FB2024_04 , released June 25, 2024
Gene: Dmel\ix
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General Information
Symbol
Dmel\ix
Species
D. melanogaster
Name
intersex
Annotation Symbol
CG13201
Feature Type
protein_coding_gene
FlyBase ID
FBgn0001276
Gene Model Status
Current
Stock Availability
13 publicly available
Gene Summary
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Required for female somatic sexual development. (UniProt, Q7KBL8)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Med29

Key Links
Genomic Location
Cytogenetic map
47F5-47F5
Sequence location
Recombination map
2-64
RefSeq locus
NT_033778 REGION:11359437..11360163
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 (10 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables DNA-binding transcription factor binding
inferred from physical interaction with FLYBASE:dsx; FB:FBgn0000504
(Yang et al., 2008)
enables transcription coregulator activity
inferred from direct assay
(Garrett-Engele et al., 2002)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables transcription coregulator activity
inferred from biological aspect of ancestor with PANTHER:PTN002001791
(GO Reference Genome Project, 2011-)
Biological Process (7 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
involved_in genital disc sexually dimorphic development
inferred from mutant phenotype
(Chatterjee et al., 2015)
involved_in imaginal disc-derived female genitalia morphogenesis
inferred from mutant phenotype
(Chatterjee et al., 2015)
involved_in regulation of transcription by RNA polymerase II
inferred from direct assay
(Garrett-Engele et al., 2002)
involved_in sex determination
inferred from mutant phenotype
(Acharyya and Chatterjee, 2002)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
involved_in female somatic sex determination
traceable author statement
(Zarkower, 2001)
involved_in regulation of transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN002001791
(GO Reference Genome Project, 2011-)
involved_in sex differentiation
traceable author statement
(Billeter et al., 2002)
involved_in somatic sex determination
non-traceable author statement
(Schutt and Nothiger, 2000)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of mediator complex
inferred from direct assay
(Garrett-Engele et al., 2002)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of mediator complex
inferred from sequence or structural similarity
(Bourbon et al., 2004)
inferred from electronic annotation with InterPro:IPR021018
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN002001791
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the Mediator complex subunit 29 family. (Q7KBL8)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
MEDIATOR CORE COMPLEX -
he Mediator (MED) complex serves as a hub for transcriptional signaling events, bridging transcriptional activators and repressors. This large multi-protein complex has a central core conserved from yeast to humans. The core is composed of three modules: head, middle, and tail. (Adapted from FBrf0226415 and FBrf0191850).
Protein Function (UniProtKB)
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Required for female somatic sexual development.
(UniProt, Q7KBL8)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
ix: intersex
Females changed into sterile intersexes with a set of reduced male and a set of irregular female external genitalia. Gonads also mixed. They have no sex combs; pigmentaion of abdomen intermediate between male and female. A large mass of chitinized tissue protrudes from vaginal opening. Homozygous males look normal but behave like intersexes (McRobert and Tompkins, 1985). They court young males as much as normal males do, and occasionally court females; however, they are attractive to normal mature males. Heterozygous ix/+ males court females and young males, but seldom court mature males. The ix locus acts with the dsx female function to allow somatic differentiation in females (Nagoshi, McKeown, Burtis, Belote, and Baker, 1988, Cell 53: 229-36).
ix2
Females homozygous for ix2 have male-like pigmentation of posterior tergites, rudimentary ovaries, and are sterile. Expression extreme and viability reduced at 27; at 17, expression less extreme and viability greater. Homozygous males appear normal but have nonmotile sperm. RK2.
ix3
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\ix 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 Q7KBL8)

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 5.49

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
ix-RA
FBtr0088154
NM_136833
727
188
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
ix-PA
FBpp0087251
21.1
188
6.95
Q7KBL8
NP_610677
AAF58653
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)

Component of the Mediator complex (By similarity). Self-associates. Interacts with dsx.

(UniProt, Q7KBL8)
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\ix 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).

