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General Information
Symbol
Dmel\Rx
Species
D. melanogaster
Name
Retinal Homeobox
Annotation Symbol
CG10052
Feature Type
FlyBase ID
FBgn0020617
Gene Model Status
Stock Availability
Gene Snapshot
Retinal Homeobox (Rx) encodes a homeodomain transcription factor required for processes of brain development. It is involved in growth regulation, proliferation and cell survival. [Date last reviewed: 2019-03-14]
Also Known As
DRx, E97, bk50, PPH17
Key Links
Genomic Location
Cytogenetic map
Sequence location
2R:20,916,753..20,937,030 [+]
Recombination map
2-92
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the paired homeobox family. Bicoid subfamily. (Q9W2Q1)
Summaries
Gene Group (FlyBase)
PAIRED-LIKE HOMEOBOX TRANSCRIPTION FACTORS -
Paired-like (PRD-like) homeobox transcription factors are sequence-specific DNA binding proteins that regulate transcription. PRD-like transcription factors lack a paired domain but possess a homeodomain characteristic of the paired homeobox transcription factors. Some members also possess an Engrailed Homology 1 (EH1) and/or an OAR motif near the C-terminus. (Adapted from FBrf0232555 and FBrf0106517).
Protein Function (UniProtKB)
Appears to function in brain development.
(UniProt, Q9W2Q1)
Summary (Interactive Fly)
homeodomain transcription factor - required for regulation of genes involved in brain morphogenesis - promotes cell growth, proliferation and survival of mushroom body neuroblasts in the brain
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\Rx or the JBrowse view of Dmel\Rx 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
Comments on Gene Model
Mutation in sequenced strain: frameshift (-1).
Gene model reviewed during 5.51
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0342783
3267
904
Additional Transcript Data and Comments
Reported size (kB)
3.2 (longest cDNA)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0309625
95.8
904
6.87
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)
902, 772 (aa); 96 (kD predicted)
Comments
External Data
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\Rx using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (5 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002518769
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN002518769
(assigned by GO_Central )
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR017970
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR032967
(assigned by InterPro )
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002518769
(assigned by GO_Central )
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

Additional Descriptive Data
Rx transcripts are first observed at embryonic stage 8 in two dorsolateral spots in the procephalic region. At the end of stage 8, additional staining is seen in the dorsal region that will give rise to the clypeolabrum. The head region expression becomes more pronounced by stage 9 and additional staining appears in the CNS. Later expression is observed in the antenno-maxillary complex. Staining at the medial edges of the two brain lobes, in the clypeolabrum, and in the antenno-maxillary complex persists until the end of embryogenesis.
Rx transcripts are detected by in situ hybridization during early embryogenesis in the eye disc primordia. They are also observed in a patch of cells in the anterior of the embryo corresponding to the clypeolabrum, in a region that gives rise to the epiphysis.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
During embryogenesis, Rx is expressed in a subset of Nrt positive brain cells, including 8-10 dpn positive neuroblasts, 4 of which are the mushroom body neuroblasts. This expression, and co-expression with dpn, persists throughout larval development where it also overlaps with Scer\GAL4insc-Mz1407 and Scer\GAL4NP1316. During the first larval instar stage, Rx positive mushroom body neuroblasts are seen within the cortex of the ey positive larval mushroom body. At the L3 stage, there are ~10 Rx and dpn co-expressing neuroblasts per hemisphere including the mushroom body neuroblasts, 2 of the dorso-lateral protocerebral DPLc lineage and ~2 that are part of the protocerebral CP or posterior deutocerebral CM lineages. Rx expression also overlaps with pros in a subset of mushroom body cells at this stage. Rx is also expressed in distally located, elav positive differentiated neurons of the type II DM neuroblast lineage, but not in neuroblasts, precursor cells or ganglion mother cells of this lineage. Finally, Rx is expressed in a subset of young Scer\GAL4insc-Mz1407 labelled Kenyon cells in adults but is not observed in mature Kenyon cells.
In stage 12 embryos, Rx protein is detected in a cluster of neuroectodermal cells alongside the dorsal midline, posterior to the pars lateralis primordium.
Protein is detected in stage 13 embryos in a restricted pattern in the central nervous system with staining in the embryonic brain hemispheres near the midline. Protein is expressed in larval central nervous system in several cell clusters near the midline. Additional expression in larvae is observed in a subset of cells in the clypeo-labral disc. Expression is detected in dorsal and posterior regions of the adult brain.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Rx in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 12 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Rx
Transgenic constructs containing regulatory region of Rx
Deletions and Duplications ( 4 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
4 of 15
Yes
Yes
2 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
4 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (3)
2 of 13
Yes
Yes
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (4)
1 of 12
Yes
Yes
1 of 12
Yes
Yes
1 of 12
Yes
No
1 of 12
Yes
Yes
Danio rerio (Zebrafish) (7)
5 of 15
Yes
Yes
5 of 15
Yes
Yes
3 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
3 of 15
Yes
Yes
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919085P )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091509WC )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0LWO )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Heliconius melpomene
Postman butterfly
Linepithema humile
Argentine ant
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0M4K )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ixodes scapularis
Black-legged tick
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (10)
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 1 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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?
    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
    esyN Network Diagram
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-92
    Cytogenetic map
    Sequence location
    2R:20,916,753..20,937,030 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    57B4-57B4
    Limits computationally determined from genome sequence between P{lacW}l(2)k06409k06409&P{PZ}insc05475 and P{PZ}l(2)0780607806
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    57B-57B
    (determined by in situ hybridisation)
    57B5-57B6
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (22)
    cDNA Clones (38)
     

    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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    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
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
       
      polyclonal
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of
      Source for database merge of
      Source for merge of: Rx E97 wom
      Additional comments
      Although extensive DNA sequence for "E97" has not been determined, no sequence overlapping that of the homeodomain of "PPH17" has been identified. Cross hybridization analysis suggests that "E97" and "PPH17" represent different homeodomain genes at 57B.
      Other Comments
      Rx is isolated in an attempt to analyse the 5' region of otp.
      Rx is cloned and sequenced and the gene structure and expression pattern determined.
      Rx encodes a prd-type homeodomain that is distinct from hbn or otp.
      57B is one of several locations where pairs of distinct homeodomains, in this case hbn and Rx, are found.
      One of the homeodomain loci identified in a screen for genes encoding DNA binding proteins capable of binding to a consensus Engrailed binding site.
      Identified on the basis of similarity to the eve homeobox sequence.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 34 )
      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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      Other crossreferences
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Linkouts
      DPiM - Drosophila Protein interaction map
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      FlyMine - An integrated database for Drosophila genomics
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (15)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (85)