A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\rb

General Information
SymbolDmel\rbSpeciesD. melanogaster
NamerubyAnnotation symbolCG11427
Feature typeprotein_coding_geneFlyBase IDFBgn0003210
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)XRecombination map1-7.5
Cytogenetic map4C7-4C7Sequence locationX:4,429,662..4,434,669 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene ruby is referred to in FlyBase by the symbol rb (CG11427, FBgn0003210). It has the cytological map location 4C7. Its sequence location is X:4429662..4434669. Its molecular function is described as: protein transporter activity; protein binding. It is involved in the biological processes described with 12 unique terms, many of which group under: transport; organelle organization and biogenesis; membrane budding; eye pigmentation; cellular localization; cellular biosynthetic process; determination of adult life span; biopolymer modification; cellular pigmentation; ocellus pigmentation. 15 alleles are reported. The phenotypes of these alleles are annotated with: pigment cell; ocellus pigment granule; testis pigment cell; Malpighian tubule; photoreceptor cell pigment granule; secondary pigment cell pigment granule; tertiary pigment cell pigment granule. It has one annotated transcript and one annotated polypeptide.

hide Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage
rb: ruby
Eye color clear ruby, white in combination with wa, orange with st, and brownish red with bw (Mainx, 1938, Z. Indukt. Abstamm. Vererbungsl. 75: 256-76). Development of pigment autonomous in rb eye disks transplanted into wild-type hosts (Beadle and Ephrussi, 1936, Genetics 21: 230). Larval Malpighian tubes pale yellow (Beadle, 1937, Genetics 22: 587-611). RK1.
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
4C7-4C7  
Limits computationally determined from genome sequence between P{EP}CG2930EP1352 and P{EP}EP425  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
4C6-4C6
 
(Kretzschmar, 2000.3.20)
4C-4C
Determined by comparing Celera genomic sequence with sequence from BDGP BAC and P1 clones.  
(Lloyd et al., 2000)
4C6-4C7
 
(Zhang, 1998.10.2)
Experimentally Determined Recombination Data
Location
1-7.5
(Lawlor, 1980, Becker, 1968)
Left of (cM)
(Schalet, 1986)
Right of (cM)
(Welshons and Welshons, 1986)
(Kokoza et al., 1982)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\rb for information on other features
detailed view FBtr0070674 FBtr0070702 FBtr0070675 FBpp0070670 FBpp0070643 FBti0034899 FBti0067188 FBti0066533 FBti0053493 FBti0035232 FBti0048922 FBti0041829 FBti0067185
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
rb-RA
FBtr0070702
 NM_080332
  4829
  1160
Additional Transcript Data & Comments
Reported size (kB)
5.4, 5.2 (northern blot)
(Kretzschmar et al., 2000)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
rb-PA  
FBpp0070670  
127.1  
1160  
6.52  
  NP_525071
  AAF45950
Additional Polypeptide Data & Comments
Reported size (kD)
1160 (aa)
(Kretzschmar et al., 2000)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Clathrin/coatomer adaptor, adaptin-like, N-terminal (IPR002553)
Armadillo-like helical (IPR011989)
Armadillo-type fold (IPR016024)
Adaptor protein complex AP-3, beta subunit (IPR017108)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA390541
 
AA817435
 
AA949182
 
AE003431
AAF45950
 
AF247194
AAF71924
 
AI238091
 
AI402500
 
AI405786
 
AJ011778
CAA09771
 
AJ131729
 
BF491265
 
BI161743
 
BI161861
 
BI167100
 
BI167360
 
BI213521
 
BI216684
 
BI234018
 
BI358664
 
BP549235
 
BT010031
AAQ22500
 
CO302236
 
CO326965
 
CZ478493
 
EC076324
 
EC087262
 
EC223268
 
EC224819
 
EC251558
 
 
UniProtKB/Swiss-Prot
    UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (Kretzschmar et al., 2000)
    (Zhang, 1999.3.3)
    (BDGP Project Members, 2000-)
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    •
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data     		Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
     adult stage | female
     
    (Kretzschmar et al., 2000)
     adult stage
     retinal basal glial cell
    (Kretzschmar et al., 2000)
     adult stage
     pigment cell
    (Kretzschmar et al., 2000)
     pupal stage | stage P13
     photoreceptor cell
    (Kretzschmar et al., 2000)
     adult stage
     retina | restricted
    (Kretzschmar et al., 2000)
     pupal stage
     
    (Kretzschmar et al., 2000)
     larval stage | third instar
     
    (Kretzschmar et al., 2000)
     pupal stage | stage P13
     pigment cell
    (Kretzschmar et al., 2000)
     pupal stage | stage P13
     cerebral cortex | restricted
    (Kretzschmar et al., 2000)
     adult stage
     
