FB2024_02 , released April 23, 2024
Gene: Dmel\spt4
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General Information
Symbol
Dmel\spt4
Species
D. melanogaster
Name
spt4
Annotation Symbol
CG12372
Feature Type
protein_coding_gene
FlyBase ID
FBgn0028683
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Summary
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. DSIF enhances transcriptional pausing at sites proximal to the promoter, which may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF may also promote transcriptional elongation within coding regions. DSIF is required for the transcriptional induction of heat shock response genes and regulation of genes which control anterior-posterior patterning during embryonic development (By similarity). (UniProt, Q9TVQ5)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

DSIF, Dspt4, l(2)k05316

Key Links
Genomic Location
Cytogenetic map
49B10-49B10
Sequence location
Recombination map
2-67
RefSeq locus
NT_033778 REGION:12633589..12634172
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (15 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
contributes_to RNA polymerase II complex binding
inferred from direct assay
(Qiu and Gilmour, 2017)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables protein heterodimerization activity
inferred from sequence or structural similarity with UniProtKB:P63272
(Gene Ontology Curators, 2002-)
enables zinc ion binding
inferred from electronic annotation with InterPro:IPR009287
(InterPro Project Members, 2004-)
Biological Process (7 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in negative regulation of DNA-templated transcription, elongation
inferred from direct assay
(Wu et al., 2003)
involved_in negative regulation of transcription by RNA polymerase II
inferred from direct assay
(Qiu and Gilmour, 2017)
inferred from direct assay
(Wu et al., 2003)
involved_in transcription elongation by RNA polymerase II
inferred from direct assay
(Wu et al., 2003)
Terms Based on Predictions or Assertions (7 terms)
CV Term
Evidence
References
involved_in negative regulation of DNA-templated transcription, elongation
inferred from sequence or structural similarity with UniProtKB:P63272
(Gene Ontology Curators, 2002-)
involved_in negative regulation of transcription by RNA polymerase II
inferred from sequence or structural similarity with UniProtKB:P63272
(Gene Ontology Curators, 2002-)
involved_in positive regulation of DNA-templated transcription, elongation
inferred from sequence or structural similarity with UniProtKB:P63272
(Gene Ontology Curators, 2002-)
involved_in positive regulation of transcription by RNA polymerase II
inferred from sequence or structural similarity with UniProtKB:P63272
(Gene Ontology Curators, 2002-)
involved_in regulation of DNA-templated transcription
inferred from electronic annotation with InterPro:IPR009287
(InterPro Project Members, 2004-)
involved_in transcription elongation by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN000306261
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with UniProtKB:P63272
(Gene Ontology Curators, 2002-)
involved_in transcription elongation-coupled chromatin remodeling
inferred from electronic annotation with InterPro:IPR009287
(InterPro Project Members, 2004-)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
part_of DSIF complex
inferred from direct assay
(Qiu and Gilmour, 2017)
located_in nucleus
inferred from direct assay
(Zhang et al., 2004)
located_in polytene chromosome interband
inferred from direct assay
(Wu et al., 2003)
located_in polytene chromosome puff
inferred from direct assay
(Wu et al., 2003)
part_of transcription elongation factor complex
inferred from direct assay
(Zhang et al., 2004)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of DSIF complex
inferred from biological aspect of ancestor with PANTHER:PTN000306261
(GO Reference Genome Project, 2011-)
located_in nucleus
inferred from electronic annotation with InterPro:IPR009287
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the SPT4 family. (Q9TVQ5)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
DRB SENSITIVITY-INDUCING FACTOR COMPLEX -
The DRB sensitivity-inducing factor (DSIF) complex is a heterodimer that acts as both a positive and negative transcription elongation factor. DSIF together with negative elongation factor (NELF) complex associates with RNA polymerase II and causes transcriptional pausing. Phosphorylation of DSIF-NELF complexes dissociates NELF from the elongation complex and transforms DSIF into a positive elongation factor. (Adapted from FBrf0235113, FBrf0211126 and FBrf0203142).
Protein Function (UniProtKB)
Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. DSIF enhances transcriptional pausing at sites proximal to the promoter, which may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF may also promote transcriptional elongation within coding regions. DSIF is required for the transcriptional induction of heat shock response genes and regulation of genes which control anterior-posterior patterning during embryonic development (By similarity).
(UniProt, Q9TVQ5)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\spt4 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9TVQ5)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.46

Low-frequency RNA-Seq exon junction(s) not annotated.

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
spt4-RA
FBtr0087840
NM_136958
457
116
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
spt4-PA
FBpp0086953
13.3
116
8.97
Q9TVQ5
NP_610802
AAF58482
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Spt5 to form DSIF. DSIF interacts with TRX, RNA polymerase II and with the FACT complex, which is composed of DRE4/SPT16 and SSRP/SSRP1. DSIF can also interact with the exosome, a complex with 3'-5' exoribonuclease activity which is composed of at least Csl4, Dis3, Mtr3, Rrp4, Rrp6, Rrp40, Rrp42, Rrp46 and Ski6. DSIF may also interact with the positive transcription elongation factor b complex (P-TEFb complex), which is composed of Cdk9 and cyclin-T (CycT).

