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SUPT4H1 Gene(Protein Coding)

SPT4 Homolog, DSIF Elongation Factor Subunit

GCID:
GC17M058345
GIFtS:
54
Genes Participants
UDN Logo

Aliases for SUPT4H1 Gene

Aliases for SUPT4H1 Gene

  • SPT4 Homolog, DSIF Elongation Factor Subunit 2 3 5
  • DRB Sensitivity-Inducing Factor 14 KDa Subunit 3 4
  • DSIF P14 3 4
  • SUPT4H 3 4
  • SPT4H 3 4
  • DRB Sensitivity-Inducing Factor Small Subunit 4
  • Suppressor Of Ty 4 Homolog 1 (S. Cerevisiae) 2
  • Suppressor Of Ty (S.Cerevisiae) 4 Homolog 1 2
  • Suppressor Of Ty 4 Homolog 1 3
  • Small HSpt4 Subunit 3
  • DSIF Small Subunit 4
  • Supt4a 3
  • HSPT4 4
  • SPT4 3

External Ids for SUPT4H1 Gene

Previous HGNC Symbols for SUPT4H1 Gene

  • SUPT4H

Previous GeneCards Identifiers for SUPT4H1 Gene

  • GC17M056166
  • GC17M058904
  • GC17M056764
  • GC17M056897
  • GC17M053777
  • GC17M056422
  • GC17M051783

Summaries for SUPT4H1 Gene

Entrez Gene Summary for SUPT4H1 Gene

  • This gene encodes the small subunit of DRB (5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole) sensitivity-inducing factor (DSIF) complex, which regulates mRNA processing and transcription elongation by RNA polymerase II. The encoded protein is localized to the nucleus and interacts with the large subunit (SUPT5H) to form the DSIF complex. Related pseudogenes have been identified on chromosomes 2 and 12. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2012]

GeneCards Summary for SUPT4H1 Gene

SUPT4H1 (SPT4 Homolog, DSIF Elongation Factor Subunit) is a Protein Coding gene. Diseases associated with SUPT4H1 include hiv-1. Among its related pathways are Chromatin Regulation / Acetylation and Formation of the HIV-1 Early Elongation Complex. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and protein heterodimerization activity.

UniProtKB/Swiss-Prot for SUPT4H1 Gene

  • Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3 terminus and may allow repeated attempts at transcription through natural pause sites. DSIF can also positively regulate transcriptional elongation and is required for the efficient activation of transcriptional elongation by the HIV-1 nuclear transcriptional activator, Tat. DSIF acts to suppress transcriptional pausing in transcripts derived from the HIV-1 LTR and blocks premature release of HIV-1 transcripts at terminator sequences.

Gene Wiki entry for SUPT4H1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SUPT4H1 Gene

Genomics for SUPT4H1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for SUPT4H1 Gene

Enhancers for SUPT4H1 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 SUPT4H1 on UCSC Golden Path with GeneCards custom track

Promoters for SUPT4H1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SUPT4H1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the SUPT4H1 gene promoter:

Genomic Location for SUPT4H1 Gene

Chromosome:
17
Start:
58,345,175 bp from pter
End:
58,353,093 bp from pter
Size:
7,919 bases
Orientation:
Minus strand

Genomic View for SUPT4H1 Gene

Genes around SUPT4H1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SUPT4H1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SUPT4H1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SUPT4H1 Gene

Proteins for SUPT4H1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SUPT4H1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P63272-SPT4H_HUMAN
    Recommended name:
    Transcription elongation factor SPT4
    Protein Accession:
    P63272
    Secondary Accessions:
    • B2R4X8
    • D3DTZ4
    • Q16550
    • Q62387
    • Q6ZP89

    Protein attributes for SUPT4H1 Gene

    Size:
    117 amino acids
    Molecular mass:
    13193 Da
    Quaternary structure:
    • Interacts with SUPT5H to form DSIF. DSIF interacts with the positive transcription elongation factor b complex (P-TEFb complex), which is composed of CDK9 and cyclin-T (CCNT1 or CCNT2). DSIF interacts with RNA polymerase II, and this interaction is reduced by phosphorylation of the C-terminal domain (CTD) of POLR2A by P-TEFb. DSIF also interacts with the NELF complex, which is composed of WHSC2/NELFA, COBRA1/NELFB, TH1L/NELFD and RDBP/NELFE, and this interaction occurs following prior binding of DSIF to RNA polymerase II. DSIF also interacts with HRMT1L2/PRMT1, HTATSF1/TATSF1, RNGTT/CAP1A, SKB1/PRMT5, SUPT6H, and can interact with PIN1.

