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General Information
Symbol
Dmel\ro
Species
D. melanogaster
Name
rough
Annotation Symbol
CG6348
Feature Type
FlyBase ID
FBgn0003267
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:26,876,771..26,881,171 [-]
Recombination map

3-92

RefSeq locus
NT_033777 REGION:26876771..26881171
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Molecular Function (GO)
[Detailed GO annotations]
Summaries
Gene Group (FlyBase)
HOX-LIKE HOMEOBOX TRANSCRIPTION FACTORS -
HOX-like (HOXL) homeobox transcription factors are sequence-specific DNA binding proteins that regulate transcription. They encompass transcription factors encoded by the Hox genes of the Antennapedia and the Bithorax gene complexes and genes closely related in sequence. HOXL transcription factors are major regulators of animal development. (Adapted from FBrf0232555).
Protein Function (UniProtKB)
Required to establish the unique cell identity of photoreceptors R2 and R5 and consequently for ommatidial assembly in the developing eye imaginal disk. Repression of expression in R8 photoreceptor by senseless (sens) is an essential mechanism of R8 cell fate determination.
(UniProt, P10181)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
ro: rough
Homozygotes have rough eyes; slightly smaller and narrower than wild type. Approximately normal numbers of facets but arrangement irregular; frequently have fewer and sometimes more than eight retinula cells; some facets missing such that three ommatidial bristles juxtaposed; other facets fused (Stemm-Tegethoff and Dicke, 1974, Theoret. Appl. Genet. 44: 262-65; Ready et al.). Fiber pathways through lamina and into medulla in considerable disarray; optic chiasma between the two replaced by parallel fibers; laminar cartridge and medullar columns deranged, ventral epithelial nuclear row absent; medulla displaced from normal position and rotated anteriorly. Mosaic studies demonstrate that phenotype is eye autonomous; i.e., the genotype of the eye dictates that of the underlying nervous elements. Expression, as determined by in situ hybridization found in the eye-antenna imaginal disk, especially in the region of the morphogenetic furrow, as well as in a specific area of the brain. No evidence of embryonic expression (Saint, Kalionis, Lockett, and Elizur, 1988, Nature (London) 334: 151-54). RK1.
Summary (Interactive Fly)

transcription factor - homeodomain - plays a critical role in restriction of the number of photoreceptor precursors in the specification of R8 photoreceptors - a bistable loop between and locks in R8 fate

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\ro or the JBrowse view of Dmel\ro 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

Gene model reviewed during 5.48

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0085090
1169
350
FBtr0085091
1241
350
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
RefSeq ID
GenBank
FBpp0084460
39.4
350
9.72
FBpp0084461
39.4
350
9.72
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

350 aa isoforms: ro-PA, ro-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
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\ro 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 (7 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR017970
(assigned by InterPro )
Biological Process (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
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
organism

Comment: maternally deposited

Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

In addition to the wild type staining in receptor cells R2, R3, R4, and R5, additional staining is observed in the position of the mystery cell in the rhohs.sev line.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\ro 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
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, and Transgenic Constructs
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) (35)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
2 of 15
Yes
No
2 of 15
Yes
No
 
2 of 15
Yes
No
2 of 15
Yes
No
2 of 15
Yes
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
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) (35)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
2 of 15
Yes
No
2 of 15
Yes
No
2 of 15
Yes
No
2 of 15
Yes
No
 
2 of 15
Yes
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (38)
2 of 13
Yes
No
2 of 13
Yes
No
2 of 13
Yes
No
2 of 13
Yes
No
2 of 13
Yes
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (28)
2 of 12
Yes
No
2 of 12
Yes
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (40)
2 of 15
Yes
No
2 of 15
Yes
No
2 of 15
Yes
No
2 of 15
Yes
Yes
2 of 15
Yes
No
2 of 15
Yes
No
2 of 15
Yes
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (6)
2 of 15
Yes
No
2 of 15
Yes
No
 
2 of 15
Yes
No
2 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (2)
1 of 15
Yes
Yes
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190DUQ )
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) ( EOG09150FBY )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Aedes aegypti
Yellow fever mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0OMA )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Danaus plexippus
Monarch butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0OWW )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G14BU )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (19)
2 of 10
2 of 10
2 of 10
2 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
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 ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    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
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    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)
    3R
    Recombination map

    3-92

    Cytogenetic map
    Sequence location
    3R:26,876,771..26,881,171 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    97D4-97D5
    Limits computationally determined from genome sequence between P{lacW}His2AvL1602 and P{PZ}sda03884
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    97D2-97D3
    (determined by in situ hybridisation)
    97D3-97D5
    (determined by in situ hybridisation)
    97D5-97D7
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location

    3-91.1

    Left of (cM)
    Right of (cM)
    Notes

    Maps adjacent to l(3)97Db.

    Stocks and Reagents
    Stocks (89)
    Genomic Clones (16)
     

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

    cDNA Clones (1)
     

    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
        Other 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
           
          Commercially Available Antibodies
           
          Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research
          Other Information
          Relationship to Other Genes
          Source for database identify of
          Source for database merge of
          Additional comments
          Other Comments

          roDOM affects morphogenetic furrow progression by interfering with hh signalling and preventing implementation of furrow-specific cell fates.

          ro expression in and around the morphogenetic furrow of the developing eye is regulated by hh.

          Spred is positively regulated by ro and gl.

          ro is a retina-specific negative regulator required for proper resolution of ato expression and proneural migration. ro acts in conjunction with the more ubiquitously used N regulatory pathway.

          The R8 fate in the developing eye is likely to be decided by the balance of the transcription factors encoded by ato and ro. The ato and ro products act as positive and negative factors, respectively, of such R8-specific genes as boss.

          Alleles of S and of ro have been identified in a screen for abnormal numbers of R8 cells.

          A 5.8kb genomic fragment contains all the information required for normal ro expression and function. Important cis-regulatory sequences are located both in the 5' promoter region (between -940 and -340, coordinates from FBrf0047664) and a tissue-specific enhancer is located in the first intron. Amino acids located in the C-terminal region of the homeodomain play an important role in binding site recognition.

          Mutagenesis of the ro locus demonstrates the ro gene product is required for the correct patterning of the developing eye.

          ro and gl gene products are required for B and B-H2 gene expression in R1 and R6.

          ro function is required during the early steps of ommatidial assembly. No R2 or R5 cells are present in ro- ommatidia as all existing out photoreceptors require svp+ function for their development.

          Mutations in ro affect early ommatidia development.

          Expression of ro in the presumptive R7 cell transforms the cell into an R1-6 type photoreceptor. The transformation is cell autonomous and depends on the presence of the sev gene. In wild type, ro may function autonomously in the specification of R2/5 photoreceptor identity but by itself may not initiate neural development.

          Adult eyes are rough with irregular facet size and shape. Ommatidia irregular size and shape. The abnormal ro phenotype is due to a developmental defect: pattern formation defect.

          Analysis of somatic mosaics suggests that the or gene function is required only in photoreceptors R2 and R5.

          Origin and Etymology
          Discoverer
          Etymology
          Identification
          External Crossreferences and Linkouts ( 36 )
          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.
          Flygut - An atlas of the Drosophila adult midgut
          GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          KEGG Genes - Molecular building blocks of life in the genomic space.
          modMine - A data warehouse for the modENCODE project
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          Developmental Studies Hybridoma Bank - Monoclonal antibodies for use in research
          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 (genetic) - An integrated Molecular Interaction Database
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Synonyms and Secondary IDs (6)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          References (225)