FB2025_02 , released April 17, 2025
Gene: Dmel\Pits
Open Close
General Information
Symbol
Dmel\Pits
Species
D. melanogaster
Name
Protein interacting with Ttk69 and Sin3A
Annotation Symbol
CG11138
Feature Type
protein_coding_gene
FlyBase ID
FBgn0030400
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
11B1-11B2
Sequence location
Recombination map
1-39
RefSeq locus
NC_004354 REGION:12569169..12583193
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 (9 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables ubiquitin protein ligase activity
inferred from direct assay
(Marcogliese et al., 2018)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables transcription corepressor activity
inferred from biological aspect of ancestor with PANTHER:PTN000775901
(GO Reference Genome Project, 2011-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in regulation of gene expression
inferred from mutant phenotype
(Liaw, 2016)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in regulation of transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN000775901
(GO Reference Genome Project, 2011-)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Liaw, 2016)
located_in nuclear periphery
inferred from direct assay
(Rohrbaugh et al., 2013)
located_in nucleoplasm
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from direct assay
(Marcogliese et al., 2018, Liaw, 2016)
colocalizes_with polytene chromosome
inferred from direct assay
(Rohrbaugh et al., 2013)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000775901
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
UNCLASSIFIED RING DOMAIN UBIQUITIN LIGASES -
This group comprises RING domain ubiquitin ligases that do not classify under other groups in FlyBase.
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\Pits 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 B7Z143)

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 5.50

Gene model reviewed during 5.45

RNA-Seq data support additional isoforms with extended 3' UTRs of differing length, some of which appear to be stage and/or tissue specific.

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Gene model reviewed during 5.55

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Pits-RC
FBtr0073662
NM_132581
5226
615
Pits-RD
FBtr0273245
NM_001144720
3811
630
Pits-RE
FBtr0331718
NM_001272557
5718
585
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
Pits-PC
FBpp0073495
60.0
615
8.50
Q9VYL7
NP_572809
AAF48175
Pits-PD
FBpp0271753
61.6
630
8.50
B7Z143
NP_001138192
ACL82924
Pits-PE
FBpp0304107
56.9
585
8.27
M9PHN7
NP_001259486
AGB95329
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\Pits 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).