    Three dimensional structures from OCA and Proteopedia for SUPT4H1 Gene

neXtProt entry for SUPT4H1 Gene

Proteomics data for SUPT4H1 Gene at MOPED

Protein Expression for SUPT4H1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SUPT4H1 Gene

  • Ubiquitination at Lys 43 and Lys 81
  • Modification sites at PhosphoSitePlus

Other Protein References for SUPT4H1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SUPT4H1 Gene

Domains & Families for SUPT4H1 Gene

Protein Domains for SUPT4H1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SUPT4H1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P63272

UniProtKB/Swiss-Prot:

SPT4H_HUMAN :
  • Belongs to the SPT4 family.
Family:
  • Belongs to the SPT4 family.
genes like me logo Genes that share domains with SUPT4H1: view

No data available for Gene Families for SUPT4H1 Gene

Function for SUPT4H1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for SUPT4H1 Gene

GENATLAS Biochemistry:
putative chromatin structure regulator,yeast spt4 (suppressor of Ty) homolog,ubiquitously expressed
UniProtKB/Swiss-Prot Function:
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3 terminus and may allow repeated attempts at transcription through natural pause sites. DSIF can also positively regulate transcriptional elongation and is required for the efficient activation of transcriptional elongation by the HIV-1 nuclear transcriptional activator, Tat. DSIF acts to suppress transcriptional pausing in transcripts derived from the HIV-1 LTR and blocks premature release of HIV-1 transcripts at terminator sequences.

Gene Ontology (GO) - Molecular Function for SUPT4H1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10075709
genes like me logo Genes that share ontologies with SUPT4H1: view

Phenotypes for SUPT4H1 Gene

MGI mutant phenotypes for SUPT4H1:
inferred from 2 alleles
GenomeRNAi human phenotypes for SUPT4H1:
genes like me logo Genes that share phenotypes with SUPT4H1: view

Animal Models for SUPT4H1 Gene

MGI Knock Outs for SUPT4H1:

Animal Model Products

CRISPR Products

miRNA for SUPT4H1 Gene

miRTarBase miRNAs that target SUPT4H1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SUPT4H1 Gene

Localization for SUPT4H1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SUPT4H1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SUPT4H1 Gene COMPARTMENTS Subcellular localization image for SUPT4H1 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for SUPT4H1 Gene

Pathways & Interactions for SUPT4H1 Gene

genes like me logo Genes that share pathways with SUPT4H1: view

Gene Ontology (GO) - Biological Process for SUPT4H1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 9450929
GO:0006355 regulation of transcription, DNA-templated IEA,TAS 8786137
GO:0006366 transcription from RNA polymerase II promoter TAS --
GO:0016032 viral process TAS --
GO:0032785 negative regulation of DNA-templated transcription, elongation IDA 9450929
genes like me logo Genes that share ontologies with SUPT4H1: view

No data available for SIGNOR curated interactions for SUPT4H1 Gene

Drugs & Compounds for SUPT4H1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SUPT4H1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for SUPT4H1 Gene

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(568) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SUPT4H1 Gene

Suppressor of Ty 4 homolog 1 (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SUPT4H1 Gene

No ASD Table

Relevant External Links for SUPT4H1 Gene

GeneLoc Exon Structure for
SUPT4H1
ECgene alternative splicing isoforms for
SUPT4H1

Expression for SUPT4H1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for SUPT4H1 Gene

mRNA expression in normal human tissues for SUPT4H1 Gene
mRNA expression by BioGPS for SUPT4H1 GenemRNA expression by GTEx for SUPT4H1 Gene

mRNA differential expression in normal tissues according to GTEx for SUPT4H1 Gene

This gene is overexpressed in Whole Blood (x4.9).

