Aliases for SUPT3H Gene

Aliases for SUPT3H Gene

  • SPT3 Homolog, SAGA And STAGA Complex Component 2 3 5
  • SPT3 2 3 4
  • Transcription Initiation Protein SPT3 Homolog 3 4
  • SPT3-Like Protein 3 4
  • SPT3L 2 3
  • Suppressor Of Ty 3 Homolog (S. Cerevisiae) 2
  • Suppressor Of Ty (S.Cerevisiae) 3 Homolog 2
  • Suppressor Of Ty 3 Homolog 3
  • SUPT3H 5

External Ids for SUPT3H Gene

Previous GeneCards Identifiers for SUPT3H Gene

  • GC06M044799
  • GC06M044844
  • GC06M044843
  • GC06M044904
  • GC06M044518
  • GC06M044807

Summaries for SUPT3H Gene

GeneCards Summary for SUPT3H Gene

SUPT3H (SPT3 Homolog, SAGA And STAGA Complex Component) is a Protein Coding gene. Diseases associated with SUPT3H include Cleidocranial Dysplasia and Hepatic Adenomas, Familial. Among its related pathways are Chromatin organization and Transcriptional misregulation in cancer. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and histone acetyltransferase activity. An important paralog of this gene is TAF13.

UniProtKB/Swiss-Prot Summary for SUPT3H Gene

Gene Wiki entry for SUPT3H Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SUPT3H Gene

Genomics for SUPT3H Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SUPT3H Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J045419 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 273.6 -45.2 -45150 8.4 ZNF654 MYC ZNF600 ZNF10 ZIC2 ZBTB10 NONO CTCF REST BHLHE40 SUPT3H ENSG00000271857 RUNX2 HSALNG0050325 CLIC5
GH06J045376 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 277.4 +0.3 332 3.4 ZNF600 MYC IKZF1 SIX5 ZNF580 ATF2 KLF9 POLR2A ZNF223 ZNF10 SUPT3H lnc-CLIC5-3 RUNX2 CDC5L
GH06J045443 Enhancer 1.7 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 12.7 -67.8 -67845 5.4 NCOR1 MYC ZNF600 SSRP1 JUND ZNF580 ZNF592 ATF2 KLF9 CEBPA SUPT3H RUNX2 HSALNG0050325 HSALNG0050326 CLIC5
GH06J044940 Enhancer 0.8 ENCODE 17.9 +437.5 437490 0.9 CEBPA YY1 FOXA1 HOMEZ THAP11 FOXA2 KDM6A MAFF SMAD4 SAP130 SUPT3H piR-60146-158 piR-39341-323 RUNX2 CDC5L
GH06J044660 Enhancer 1.5 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 8.7 +713.4 713350 8.6 JUND CEBPA TRIM22 CTCF ZNF217 RAD21 SMC3 RARA YY1 TEAD3 SUPT3H lnc-CDC5L-6 HSALNG0050306 CDC5L RUNX2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SUPT3H on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SUPT3H

Top Transcription factor binding sites by QIAGEN in the SUPT3H gene promoter:
  • AREB6
  • HNF-1
  • HNF-1A
  • POU2F1
  • POU2F1a

Genomic Locations for SUPT3H Gene

Latest Assembly
568,995 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
568,878 bases
Minus strand

(GRCh37/hg19 by Ensembl)
568,637 bases
Minus strand

Genomic View for SUPT3H Gene

Genes around SUPT3H on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SUPT3H Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SUPT3H Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SUPT3H Gene

Proteins for SUPT3H Gene

  • Protein details for SUPT3H Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transcription initiation protein SPT3 homolog
    Protein Accession:
    Secondary Accessions:
    • A6NKG9
    • B2R9Q5
    • O76066
    • Q5TAV9
    • Q86VN7

