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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 61
  • HSET1A 3 4
  • Set1A 3 4
  • KMT2F 3 4
  • Set1 3 4
  • Histone-Lysine N-Methyltransferase SETD1A 3
  • 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. 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) is a Protein Coding gene. Diseases associated with SETD1A include Schizophrenia and Cerebritis. Among its related pathways are Lysine degradation and PKMTs methylate histone lysines. GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SETD1B.

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-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 , fRNAdb sequence ontologies and piRNA Summary for SETD1A Gene

Genomics for SETD1A Gene

Regulatory Elements for SETD1A Gene

Enhancers for SETD1A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16G031178 1.2 ENCODE 11 +232.3 232329 4.7 MLX CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 ZNF785 ZNF720 PYCARD MIR762HG ZNF668 LOC730183 PYDC1 ZNF771 PRSS36 PRSS8
GH16G031001 1.1 Ensembl ENCODE 11.6 +54.3 54346 2.5 ELF3 PKNOX1 ARID4B SIN3A RAD21 THRB ZNF48 RARA ZNF366 EGR1 KAT8 ZNF668 STX4 SETD1A ZNF646 HSD3B7 PRSS36 PRSS8 FUS GC16P031002
GH16G031386 1.1 Ensembl ENCODE 10.8 +438.1 438130 0.9 HDAC1 TBP MXI1 AGO1 JUN MAX SIN3A CEBPG BMI1 ZIC2 ITGAX PYCARD COX6A2 HSD3B7 SETD1A PRSS36 STX4 STX1B LOC105371171 CLUHP3
GH16G031176 0.9 Ensembl ENCODE 11 +228.8 228765 1.1 SMAD5 POLR2A ZNF600 ZNF652 RBFOX2 EGR2 SUPT5H ZBTB20 PYCARD PRSS36 PRSS8 TRIM72 HSD3B7 SETD1A ZNF668 ZNF646 NDUFA3P6 FUS
GH16G031187 0.8 ENCODE 10.1 +240.3 240349 2.1 NFXL1 RAD21 TCF12 SCRT2 ZNF263 PAF1 ZNF362 SMAD5 ZEB2 REST PYDC1 PRSS8 PRSS36 PYCARD SETD1A HSD3B7 PIR60441 PIR50410
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000085270 695 2001 HDGF PKNOX1 MLX CREB3L1 ARNT AGO1 ZFP64 WRNIP1 ARID4B SIN3A

Genomic Location for SETD1A Gene

Chromosome:
16
Start:
30,948,505 bp from pter
End:
30,984,664 bp from pter
Size:
36,160 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

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

Suggested Antigen Peptide Sequences for SETD1A Gene

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 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 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: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

Clone 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
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 2

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 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 GeneTex pathway for SETD1A Gene
1 Cell Signaling Technology pathway for SETD1A Gene
1 BioSystems 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:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0032259 methylation IEA --
GO:0034968 histone lysine methylation IEA --
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:

CRISPR Products

Inhibitory RNA Products

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for SETD1A Gene



Protein tissue co-expression partners for SETD1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SETD1A Gene:

SETD1A

SOURCE GeneReport for Unigene cluster for SETD1A Gene:

Hs.297483

Evidence on tissue expression from TISSUES for SETD1A Gene

  • Liver(4.3)
  • Muscle(2.3)
  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with SETD1A: view

Primer Products

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 34 35
  • 99.32 (n)
dog
(Canis familiaris)
Mammalia SETD1A 34 35
  • 88.62 (n)
cow
(Bos Taurus)
Mammalia SETD1A 34 35
  • 88.55 (n)
mouse
(Mus musculus)
Mammalia Setd1a 34 16 35
  • 84.31 (n)
oppossum
(Monodelphis domestica)
Mammalia SETD1A 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETD1A 35
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETD1A 35
  • 55 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii setd1a 35
  • 38 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Set1 35
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-2 35
  • 20 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SET1 35 37
  • 22 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.8820 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7781 35
  • 39 (a)
OneToMany
Species where no ortholog for SETD1A 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)
  • 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
rs770913157 Pathogenic 30,965,819(+) GAGTA(C/G/T)CCCCC reference, synonymous-codon
rs869312829 Pathogenic 30,963,431(+) CCTCC(A/G)GGACA splice-acceptor-variant
rs869312830 Pathogenic 30,965,014(+) CAGGA(-/C)TACCG reference, frameshift-variant
rs869312831 Pathogenic 30,966,090(+) AGGGG(C/T)AGGAG reference, stop-gained
rs869312832 Pathogenic 30,966,052(+) GAGGC(-/C)AGCCT reference, frameshift-variant

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)

Relevant External Links 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

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

Disorder Aliases PubMed IDs
schizophrenia
  • schizophrenia 12
cerebritis
cerebral lymphoma
  • brain primary lymphoma
hemometra
  • hematometra
anus cancer
  • anal cancer
- 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. 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 4 22 64
  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 Dev. 2003) 2 3 4 64
  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 64
  4. The histone chaperone Spt6 is required for activation-induced cytidine deaminase target determination through H3K4me3 regulation. (PMID: 22843687) Begum N.A. … Honjo T. (J. Biol. Chem. 2012) 3 4 64
  5. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. (PMID: 20819778) Zhang X. … Wu X. (Carcinogenesis 2010) 3 46 64

Products for SETD1A Gene

Sources for SETD1A Gene

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