Protein differential expression in normal tissues from HIPED for SUPT4H1 Gene

This gene is overexpressed in Breast (14.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SUPT4H1 Gene



SOURCE GeneReport for Unigene cluster for SUPT4H1 Gene Hs.439481

mRNA Expression by UniProt/SwissProt for SUPT4H1 Gene

P63272-SPT4H_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with SUPT4H1: view

Protein tissue co-expression partners for SUPT4H1 Gene

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for SUPT4H1 Gene

Orthologs for SUPT4H1 Gene

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

Orthologs for SUPT4H1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia SUPT4H1 35
  • 94.02 (n)
  • 100 (a)
SUPT4H1 36
  • 100 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia SUPT4H1 35
  • 96.3 (n)
  • 100 (a)
SUPT4H1 36
  • 100 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Supt4a 35
  • 94.87 (n)
  • 100 (a)
Supt4a 16
Supt4a 36
  • 100 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia SUPT4H1 35
  • 100 (n)
  • 100 (a)
SUPT4H1 36
  • 100 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Supt4h1 35
  • 93.73 (n)
  • 100 (a)
oppossum
(Monodelphis domestica)
 Mammalia -- 36
  • 97 (a)
 OneToMany
-- 36
  • 83 (a)
 OneToMany
chicken
(Gallus gallus)
 Aves SUPT4H1 35
  • 81.77 (n)
  • 97.44 (a)
SUPT4H1 36
  • 95 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia Str.5867 35
supt4h1 35
  • 79.77 (n)
  • 95.73 (a)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.23755 35
zebrafish
(Danio rerio)
 Actinopterygii Dr.29315 35
supt4h1 35
  • 78.63 (n)
  • 88.03 (a)
supt4h1 36
  • 88 (a)
 OneToOne
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.1288 35
fruit fly
(Drosophila melanogaster)
 Insecta spt4 37
  • 62 (a)
spt4 35
  • 63.1 (n)
  • 62.5 (a)
spt4 36
  • 59 (a)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP005428 35
  • 65.79 (n)
  • 65.79 (a)
worm
(Caenorhabditis elegans)
 Secernentea spt-4 37
  • 58 (a)
spt-4 35
  • 57.46 (n)
  • 58.1 (a)
spt-4 36
  • 51 (a)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes SPT4 36
  • 44 (a)
 OneToOne
SPT4 38
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.956 35
bread mold
(Neurospora crassa)
 Ascomycetes NCU03838 35
  • 48.6 (n)
  • 42.06 (a)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.5304 36
  • 68 (a)
 OneToOne
Species with no ortholog for SUPT4H1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 SUPT4H1 Gene

ENSEMBL:
Gene Tree for SUPT4H1 (if available)
TreeFam:
Gene Tree for SUPT4H1 (if available)

Paralogs for SUPT4H1 Gene

Pseudogenes.org Pseudogenes for SUPT4H1 Gene

genes like me logo Genes that share paralogs with SUPT4H1: view

No data available for Paralogs for SUPT4H1 Gene

Variants for SUPT4H1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SUPT4H1 Gene

Variant ID Type Subtype PubMed ID
nsv517229 CNV Gain+Loss 19592680
nsv509663 CNV Insertion 20534489
nsv819948 CNV Loss 19587683
nsv908641 CNV Loss 21882294

Variation tolerance for SUPT4H1 Gene

Residual Variation Intolerance Score: 48.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.17; 3.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SUPT4H1 Gene

HapMap Linkage Disequilibrium report
SUPT4H1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations from dbSNP and Humsavar for SUPT4H1 Gene

Disorders for SUPT4H1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SUPT4H1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
hiv-1
  • aids, slow progression to
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SUPT4H1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SUPT4H1
genes like me logo Genes that share disorders with SUPT4H1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SUPT4H1 Gene

Publications for SUPT4H1 Gene

  1. Structure and function of the human transcription elongation factor DSIF. (PMID: 10075709) Yamaguchi Y. … Handa H. (J. Biol. Chem. 1999) 2 3 4 67
  2. The small hSpt4 subunit of the human transcription elongation factor DSIF is a Zn-finger protein with alpha/beta type topology. (PMID: 18373978) Wenzel S. … WAPhrl B.M. (Biochem. Biophys. Res. Commun. 2008) 3 23
  3. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. (PMID: 9450929) Wada T. … Handa H. (Genes Dev. 1998) 3 23
  4. Isolation and characterization of the human and mouse homologues (SUPT4H and Supt4h) of the yeast SPT4 gene. (PMID: 8786137) Chiang P.-W. … Kurnit D.M. (Genomics 1996) 2 3
  5. Identification and analysis of a functional human homolog of the SPT4 gene of Saccharomyces cerevisiae. (PMID: 8649394) Hartzog G.A. … Winston F. (Mol. Cell. Biol. 1996) 3 23

Products for SUPT4H1 Gene

Sources for SUPT4H1 Gene

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