    Protein attributes for SUPT3H Gene

    317 amino acids
    Molecular mass:
    35793 Da
    Quaternary structure:
    • Component of the PCAF complex, at least composed of TADA2L/ADA2, SUPT3H, TADA3L/ADA3, TAF5L/PAF65-beta, TAF6L/PAF65-alpha, TAF10/TAFII30, TAF12/TAFII20, TAF9/TAFII31 and TRRAP. Associates with TAFII31 and GCN5L2. Component of the TFTC-HAT complex, at least composed of TAF5L, TAF6L, TADA3L, SUPT3H/SPT3, TAF2/TAFII150, TAF4/TAFII135, TAF5/TAFII100, GCN5L2/GCN5, TAF10 and TRRAP. Component of the STAGA transcription coactivator-HAT complex, at least composed of SUPT3H, GCN5L2, TAF5L, TAF6L, SUPT7L, TADA3L, TAD1L, TAF10, TAF12, TRRAP and TAF9. The STAGA core complex is associated with a subcomplex required for histone deubiquitination composed of ATXN7L3, ENY2 and USP22.
    • Sequence=AAC70014.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=AAC70014.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAC70014.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA.; Evidence={ECO:0000305};

    Alternative splice isoforms for SUPT3H Gene


neXtProt entry for SUPT3H Gene

Post-translational modifications for SUPT3H Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SUPT3H Gene

Domains & Families for SUPT3H Gene

Gene Families for SUPT3H Gene

Protein Domains for SUPT3H Gene

  • Transcription initiation factor IID, 18 kDa subunit

Suggested Antigen Peptide Sequences for SUPT3H Gene

GenScript: Design optimal peptide antigens:
  • SUPT3H protein (Q5U608_HUMAN)
  • SPT3-like protein (SUPT3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SPT3 family.
  • Belongs to the SPT3 family.
genes like me logo Genes that share domains with SUPT3H: view

Function for SUPT3H Gene

Molecular function for SUPT3H Gene

UniProtKB/Swiss-Prot Function:
Probable transcriptional activator.
GENATLAS Biochemistry:
putative chromatin structure regulator,yeasqt spt3 (suppressor of Ty) homolog

Phenotypes From GWAS Catalog for SUPT3H Gene

Gene Ontology (GO) - Molecular Function for SUPT3H Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IBA,IDA 11564863
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with SUPT3H: view
genes like me logo Genes that share phenotypes with SUPT3H: view

Animal Models for SUPT3H Gene

MGI Knock Outs for SUPT3H:
  • Supt3 Supt3<tm1a(EUCOMM)Hmgu>

Animal Models for research

miRNA for SUPT3H Gene

miRTarBase miRNAs that target SUPT3H

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SUPT3H

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SUPT3H Gene

Localization for SUPT3H Gene

Subcellular locations from UniProtKB/Swiss-Prot for SUPT3H Gene

Subcellular locations from

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 SUPT3H gene
Compartment Confidence
nucleus 5
cytoskeleton 3
extracellular 1
cytosol 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SUPT3H Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 9726987
GO:0005654 nucleoplasm IDA --
GO:0030914 STAGA complex IBA,IDA 11564863
GO:0033276 transcription factor TFTC complex IDA 10373431
genes like me logo Genes that share ontologies with SUPT3H: view

Pathways & Interactions for SUPT3H Gene

genes like me logo Genes that share pathways with SUPT3H: view

Pathways by source for SUPT3H Gene

1 KEGG pathway for SUPT3H Gene
1 GeneGo (Thomson Reuters) pathway for SUPT3H Gene
  • Transcription Ligand-Dependent Transcription of Retinoid-Target genes

Gene Ontology (GO) - Biological Process for SUPT3H Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated NAS 9787080
GO:0006357 regulation of transcription by RNA polymerase II TAS 9787080
GO:0006366 transcription by RNA polymerase II IEA --
GO:0016578 histone deubiquitination IDA 18206972
GO:0043966 histone H3 acetylation IBA,IDA 11564863
genes like me logo Genes that share ontologies with SUPT3H: view

