FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\IntS1
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General Information
Symbol
Dmel\IntS1
Species
D. melanogaster
Name
Integrator 1
Annotation Symbol
CG3173
Feature Type
protein_coding_gene
FlyBase ID
FBgn0034964
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Summary
Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes (PubMed:21078872, PubMed:23097424, PubMed:32966759). The integrator complex provides a quality checkpoint during transcription elongation by driving premature transcription termination of transcripts that are unfavorably configured for transcriptional elongation: the complex terminates transcription by (1) catalyzing dephosphorylation of the C-terminal domain (CTD) of Pol II subunit Polr2A/Rbp1 and Spt5, and (2) degrading the exiting nascent RNA transcript via endonuclease activity (PubMed:32966759). The integrator complex is also involved in the 3'-end processing of the U7 snRNA, and also the spliceosomal snRNAs U1, U2, U4 and U5 (PubMed:21078872, PubMed:23097424, PubMed:23288851). Required for the normal expression of the Integrator complex component IntS12 (PubMed:23288851). (UniProt, Q9W1C5)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
60B5-60B5
Sequence location
Recombination map
2-106
RefSeq locus
NT_033778 REGION:24037943..24044458
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 (8 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (5 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in positive regulation of neuron differentiation
inferred from mutant phenotype
(Zhang et al., 2019)
involved_in RNA polymerase II transcription initiation surveillance
inferred from direct assay
(Fujiwara et al., 2023, Huang et al., 2020, Tatomer et al., 2019)
involved_in snRNA 3'-end processing
inferred from direct assay
(Ezzeddine et al., 2011)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in snRNA processing
inferred from sequence or structural similarity with UniProtKB:Q8N201
(Baillat et al., 2005)
involved_in U2 snRNA 3'-end processing
inferred from electronic annotation with InterPro:IPR038902
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN001081376
(GO Reference Genome Project, 2011-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
part_of INTAC complex
inferred from direct assay
(Fujiwara et al., 2023, Huang et al., 2020)
part_of integrator complex
inferred from direct assay
(Lin et al., 2024)
inferred from direct assay
(Tatomer et al., 2019)
is_active_in nucleus
inferred from direct assay
(Lin et al., 2024)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of integrator complex
inferred from biological aspect of ancestor with PANTHER:PTN001081376
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with UniProtKB:Q8N201
(Baillat et al., 2005)
inferred from electronic annotation with InterPro:IPR038902
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the Integrator subunit 1 family. (Q9W1C5)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
INTEGRATOR COMPLEX -
The Integrator complex is an RNA Polymerase II (Pol II)-associated endonucleolytic complex that mediates 3'-end generation of small nuclear RNAs (snRNAs) and other non-coding RNAs, and modulates Pol II promoter-proximal pausing and transcript elongation. (Adapted from PMID:36180603.)
INTEGRATOR-PP2A COMPLEX -
The Integrator-PP2A complex (INTAC) is a complex formed between the endonucleolytic integrator complex and a serine/threonine-protein phosphatase 2A (PP2A) module. The PP2A module is formed from a PP2A-A scaffold subunit and a PP2A-C catalytic subunit, but lacks the PP2A-B regulatory subunit characteristic of canonical PP2A complexes. INTAC inhibits promoter-proximal pause release of RNA polymerase II (Pol II) by the dephosphorylation of a number of targets including the C-terminal domain of Pol II. (Adapted from PMID:36180603.)
Protein Function (UniProtKB)
Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes (PubMed:21078872, PubMed:23097424, PubMed:32966759). The integrator complex provides a quality checkpoint during transcription elongation by driving premature transcription termination of transcripts that are unfavorably configured for transcriptional elongation: the complex terminates transcription by (1) catalyzing dephosphorylation of the C-terminal domain (CTD) of Pol II subunit Polr2A/Rbp1 and Spt5, and (2) degrading the exiting nascent RNA transcript via endonuclease activity (PubMed:32966759). The integrator complex is also involved in the 3'-end processing of the U7 snRNA, and also the spliceosomal snRNAs U1, U2, U4 and U5 (PubMed:21078872, PubMed:23097424, PubMed:23288851). Required for the normal expression of the Integrator complex component IntS12 (PubMed:23288851).
(UniProt, Q9W1C5)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\IntS1 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 Q9W1C5)

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 5.52

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
IntS1-RA
FBtr0072168
NM_138031
6401
2053
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
IntS1-PA
FBpp0072077
235.1
2053
6.58
Q9W1C5
NP_611875
AAF47145
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)

Belongs to the multiprotein complex Integrator, at least composed of IntS1, IntS2, IntS3, IntS4, omd/IntS5, IntS6, defl/IntS7, IntS8, IntS9, IntS10, IntS11, IntS12, asun/IntS13, IntS14 and IntS15 (PubMed:23097424, PubMed:31530651, PubMed:32966759, PubMed:39032490). The core complex associates with protein phosphatase 2A subunits mts/PP2A and Pp2A-29B, to form the Integrator-PP2A (INTAC) complex (PubMed:32966759, PubMed:37995689). Within the complex, interacts with IntS12 and IntS9 (PubMed:23288851). Interaction with IntS12 is likely to be important for promoting 3'-end processing of snRNAs (PubMed:23288851). Interacts with Mediator complex members Cdk8 and CycC (PubMed:23097424).

(UniProt, Q9W1C5)
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\IntS1 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).

