNV deletion 23128226
esv33379 CNV loss 17666407
esv3582130 CNV loss 25503493
esv3638390 CNV loss 21293372
nsv457483 CNV loss 19166990
nsv571820 CNV loss 21841781
nsv833193 CNV gain+loss 17160897
nsv953802 CNV deletion 24416366

Variation tolerance for SETD1A Gene

Residual Variation Intolerance Score: 0.741% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.02; 60.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETD1A Gene

Human Gene Mutation Database (HGMD)
SETD1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETD1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD1A Gene

Disorders for SETD1A Gene

MalaCards: The human disease database

(9) MalaCards diseases for SETD1A Gene - From: OMIM, ClinVar, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SETD1A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SETD1A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SETD1A Gene

Publications for SETD1A Gene

  1. CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. (PMID: 16253997) Lee JH … Skalnik DG (The Journal of biological chemistry 2005) 3 4 23
  2. Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. (PMID: 12670868) Wysocka J … Herr W (Genes & development 2003) 2 3 4
  3. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4
  4. 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
  5. 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

Products for SETD1A Gene

Sources for SETD1A Gene