No data available for SIGNOR curated interactions for SUPT3H Gene

Drugs & Compounds for SUPT3H Gene

No Compound Related Data Available

Transcripts for SUPT3H Gene

mRNA/cDNA for SUPT3H Gene

9 NCBI additional mRNA sequence :
7 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 SUPT3H

Alternative Splicing Database (ASD) splice patterns (SP) for SUPT3H Gene

No ASD Table

Relevant External Links for SUPT3H Gene

GeneLoc Exon Structure for

Expression for SUPT3H Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SUPT3H Gene

Protein differential expression in normal tissues from HIPED for SUPT3H Gene

This gene is overexpressed in Adrenal (25.9), Peripheral blood mononuclear cells (25.7), and CD8 Tcells (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SUPT3H Gene

Protein tissue co-expression partners for SUPT3H Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SUPT3H

SOURCE GeneReport for Unigene cluster for SUPT3H Gene:


mRNA Expression by UniProt/SwissProt for SUPT3H Gene:

Tissue specificity: Expressed in all tissues tested including pancreas, kidney, skeletal muscle, liver, lung, placenta, brain and heart.

Evidence on tissue expression from TISSUES for SUPT3H Gene

  • Intestine(4.1)
  • Heart(4.1)
genes like me logo Genes that share expression patterns with SUPT3H: 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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for SUPT3H Gene

Orthologs for SUPT3H Gene

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

Orthologs for SUPT3H Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SUPT3H 29 30
  • 99.76 (n)
(Ornithorhynchus anatinus)
Mammalia SUPT3H 30
  • 97 (a)
(Canis familiaris)
Mammalia SUPT3H 29 30
  • 93.33 (n)
(Bos Taurus)
Mammalia SUPT3H 29 30
  • 92.5 (n)
(Rattus norvegicus)
Mammalia Supt3h 29
  • 88.06 (n)
(Mus musculus)
Mammalia Supt3 29 16 30
  • 87.85 (n)
(Monodelphis domestica)
Mammalia SUPT3H 30
  • 68 (a)
(Gallus gallus)
Aves SUPT3H 29 30
  • 80.65 (n)
(Anolis carolinensis)
Reptilia SUPT3H 30
  • 64 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia supt3h 29
  • 72.85 (n)
MGC75923 29
(Danio rerio)
Actinopterygii supt3h 29 30
  • 68.57 (n)
wufd11f09 29
Fruit Fly
(Drosophila melanogaster)
Insecta Spt3 30
  • 23 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SPT3 30 32
  • 26 (a)
Species where no ortholog for SUPT3H 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for SUPT3H Gene

Gene Tree for SUPT3H (if available)
Gene Tree for SUPT3H (if available)
Evolutionary constrained regions (ECRs) for SUPT3H: view image
Alliance of Genome Resources:
Additional Orthologs for SUPT3H

Paralogs for SUPT3H Gene

Paralogs for SUPT3H Gene

(1) SIMAP similar genes for SUPT3H Gene using alignment to 3 proteins:

  • Q5U608_HUMAN
genes like me logo Genes that share paralogs with SUPT3H: view

Variants for SUPT3H Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SUPT3H Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
911151 Uncertain Significance: Cleidocranial dysostosis 45,328,780(-) T/C
NM_001024630.4(RUNX2):c.54T>C (p.Phe18=)
916707 Pathogenic: Cleidocranial dysostosis 45,328,754(-) G/GT
rs139788537 Benign/Likely Benign: Cleidocranial dysostosis; none provided 45,328,715(-) AAAG/A
rs1562961725 Pathogenic: not provided 45,328,729(-) G/A
NM_001024630.4(RUNX2):c.3G>A (p.Met1Ile)
rs188596507 Likely Benign: not provided 45,321,795(-) C/A

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SUPT3H 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 SUPT3H Gene