    (Kretzschmar et al., 2000)
     embryonic stage
     
    (Kretzschmar et al., 2000)
     embryonic stage
     
    (Kretzschmar et al., 2000)
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        hide Microarray Data
        Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)
        Untitled Document detailed view FBtr0070674 FBtr0070702 FBtr0070675
        AI238091
        hide External Data & Images
        Linkouts
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        viable
        Other Phenotypes
        Allele
        visible | recessive
        eye color defective
        eye color defective | recessive
        short lived | male
        visual behavior defective (with Df(1)rb1)
        visual behavior defective (with rbD1)
        visual behavior defective (with rb10)
        visual behavior defective (with rbS1)
        Sterility
        Allele
        fertile
        Phenotype manifest in
        Allele
        pigment cell
        ocellus pigment granule
        testis pigment cell
        Malpighian tubule
        photoreceptor cell pigment granule
        secondary pigment cell pigment granule
        tertiary pigment cell pigment granule
        subretinal glial cell & pigment granule
        hide Classical Alleles ( 14 )
        For All Classical Alleles Show

        Allele of rbClassMutagenStocksKnown lesion
        rb100 Yes
        rb1
          		25 --
          rb48a0 --
          rb50j
            		0 --
            rb64d140 --
            rb64f0 --
            rb66a0 --
            rbD11 Yes
            rbH
              		0 --
              rbP20 Yes
              rbS1
                		0 --
                rbe006280 --
                rbntg0 --
                rbunspecified
                  		0 --
                  hide Alleles Carried on Transgenic Constructs ( 1 )
                  For All Alleles Carried on Transgenic Constructs Show

                  Allele of rbClassMutagenStocksKnown lesion
                  rbGD73002 Yes
                  hide Aneuploid Aberrations
                  Useful deficiency
                   
                  Disrupted in
                  (Christensen et al., 2008.6.11)
                  (Lawlor, 1980, Banga et al., 1986, Oliver et al., 1988, Pflugfelder et al., 1990)
                  (Lawlor, 1980)
                  (Lawlor, 1980)
                  (Craymer and Roy, 1980, Steinmann-Zwicky, 1988, Oliver et al., 1988)
                  (Craymer and Roy, 1980, Oliver et al., 1988)
                  (Craymer and Roy, 1980, Lawlor, 1980, Banga et al., 1986, Steinmann-Zwicky, 1988, Oliver et al., 1988)
                  (Schalet, 1986)
                  (Banga et al., 1986)
                  (Banga et al., 1986, Oliver et al., 1988)
                  (Banga et al., 1986)
                  (Banga et al., 1986)
                  (Banga et al., 1986)
                  (Oliver et al., 1988)
                  (Banga et al., 1986)
                  (Oliver et al., 1988)
                  (Banga et al., 1986)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Pflugfelder et al., 1990)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Oliver et al., 1988, Pflugfelder et al., 1990)
                  (Valencia, 1966)
                  (Banga et al., 1986, Oliver et al., 1988)
                  (Banga et al., 1986, Steinmann-Zwicky, 1988, Oliver et al., 1988, Pflugfelder et al., 1990)
                  (Pflugfelder et al., 1990)
                  (Steinmann-Zwicky, 1988)
                  (Banga et al., 1986, Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Banga et al., 1986, Oliver et al., 1988)
                  (Banga et al., 1986)
                  (Oliver et al., 1988)
                  (Banga et al., 1986, Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Banga et al., 1986)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Banga et al., 1986, Oliver et al., 1988, Pflugfelder et al., 1990)
                  (Oliver et al., 1988)
                  (Steinmann-Zwicky, 1988)
                  (Banga et al., 1986, Pflugfelder et al., 1990, Poeck et al., 1991)
                  (Steinmann-Zwicky, 1988)
                   
                  (Banga et al., 1986)
                  (Banga et al., 1986)
                  Duplicated in
                  (Dobzhansky, 1932)
                  (Kretzschmar et al., 2000)
                  (Dobzhansky, 1932)
                   