(UniProt, Q9TVQ5)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\spt4 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.52

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of DSIF complex
inferred from direct assay
(Qiu and Gilmour, 2017)
located_in nucleus
inferred from direct assay
(Zhang et al., 2004)
located_in polytene chromosome interband
inferred from direct assay
(Wu et al., 2003)
located_in polytene chromosome puff
inferred from direct assay
(Wu et al., 2003)
part_of transcription elongation factor complex
inferred from direct assay
(Zhang et al., 2004)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\spt4 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of spt4
Transgenic constructs containing regulatory region of spt4
Aberrations (Deficiencies and Duplications) ( 6 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal | recessive
partially lethal - majority die | recessive
Other Phenotypes
Allele
melanotic mass phenotype, with Scer\GAL4SPARC-MI00329-GAL4
Phenotype manifest in
Allele
fat body, with Scer\GAL4SPARC-MI00329-GAL4
melanotic mass, with Scer\GAL4SPARC-MI00329-GAL4
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\SUPT4H1
14 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Supt4h1
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (2)
Mmus\Supt4a
14 of 14
Yes
Yes
Mmus\Supt4b
9 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\supt4h1
7 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\supt4h1
13 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\spt-4
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP005428
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\AT5G08565
12 of 13
Yes
Yes
Atha\SPT42
12 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\SPT4
12 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\spt4
11 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:spt4. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 1 )
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    SUPT4H1; SPT4 homolog, DSIF elongation factor subunit
    14 of 14
    603555
        Functional Complementation Data
        Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
        Interactions
        Summary of Physical Interactions
        esyN Network Diagram
        Show neighbor-neighbor interactions:
        Show/hide secondary interactors 
        (data from AllianceMine provided by esyN)
        Select Layout:
        Legend:
        Protein
        RNA
        Selected Interactor(s)
        Interactions Browser
        View in Interactions Browser
        Please see the Physical Interaction reports below for full details
        MIST Molecular Interaction Search Tool
        View in MIST tool (external link)
        Please see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        spt4 - Cbp20
        anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
        (Rhee et al., 2014)
        spt4 - Spt5
        anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based, anti tag western blot, pull down, molecular weight estimation by staining, affinity chromatography technology
        (Dollinger et al., 2023, Pereira and Paro, 2017, Qiu and Gilmour, 2017, Rhee et al., 2014, Harvey et al., 2013)
        Summary of Genetic Interactions
        esyN Network Diagram
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Interacts with Spt5 to form DSIF. DSIF interacts with TRX, RNA polymerase II and with the FACT complex, which is composed of DRE4/SPT16 and SSRP/SSRP1. DSIF can also interact with the exosome, a complex with 3'-5' exoribonuclease activity which is composed of at least Csl4, Dis3, Mtr3, Rrp4, Rrp6, Rrp40, Rrp42, Rrp46 and Ski6. DSIF may also interact with the positive transcription elongation factor b complex (P-TEFb complex), which is composed of Cdk9 and cyclin-T (CycT).
        (UniProt, Q9TVQ5 )
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map
        2-67
        Cytogenetic map
        49B10-49B10
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        49B10-49B10
        Limits computationally determined from genome sequence between P{EP}AmphEP2175&P{lacW}spt4k05316 and P{PZ}ox1
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        49B7-49B11
        (Chiang et al., 1999, Chiang, 1998.11.20, BDGP Project Members, 1994-1999)
        49B7-49B11
        (determined by in situ hybridisation)
        (Spradling et al., 1999)
        Experimentally Determined Recombination Data
        Location

        2-67

        (FlyBase, 2016)

        2-69.7

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (6)
        Genomic Clones (16)
         

        Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

        cDNA Clones (3)
         

        Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

        cDNA clones, fully sequenced
        BDGP DGC clones
        Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
          Other clones
          RNAi and Array Information
          Linkouts
          DRSC - Results frm RNAi screens
          Antibody Information
          Laboratory Generated Antibodies
           
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments
              Relationship to Other Genes
              Source for database merge of
              Additional comments
              Nomenclature History
              Source for database identify of
              Nomenclature comments
              Etymology
              Synonyms and Secondary IDs (11)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 45 )
              Sequence Crossreferences
              NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
              GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
              GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
              RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
              UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
              UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
              Other crossreferences
              AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
              DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
              EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
              FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
              FlyMine - An integrated database for Drosophila genomics
              InterPro - A database of protein families, domains and functional sites
              KEGG Genes - Molecular building blocks of life in the genomic space.
              MARRVEL_MODEL - MARRVEL (model organism gene)
              Linkouts
              BioGRID - A database of protein and genetic interactions.
              Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
              DroID - A comprehensive database of gene and protein interactions.
              DRSC - Results frm RNAi screens
              Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
              FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
              Flygut - An atlas of the Drosophila adult midgut
              FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
              KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
              MIST (protein-protein) - An integrated Molecular Interaction Database
              Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
              References (81)