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Aliases for SETD1A Gene

Aliases for SETD1A Gene

  • SET Domain Containing 1A 2 3 5
  • Set1/Ash2 Histone Methyltransferase Complex Subunit SET1 3 4
  • SET Domain-Containing Protein 1A 3 4
  • Lysine N-Methyltransferase 2F 3 4
  • EC 2.1.1.43 4 63
  • HSET1A 3 4
  • Set1A 3 4
  • KMT2F 3 4
  • Set1 3 4
  • KIAA0339 4

External Ids for SETD1A Gene

Previous GeneCards Identifiers for SETD1A Gene

  • GC16P030877
  • GC16P030878
  • GC16P030968
  • GC16P028531

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. 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, Jan 2015]

GeneCards Summary for SETD1A Gene

SETD1A (SET Domain Containing 1A) is a Protein Coding gene. Diseases associated with SETD1A include Schizophrenia and Cerebritis. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is KMT2C.

UniProtKB/Swiss-Prot 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-overalpping 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 Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETD1A Gene

Genomics for SETD1A Gene

Regulatory Elements for SETD1A Gene

Enhancers for SETD1A Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SETD1A on UCSC Golden Path with GeneCards custom track

Promoters for SETD1A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SETD1A on UCSC Golden Path with GeneCards custom track

Genomic Location for SETD1A Gene

Chromosome:
16
Start:
30,948,505 bp from pter
End:
30,985,116 bp from pter
Size:
36,612 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, WDR5 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.
    SequenceCaution:
    • Sequence=AAH35795.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA20797.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SETD1A Gene

neXtProt entry for SETD1A Gene

Proteomics data for SETD1A Gene at MOPED

Post-translational modifications for SETD1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SETD1A Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SETD1A (SETD1A)

Domains & Families for SETD1A Gene

Suggested Antigen Peptide Sequences for SETD1A Gene

Graphical View of Domain Structure for InterPro Entry

O15047

UniProtKB/Swiss-Prot:

SET1A_HUMAN :
  • Contains 1 post-SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Domain:
  • Contains 1 post-SET domain.
  • Contains 1 RRM (RNA recognition motif) domain.
  • Contains 1 SET domain.
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 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-overalpping localization with SETD1B suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression.

Enzyme Numbers (IUBMB) for SETD1A Gene

Gene Ontology (GO) - Molecular Function for SETD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003723 RNA binding IEA --
GO:0008013 beta-catenin binding IDA 22723415
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

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
Jensen Localization Image for SETD1A Gene COMPARTMENTS Subcellular localization image for SETD1A gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for SETD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0016607 nuclear speck IEA --
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 GeneTex pathway for SETD1A Gene
1 Cell Signaling Technology pathway for SETD1A Gene
1 KEGG pathway for SETD1A Gene

Gene Ontology (GO) - Biological Process for SETD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034968 histone lysine methylation TAS --
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

(2) Drugs for SETD1A Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with SETD1A: view

Transcripts for SETD1A Gene

Unigene Clusters for SETD1A Gene

SET domain containing 1A:
Representative Sequences:

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

No ASD Table

Relevant External Links for SETD1A Gene

GeneLoc Exon Structure for
SETD1A
ECgene alternative splicing isoforms for
SETD1A

Expression for SETD1A Gene

mRNA expression in normal human tissues 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, PaxDb, MOPED, and MaxQB for SETD1A Gene



SOURCE GeneReport for Unigene cluster for SETD1A Gene Hs.297483

genes like me logo Genes that share expression patterns with SETD1A: view

Protein tissue co-expression partners for SETD1A Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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
cow
(Bos Taurus)
Mammalia SETD1A 35
  • 88.55 (n)
  • 92.76 (a)
SETD1A 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETD1A 35
  • 88.62 (n)
  • 92.56 (a)
SETD1A 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setd1a 35
  • 84.31 (n)
  • 89.81 (a)
Setd1a 16
Setd1a 36
  • 90 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SETD1A 35
  • 99.32 (n)
  • 99.59 (a)
SETD1A 36
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SETD1A 36
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETD1A 36
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETD1A 36
  • 55 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii setd1a 36
  • 38 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Set1 36
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-2 36
  • 20 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET1 36
  • 22 (a)
OneToMany
SET1 38
rice
(Oryza sativa)
Liliopsida Os.8820 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7781 36
  • 39 (a)
OneToMany
Species with no ortholog for SETD1A:
  • 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)
  • 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 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)

Paralogs for SETD1A Gene

Paralogs for SETD1A Gene

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

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

Variants for SETD1A Gene

Sequence variations from dbSNP and Humsavar for SETD1A Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs897985 - 30,965,796(-) CCCAT(C/T)AGGTC reference, missense
rs4321212 -- 30,958,495(+) CAGGC(A/C/G/T)CGTCT intron-variant, upstream-variant-2KB
rs4346218 -- 30,968,809(-) tatat(A/T)ttttt intron-variant
rs4502227 -- 30,968,733(-) gcctc(C/T)gcctc intron-variant
rs4573943 -- 30,958,735(-) CTGAT(A/C/T)CATCT reference, missense

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

Variant ID Type Subtype PubMed ID
nsv905729 CNV Loss 21882294
nsv905733 CNV Loss 21882294
dgv35n68 CNV Loss 17160897
dgv2670n71 CNV Loss 21882294
dgv2671n71 CNV Loss 21882294
nsv457483 CNV Loss 19166990
nsv905738 CNV Loss 21882294
nsv833193 CNV Gain+Loss 17160897
esv2673466 CNV Deletion 23128226
esv33379 CNV Loss 17666407
nsv905739 CNV Loss 21882294

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)

Relevant External Links for SETD1A Gene

Human Gene Mutation Database (HGMD)
SETD1A

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

Disorders for SETD1A Gene

MalaCards: The human disease database

(6) MalaCards diseases for SETD1A Gene - From: ClinVar and DISEASES

Disorder Aliases PubMed IDs
schizophrenia
  • schizophrenia 12
cerebritis
hemometra
  • hematometra
cerebral lymphoma
  • brain primary lymphoma
mesenchymoma
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SETD1A

Genetic Association Database (GAD)
SETD1A
Human Genome Epidemiology (HuGE) Navigator
SETD1A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SETD1A
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. 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 Dev. 2003) 2 3 4 67
  2. 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 J.-H. … Skalnik D.G. (J. Biol. Chem. 2005) 3 23
  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 Res. 1997) 2 3
  4. Histone Methyltransferase hSETD1A Is a Novel Regulator of Metastasis in Breast Cancer. (PMID: 25373480) Salz T. … Huang S. (Mol. Cancer Res. 2015) 3
  5. Structural implications of Dpy30 oligomerization for MLL/SET1 COMPASS H3K4 trimethylation. (PMID: 25542209) Zhang H. … Chang W. (Protein Cell 2015) 3

Products for SETD1A Gene

Sources for SETD1A Gene

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