-1.18

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 mediator complex
inferred from direct assay
(Garrett-Engele et al., 2002)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\ix 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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 10 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 14 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of ix
Transgenic constructs containing regulatory region of ix
Aberrations (Deficiencies and Duplications) ( 11 )
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\MED29
11 of 14
Yes
Yes
1  
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\Med29
12 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Med29
11 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\med29
10 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\med29
12 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
Agam\MED29_ANOGA
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:ix. 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 ( 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?
    MED29; mediator complex subunit 29
    11 of 14
    612914
         
        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)
        Other 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
        ix - Bap60
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - CG17002
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - CG3008
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - CG34159
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - Cdk8
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - Cpsf6
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - Gtpbp2
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - Larp4B
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED10
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED11
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED14
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED15
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED16
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED17
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED18
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED20
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED23
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED27
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED30
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED4
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED6
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED7
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - MED8
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - Ptip
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - Ssdp
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - boca
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - dsh
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - dsx
        two hybrid, anti tag coimmunoprecipitation, anti tag western blot
        (Yang et al., 2008)
        ix - ebi
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - enc
        experimental knowledge based
        (Guruharsha et al., 2011)
        ix - mor
        experimental knowledge based
        (Guruharsha et al., 2011)
        Summary of Genetic Interactions
        esyN Network Diagram
        Show/hide secondary interactors 
        (data from AllianceMine provided by esyN)
        esyN Network Key:
        Suppression
        Enhancement
        Other 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
        ix
        enhanceable
        dpp
        (Chatterjee et al., 2015)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        dsx
        enhanceable
        ix
        (Nothiger et al., 1987)
        External Data
        Subunit Structure (UniProtKB)
        Component of the Mediator complex (By similarity). Self-associates. Interacts with dsx.
        (UniProt, Q7KBL8 )
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map
        2-64
        Cytogenetic map
        47F5-47F5
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        47F5-47F5
        Limits computationally determined from genome sequence between P{lacW}Fppsk06103&P{lacW}Fppsk03514 and P{lacW}Tapδk17005&P{lacW}k05103
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-64

        (FlyBase, 2016)

        2-64.2

        (Comeron et al., 2012)

        2-60.5

        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (13)
        Genomic Clones (16)
         

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

        cDNA Clones (23)
         

        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

              ix is required for complete differentiation of female but not male specific adult cuticular structures.

              (Garrett-Engele et al., 2002)

              her acts together with the last genes in the determination hierarchy, dsx and ix, to control female sexual differentiation.

              (Li and Baker, 1998)

              Sex determining genes tra, ix and dsx have no role in regulating the template organisation of the X chromosome(s) for dosage compensation.

              (Acharyya and Chatterjee, 1997)

              Levels of haemolymph vitellogenin of ix flies tentatively suggest ix gene function is neither required for vitellogenin synthesis nor for maintaining proper level of dosage compensation of yolk protein genes. In ix mutant males the yolk protein gene expression is further repressed which suggests the gene is inactive at least in the fat body cells of the males.

              (Chatterjee and Mukherjee, 1996)

              At the morphological level, a loss of ix+ function results in the simultaneous realization of both male and female developmental pathways in diplo-X individuals. The ix product is required to function with the female-specific product of dsx to implement appropriate female sexual differentiation in diplo-X individuals. ix does not have a role in sexual behaviour in haplo-X individuals. Clonal analysis suggests that ix functions in a cell-autonomous manner in the abdomen and that it is required in the abdominal histoblasts after the resumption of cell division at pupariation for the normal sexual development of the abdominal tergites.

              (Chase and Baker, 1995)

              Mutant analysis of ix suggests that ix is active in both males and females for sexual differentiation.

              (Chatterjee, 1995)

              ix plays no role in the development of sexually dimorphic skeletal muscles.

              (Taylor, 1992)
              Relationship to Other Genes
              Source for database merge of

              Source for merge of: ix CG13201

              (FlyBase, 1996-)
              Additional comments

              Source for merge of ix CG13201 was sequence comparison ( date:021108 ).

              (FlyBase, 1996-)
              Nomenclature History
              Source for database identify of
              Nomenclature comments
              Etymology
              Synonyms and Secondary IDs (8)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 28 )
              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
              Flygut - An atlas of the Drosophila adult midgut
              iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
              MIST (genetic) - An integrated Molecular Interaction Database
              MIST (protein-protein) - An integrated Molecular Interaction Database
              References (100)