-0.98

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 2 -- 3
organism
(Liaw, 2016)
embryonic stage 10 -- 13
anterior midgut primordium
(Liaw, 2016)
posterior midgut primordium
(Liaw, 2016)
fused midgut primordium
(Liaw, 2016)
presumptive embryonic/larval central nervous system
(Liaw, 2016)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Liaw, 2016)
located_in nuclear periphery
inferred from direct assay
(Rohrbaugh et al., 2013)
located_in nucleoplasm
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from direct assay
(Marcogliese et al., 2018, Liaw, 2016)
colocalizes_with polytene chromosome
inferred from direct assay
(Rohrbaugh et al., 2013)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Pits 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 ( 19 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pits
Transgenic constructs containing regulatory region of Pits
Aberrations (Deficiencies and Duplications) ( 2 )
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 | female, with PitsMI02926-TG4.1, Scer\GAL4Pits-MI02926-TG4.1
lethal | female, with PitsRC.UAS.Tag:HA, Scer\GAL4Pits-MI02926-TG4.1
lethal - all die before end of first instar larval stage | male
partially lethal
partially lethal - majority die, with Scer\GAL4Act5C.PI
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4GMR.PU
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
abnormal locomotor behavior | adult stage, with Scer\GAL4Act5C.PI, Zzzz\VHHdeGradFP.UAS
abnormal locomotor behavior | adult stage | progressive, with Scer\GAL4Act5C.PI, Zzzz\VHHdeGradFP.UAS
abnormal locomotor behavior | adult stage | progressive, with Scer\GAL4nSyb.PS, Zzzz\VHHdeGradFP.UAS
abnormal locomotor behavior | progressive, with Scer\GAL4nSyb.PS
abnormal neuroanatomy | adult stage | progressive, with Scer\GAL4nSyb.PS, Zzzz\VHHdeGradFP.UAS
bang sensitive | progressive, with Scer\GAL4nSyb.PS
decreased cell number | progressive, with Scer\GAL4ninaE.PT
short lived, with Scer\GAL4Act5C.PI, Zzzz\VHHdeGradFP.UAS
short lived, with Scer\GAL4nSyb.PS, Zzzz\VHHdeGradFP.UAS
visible | adult stage, with Scer\GAL4nub-AC-62
Phenotype manifest in
Allele
axon | adult stage | decreased number, with Scer\GAL4Act5C.PI, Zzzz\VHHdeGradFP.UAS
axon | adult stage | decreased number, with Scer\GAL4nSyb.PS, Zzzz\VHHdeGradFP.UAS
lipid droplet | adult stage, with Scer\GAL4ninaE.PT
marginal nerve, with Scer\GAL4Act5C.PI, Zzzz\VHHdeGradFP.UAS
marginal nerve, with Scer\GAL4nSyb.PS, Zzzz\VHHdeGradFP.UAS
ommatidium | progressive, with Scer\GAL4ninaE.PT
photoreceptor | progressive, with Scer\GAL4ninaE.PT
wing margin, with Scer\GAL4nub-AC-62
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) (6)
Hsap\IRF2BP1
11 of 14
Yes
Yes
1  
Hsap\IRF2BP2
11 of 14
Yes
Yes
1  
Hsap\IRF2BPL
11 of 14
Yes
Yes
14  
Hsap\MYT1
1 of 14
No
No
1  
Hsap\MYT1L
1 of 14
No
No
Hsap\ST18
1 of 14
No
No
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) (6)
Rnor\Irf2bp1
11 of 14
Yes
Yes
Rnor\Irf2bp2
11 of 14
Yes
Yes
Rnor\Irf2bpl
11 of 14
Yes
Yes
Rnor\Myt1l
1 of 14
No
No
Rnor\Myt1
1 of 14
No
No
Rnor\St18
1 of 14
No
No
Mus musculus (laboratory mouse) (6)
Mmus\Irf2bp2
12 of 14
Yes
Yes
Mmus\Irf2bpl
11 of 14
No
Yes
Mmus\Irf2bp1
10 of 14
No
Yes
Mmus\Myt1l
1 of 14
No
No
Mmus\Myt1
1 of 14
No
No
Mmus\St18
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\irf2bpl
9 of 13
Yes
Yes
Xtro\irf2bp2
8 of 13
No
Yes
Xtro\gja8
1 of 13
No
No
Xtro\rere
1 of 13
No
No
Danio rerio (Zebrafish) (7)
Drer\irf2bp1
11 of 14
Yes
Yes
Drer\irf2bp2b
11 of 14
Yes
Yes
Drer\irf2bpl
11 of 14
Yes
Yes
Drer\irf2bp2a
10 of 14
No
Yes
Drer\myt1a
1 of 14
No
No
Drer\myt1b
1 of 14
No
No
Drer\myt1la
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\ifbp-1
8 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP012958
10 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:Pits. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (2)
CG43689
1 of 13
shot
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 4 )
Potential Models Based on Orthology ( 2 )
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?
IRF2BP1; interferon regulatory factor 2 binding protein 1
11 of 14
615331
       
      IRF2BP2; interferon regulatory factor 2 binding protein 2
      11 of 14
      615332
       
      IRF2BPL; interferon regulatory factor 2 binding protein like
      11 of 14
      611720
       
      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
      Summary of Genetic Interactions
      Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Pits
      suppressible
      CkIα
      (Marcogliese et al., 2022)
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      pnr
      enhanceable
      Pits
      (Pena-Rangel et al., 2002)
      Tgi
      suppressible
      Pits
      (Vissers et al., 2020)
      Tgi
      enhanceable
      Pits
      (Vissers et al., 2020)
      External Data
      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
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map
      1-39
      Cytogenetic map
      11B1-11B2
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      11B1-11B2
      Limits computationally determined from genome sequence between P{EP}EP1451&P{EP}EP1629 and P{EP}CG11138EP1313
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      1-39

      (FlyBase, 2016)

      1-39.1

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (10)
      Genomic Clones (26)
      cDNA Clones (54)
       

      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

        (Liaw, 2016, Rohrbaugh et al., 2013)
        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

            Source for merge of: CG11138 BEST:RE18684

            (FlyBase, 1996-)

            Source for merge of: CG11138 CG1855

            (FlyBase Genome Annotators, 2002-2003)

            Source for merge of: CG11138 BcDNA:RE48052

            (FlyBase, 1996-)
            Additional comments

            Annotations CG11138 and CG1855 merged as CG11138 in release 3 of the genome annotation.

            (FlyBase Genome Annotators, 2002-2003)

            Source for merge of CG11138 BEST:RE18684 was sequence comparison ( date:040521 ).

            (FlyBase, 1996-)

            Source for merge of CG11138 BcDNA:RE48052 was a shared cDNA ( date:030728 ).

            (FlyBase, 1996-)
            Nomenclature History
            Source for database identify of

            Source for identity of: Pits CG11138

            (Liaw, 2016)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (9)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 46 )
            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/TrEMBL - Automatically annotated and unreviewed 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
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            MIST (protein-protein) - An integrated Molecular Interaction Database
            References (54)