0.95

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 INTAC complex
inferred from direct assay
(Fujiwara et al., 2023, Huang et al., 2020)
part_of integrator complex
inferred from direct assay
(Lin et al., 2024)
inferred from direct assay
(Tatomer et al., 2019)
is_active_in nucleus
inferred from direct assay
(Lin et al., 2024)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\IntS1 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 ( 5 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of IntS1
Transgenic constructs containing regulatory region of IntS1
Aberrations (Deficiencies and Duplications) ( 7 )
Inferred from experimentation ( 7 )
Gene disrupted in
Df(2R)Exel6080
(Ryder, 2004.4.26)
Df(2R)Exel6081
(Ryder, 2004.4.26)
Gene not disrupted in
Df(2R)MAN1Δ6
(Pinto et al., 2008)
Df(2R)MAN1Δ26
(Pinto et al., 2008)
Df(2R)MAN1Δ47
(Pinto et al., 2008)
Df(2R)MAN1Δ128
(Pinto et al., 2008)
Gene partially disrupted in
Df(2R)MAN1Δ296
(Pinto et al., 2008)
Inferred from location ( 2 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
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\INTS1
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\Ints1
9 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Ints1
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\gcnt4
6 of 13
Yes
Yes
Xtro\ints1
2 of 13
No
Yes
Danio rerio (Zebrafish) (1)
Drer\ints1
13 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\ints-1
7 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP008047
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:IntS1. 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 ( 1 )
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
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?
INTS1; integrator complex subunit 1
14 of 14
611345
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
Interaction Browsers
View in FlyBase Interactions Browser   View in MIST tool (external link)
Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
IntS1 - Cdk8
anti tag coimmunoprecipitation, western blot
(Chen et al., 2012)
IntS1 - CycC
anti tag coimmunoprecipitation, western blot
(Chen et al., 2012)
IntS1 - IntS11
anti tag coimmunoprecipitation, Identification by mass spectrometry, western blot, pull down
(Lin et al., 2024, Lin et al., 2022, Huang et al., 2020, Tatomer et al., 2019)
IntS1 - IntS12
anti tag coimmunoprecipitation, Identification by mass spectrometry, two hybrid, western blot
(Lin et al., 2024, Huang et al., 2020, Chen et al., 2013)
IntS1 - IntS14
anti tag coimmunoprecipitation, western blot
(Chen et al., 2012)
IntS1 - IntS4
anti tag coimmunoprecipitation, Identification by mass spectrometry, western blot
(Huang et al., 2020)
IntS1 - IntS6
anti tag coimmunoprecipitation, western blot, Identification by mass spectrometry
(Lin et al., 2024)
IntS1 - IntS8
anti tag coimmunoprecipitation, Identification by mass spectrometry, western blot
(Lin et al., 2024, Huang et al., 2020)
IntS1 - IntS9
anti tag coimmunoprecipitation, western blot, Identification by mass spectrometry, pull down
(Lin et al., 2024, Lin et al., 2022, Huang et al., 2020, Tatomer et al., 2019)
IntS1 - Pp2A-29B
anti tag coimmunoprecipitation, western blot, Identification by mass spectrometry
(Huang et al., 2020)
IntS1 - Rrp40
anti tag coimmunoprecipitation, Identification by mass spectrometry, western blot
(Tatomer et al., 2019)
IntS1 - asun
anti tag coimmunoprecipitation, western blot
(Chen et al., 2012)
IntS1 - defl
anti tag coimmunoprecipitation, western blot, Identification by mass spectrometry
(Lin et al., 2024, Huang et al., 2020)
IntS1 - mts
anti tag coimmunoprecipitation, western blot, Identification by mass spectrometry
(Huang et al., 2020)
IntS1 - omd
anti tag coimmunoprecipitation, western blot, Identification by mass spectrometry
(Lin et al., 2024, Huang et al., 2020, Tatomer et al., 2019)
Summary of Genetic Interactions
Interaction Browsers
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Belongs to the multiprotein complex Integrator, at least composed of IntS1, IntS2, IntS3, IntS4, omd/IntS5, IntS6, defl/IntS7, IntS8, IntS9, IntS10, IntS11, IntS12, asun/IntS13, IntS14 and IntS15 (PubMed:23097424, PubMed:31530651, PubMed:32966759, PubMed:39032490). The core complex associates with protein phosphatase 2A subunits mts/PP2A and Pp2A-29B, to form the Integrator-PP2A (INTAC) complex (PubMed:32966759, PubMed:37995689). Within the complex, interacts with IntS12 and IntS9 (PubMed:23288851). Interaction with IntS12 is likely to be important for promoting 3'-end processing of snRNAs (PubMed:23288851). Interacts with Mediator complex members Cdk8 and CycC (PubMed:23097424).
(UniProt, Q9W1C5 )
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
FlyBase
External Links
External Data
Linkouts
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2R
Recombination map
2-106
Cytogenetic map
60B5-60B5
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
60B5-60B5
Limits computationally determined from genome sequence between P{lacW}Phmk07623&P{lacW}tsrk05633 and P{EP}EP503
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

2-106

(FlyBase, 2016)

2-109.9

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (8)
Genomic Clones (14)
 

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

cDNA Clones (18)
 

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
           

          polyclonal

          (Ezzeddine et al., 2011)
          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

              Source for identity of: IntS1 CG3173

              (Baillat et al., 2005)
              Nomenclature comments
              Etymology
              Synonyms and Secondary IDs (6)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 35 )
              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.
              iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
              MIST (protein-protein) - An integrated Molecular Interaction Database
              Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
              References (50)