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General Information
Symbol
Dmel\rg
Species
D. melanogaster
Name
rugose
Annotation Symbol
CG44835
Feature Type
FlyBase ID
FBgn0266098
Gene Model Status
Stock Availability
Gene Snapshot
rugose (rg) encodes a protein involved in synaptic architecture, brain morphology and associative learning. [Date last reviewed: 2019-09-26]
Also Known As

DAKAP550, Akap550

Key Links
Genomic Location
Cytogenetic map
Sequence location
X:5,085,759..5,254,864 [+]
Recombination map

1-10

RefSeq locus
NC_004354 REGION:5085759..5254864
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 WD repeat neurobeachin family. (Q9W4E2)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
Predictions / Assertions
-
Summaries
Protein Function (UniProtKB)
Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the membrane. May anchor the kinase to cytoskeletal and/or organelle-associated proteins. Required for correct retinal pattern formation and may function in cell fate determination through its interactions with the EGFR and Notch signaling pathways. Required for associative odor learning and short-term memory. Involved in development of the neuromuscular junction and the mushroom body.
(UniProt, Q9W4E2)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
rg: rugose
Eyes variably rough depending on strength of allele; stronger alleles display reduced viability. Additional traits include wings thin, curled upward (rgP), margins somewhat frayed (rg1); eclosion delayed (rg7); body pale (rgP).
Summary (Interactive Fly)

protein kinase A anchor protein - required for correct retinal pattern formation through its interactions with Egfr and Notch pathways - mutants of the autism candidate gene exhibit neuro-developmental disorders, aberrant synaptic properties, altered locomotion, impaired adult social behavior and activity patterns

Gene Model and Products
Number of Transcripts
7
Number of Unique Polypeptides
7

Please see the GBrowse view of Dmel\rg or the JBrowse view of Dmel\rg 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 5.54

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.52

gene_with_dicistronic_mRNA ; SO:0000722

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0344647
15981
3719
FBtr0344648
14745
3203
FBtr0344649
15534
3466
FBtr0344650
11424
3400
FBtr0344651
19353
3446
FBtr0344652
16491
3785
FBtr0344668
16076
3239
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
FBpp0310994
411.8
3719
5.43
FBpp0310995
358.6
3203
4.97
FBpp0310996
384.5
3466
5.04
FBpp0310997
377.3
3400
4.97
FBpp0310998
381.1
3446
5.05
FBpp0310999
419.0
3785
5.54
FBpp0311009
361.0
3239
5.05
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with RII subunit of PKA and components of the EGFR-mediated and Notch-mediated signaling pathways.

(UniProt, Q9W4E2)
Domain

RII-alpha binding site, predicted to form an amphipathic helix, could participate in protein-protein interactions with a complementary surface on the R-subunit dimer.

(UniProt, Q9W4E2)
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\rg 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 (10 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
Terms Based on Predictions or Assertions (0 terms)
Biological Process (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
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
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

rg protein is detected in the cell bodies in the larval and adult brain, opposite to the cis-Golgi marker GM130.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
Expression Deduced from Reporters
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\rg 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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 58 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of rg
Transgenic constructs containing regulatory region of rg
Deletions and Duplications ( 35 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
eye (with rg41)
eye (with rgγ1)
eye (with rgγ2)
eye (with rgγ3)
eye (with rgγ4)
eye (with rgγ5)
eye (with rgγ6)
eye (with rgγ7)
eye (with rgγ8)
eye (with rgγ9)
eye (with rgγ10)
eye (with rgγ11)
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
11 of 15
No
Yes
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?
12 of 15
Yes
Yes
Mmus\Nbea
12 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (4)
5 of 13
Yes
Yes
2 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (4)
5 of 12
Yes
Yes
2 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (4)
10 of 15
Yes
Yes
9 of 15
No
Yes
6 of 15
No
Yes
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
13 of 15
Yes
Yes
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (4)
4 of 9
Yes
Yes
1 of 9
No
Yes
1 of 9
No
No
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
1 of 12
Yes
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190037 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila sechellia
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150027 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Musca domestica
House fly
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Aedes aegypti
Yellow fever mosquito
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) ( EOG090W00A4 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis florea
Little honeybee
Apis florea
Little honeybee
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
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X009K )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G024D )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (4)
3 of 10
2 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 ( 4 )
Potential Models Based on Orthology ( 1 )
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.
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
RNA-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
Subunit Structure (UniProtKB)
Interacts with RII subunit of PKA and components of the EGFR-mediated and Notch-mediated signaling pathways.
(UniProt, Q9W4E2 )
Linkouts
DroID - A comprehensive database of gene and protein interactions.
MIST (genetic) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
Genomic Location and Detailed Mapping Data
Chromosome (arm)
X
Recombination map

1-10

Cytogenetic map
Sequence location
X:5,085,759..5,254,864 [+]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
4F2-4F3
Limits computationally determined from genome sequence between P{EP}EP425 and P{EP}CG3249EP1400
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
4F1-4F2
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (20)
Genomic Clones (65)
cDNA Clones (42)
 

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)
RNAi and Array Information
Linkouts
GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
Antibody Information
Laboratory Generated Antibodies
 
Commercially Available Antibodies
 
Other Information
Relationship to Other Genes
Source for database identify of

Source for identity of: Akap550 CG6775

Source for database merge of

Source for merge of: rg Akap550

Source for merge of: rg CG15466

Source for merge of: rg CG15464

Additional comments

One or more of the processed transcripts for these genes contain two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG44835 (FBgn0266098), CG15465 (FBgn0029746).

Annotations CG6775 and CG15464 merged as CG44835 in release 5.52 of the genome annotation. Merge based on RNA-Seq junction and expression data.

Release 2 annotation CG15466 (which was eliminated in release 3 of the genome annotation) has been merged with CG6775 (which corresponds to rg) in release 5.1 of the genome annotation.

Not allelic to N or rst.

may be allelic to lzl: lozenge-like

Other Comments

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

Annotation CG15466 was eliminated in release 3 of the genome annotation, October 2002.

Cloning and sequencing of rg cDNA, the differential expression of the protein during embryogenesis and the mapping of the binding site are studied.

The interaction of rap and rg with S is synergistic and dosage sensitive.

lzl may be allelic to rg.

The abnormal rg phenotype is due to a developmental defect: late occurring defects. Adult eye is rough with variable facet shape, variable number of rhabdomeres per ommatidium, eye disc pattern appears normal.

Origin and Etymology
Discoverer
Etymology
Identification
External Crossreferences and Linkouts ( 67 )
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
UniProt/TrEMBL - Automatically annotated and unreviewed 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
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.
Linkouts
DroID - A comprehensive database of gene and protein interactions.
Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
MIST (genetic) - An integrated Molecular Interaction Database
Synonyms and Secondary IDs (15)
Reported As
Secondary FlyBase IDs
  • FBgn0086911
  • FBgn0003244
  • FBgn0021748
  • FBgn0040912
  • FBgn0029748
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
References (114)