Variant ID Type Subtype PubMed ID
dgv1004e201 CNV deletion 23290073
dgv1179e214 CNV loss 21293372
dgv1180e214 CNV loss 21293372
dgv1764e212 CNV loss 25503493
dgv5958n100 CNV loss 25217958
esv1627992 CNV insertion 17803354
esv1738028 CNV insertion 17803354
esv2380124 CNV deletion 18987734
esv2476554 CNV deletion 19546169
esv2516025 CNV deletion 19546169
esv2554212 CNV deletion 19546169
esv2657532 CNV deletion 23128226
esv2665320 CNV deletion 23128226
esv2666379 CNV deletion 23128226
esv2668261 CNV deletion 23128226
esv2675500 CNV deletion 23128226
esv2678447 CNV deletion 23128226
esv2732018 CNV deletion 23290073
esv2732019 CNV deletion 23290073
esv2732020 CNV deletion 23290073
esv2732023 CNV deletion 23290073
esv2732024 CNV deletion 23290073
esv2732025 CNV deletion 23290073
esv2759423 CNV gain+loss 17122850
esv2762589 CNV loss 21179565
esv2763550 CNV loss 21179565
esv3305631 CNV mobile element insertion 20981092
esv3306539 CNV mobile element insertion 20981092
esv3307979 CNV mobile element insertion 20981092
esv3340653 CNV insertion 20981092
esv3342218 CNV insertion 20981092
esv3384552 CNV insertion 20981092
esv3385505 CNV insertion 20981092
esv3401379 CNV insertion 20981092
esv3409563 CNV insertion 20981092
esv3567735 CNV deletion 23714750
esv3571034 CNV loss 25503493
esv3571035 CNV loss 25503493
esv3571036 CNV loss 25503493
esv3608841 CNV loss 21293372
esv3608843 CNV loss 21293372
esv3608845 CNV loss 21293372
esv3608847 CNV gain 21293372
esv3608851 CNV gain 21293372
esv3608853 CNV loss 21293372
esv3608854 CNV loss 21293372
esv3608855 CNV loss 21293372
esv3608857 CNV loss 21293372
esv3608858 CNV loss 21293372
esv3608860 CNV loss 21293372
esv3608861 CNV loss 21293372
esv3890844 CNV loss 25118596
nsv1024370 CNV loss 25217958
nsv1028068 CNV loss 25217958
nsv1032906 CNV loss 25217958
nsv1033815 CNV gain 25217958
nsv1109773 CNV deletion 24896259
nsv1117618 CNV deletion 24896259
nsv462938 CNV loss 19166990
nsv470817 CNV loss 18288195
nsv528130 CNV loss 19592680
nsv5286 CNV deletion 18451855
nsv5288 CNV insertion 18451855
nsv603007 CNV loss 21841781
nsv603008 CNV loss 21841781
nsv830652 CNV loss 17160897

Variation tolerance for SUPT3H Gene

Residual Variation Intolerance Score: 48.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.37; 42.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SUPT3H Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SUPT3H Gene

Disorders for SUPT3H Gene

MalaCards: The human disease database

(4) MalaCards diseases for SUPT3H Gene - From: CVR, COP, and GCD

Disorder Aliases PubMed IDs
cleidocranial dysplasia
  • ccd
hepatic adenomas, familial
  • liver cell adenomas, familial
  • dysostoses
generalized atherosclerosis
  • generalised atherosclerosis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SUPT3H

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SUPT3H: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SUPT3H Gene

Publications for SUPT3H Gene

  1. Characterization of a human homologue of the Saccharomyces cerevisiae transcription factor spt3 (SUPT3H). (PMID: 9787080) Yu J … Olsen BR (Genomics 1998) 3 4 22
  2. Histone-like TAFs within the PCAF histone acetylase complex. (PMID: 9674425) Ogryzko VV … Nakatani Y (Cell 1998) 2 3 4
  3. A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID. (PMID: 9726987) Martinez E … Roeder RG (The Journal of biological chemistry 1998) 2 3 4
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40

Products for SUPT3H Gene

Sources for SUPT3H Gene