                   
                  Not disrupted in
                  (Patterson, 1932)
                  (Patterson, 1932)
                  (Patterson, 1932)
                  (Patterson, 1932)
                  (Patterson, 1932)
                  (Patterson, 1932)
                  (Patterson, 1932)
                  (Patterson, 1932)
                  (Oliver et al., 1988)
                  (Oliver et al., 1988)
                  (Craymer and Roy, 1980, Schalet, 1986, Oliver et al., 1988)
                  (Oliver et al., 1988)
                  (Banga et al., 1986, Pflugfelder et al., 1990)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Steinmann-Zwicky, 1988)
                  (Oliver et al., 1988, Pflugfelder et al., 1990)
                  (Pflugfelder et al., 1990)
                  (Pflugfelder et al., 1990)
                  (Patterson, 1932)
                  Not duplicated in
                  (Dobzhansky, 1932)
                  (Dobzhansky, 1932)
                  (Schalet, 1986)
                  (Schalet, 1986)
                  (Dobzhansky, 1932)
                  (Dobzhansky, 1932)
                  (Dobzhansky, 1932)
                  (Dobzhansky, 1932)
                  (Dobzhansky, 1932)
                  hide Transgenic Constructs & Insertions
                  Transgenic Constructs
                  Type of construct
                  Name
                  Expression data
                  UAS construct
                  P{GD7300}
                  NA
                  Insertions
                  Type of insertions
                  Name
                  Expression data
                  miscellaneous insertions
                  ?{}rb10
                  NA
                  PBac{RB}rbe00628
                  NA
                  hide Related Comments
                  Please look at the allele reports for the complete phenotype data
                  Lesions in rb reduce or eliminate pigmentation in the eyes and ocelli and block pigmentation of the fat body and tubules: rb is required for normal pigmentation of all four tissues.
                  (Tearle, 1991)
                  rb mutations lead to a decreased number and altered size of pigment granules in various cell types in and adjacent to the retina. rb mutants also show defective behaviour in alternating pattern fixation in Buridan's paradigm.
                  (Kretzschmar et al., 2000)
                  hide Gene Ontology: Function, Process & Cellular Component ( 18 )
                  hide Molecular Function
                  CV term
                  Evidence
                  References
                  protein binding
                  inferred from electronic annotation with InterPro:IPR002553, InterPro:IPR017108
                  (FlyBase Curators et al., 2004-)
                  protein transporter activity
                  inferred from electronic annotation with InterPro:IPR017108
                  (FlyBase Curators et al., 2004-)
                  hide Biological Process
                  CV term
                  Evidence
                  References
                  determination of adult life span
                  inferred from mutant phenotype
                  (Simonsen et al., 2007)
                  endocytosis
                  inferred from electronic annotation with InterPro:IPR017108
                  (FlyBase Curators et al., 2004-)
                  eye pigment biosynthetic process
                  traceable author statement
                  (Mullins et al., 2000)
                  eye pigment granule organization and biogenesis
                  non-traceable author statement
                  (Kretzschmar, 2000.3.20)
                  intracellular protein transport
                  inferred from electronic annotation with InterPro:IPR002553
                  (FlyBase Curators et al., 2004-)
                  intracellular transport
                  traceable author statement
                  (Narayanan and Ramaswami, 2001)
                  lysosome organization and biogenesis
                  inferred from sequence or structural similarity
                  (Mullins and Bonifacino, 2001)
                  ommochrome biosynthetic process
                  inferred from mutant phenotype
                  (Tearle, 1991)
                  regulation of protein ubiquitination
                  inferred from mutant phenotype
                  (Simonsen et al., 2007)
                  synaptic vesicle coating
                  traceable author statement
                  (Stimson and Ramaswami, 1999)
                  vesicle coating
                  traceable author statement
                  (Stimson and Ramaswami, 1999)
                  vesicle-mediated transport
                  non-traceable author statement
                  (Mazzarelli, 2001.8.15)
                  hide Cellular Component
                  CV term
                  Evidence
                  References
                  Golgi apparatus
                  inferred from electronic annotation with InterPro:IPR017108
                  (FlyBase Curators et al., 2004-)
                  coated vesicle
                  traceable author statement
                  (Stimson and Ramaswami, 1999)
                  membrane coat
                  inferred from electronic annotation with InterPro:IPR002553
                  (FlyBase Curators et al., 2004-)
                  synaptic vesicle
                  traceable author statement
                  (Stimson and Ramaswami, 1999)
                  hide Sequence Ontology: Class of Gene
                  protein_coding_gene
                   
                  nuclear_gene
                   
                  hide Interactions & Pathways
                  hide Summary of Genetic Interactions
                  Interacts with
                  Please look at the allele data for full details of the genetic interactions
                  rb allele
                  Gene
                  References
                  rb1
                  ltd
                  (Silva and Mensua, 1985)
                  rb66a
                  w
                  (Becker, 1968)
                  rbunspecified
                  w
                  (Lloyd et al., 2002)
                  unspecified
                  w
                  (Green, 1959)
                  bchs
                  (Simonsen et al., 2007)
                  hide External Data
                  Linkouts
                  BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
                  •
                  Drosophila PIMRider - The Drosophila Protein Interaction map
                  •
                  hide Orthologs
                  Genome-wide drosophilid orthologs
                  Curated drosophilid orthologs
                   
                   
                   
                  (Sturtevant, 1921, Sturtevant, 1929, Rux and Coyne, 1991)
                  (