A Database of Drosophila Genes & Genomes

FB2012_01, released January 20th, 2012
 

Gene Dmel\boca

General Information
SymbolDmel\bocaSpeciesD. melanogaster
NamebocaAnnotation symbolCG30498
Feature typeprotein_coding_geneFlyBase IDFBgn0004132
Gene Model StatusCurrent Stock availability 5 publicly available
Also Known AsCG1364, l(2)43Ea
Genomic Location
Chromosome (arm)2RRecombination map2-[57]
Cytogenetic map43D7-43D7Sequence location2R:3,453,378..3,454,240 [-]

Genomic Maps

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modENCODE GBrowse
detailed view
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Automatically generated summary

See sections below for more information
The gene boca is referred to in FlyBase by the symbol Dmel\boca (CG30498, FBgn0004132). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. There is experimental evidence that it is involved in the biological process: ER to Golgi vesicle-mediated transport; proboscis development; low-density lipoprotein receptor particle metabolic process; oogenesis; Wnt receptor signaling pathway; protein targeting to membrane. 8 alleles are reported. The phenotypes of these alleles are annotated with: wing disc; proboscis. It has one annotated transcript and one annotated polypeptide. Protein features are: Mesoderm development candidate 2. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-12 hour embryonic stages, during early pupal stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Nearly all larval and adult tissues/organs expressed at moderate levels. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval/adult central nervous system, adult crop, larval/adult hindgut, larval/adult Malpighian tubules, adult heart, larval/adult fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval/adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1623599_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of boca. Gene sequence location is 2R:3453378..3454240.

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Description
What does this section display?
This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms).
What does this section not display?
This section does not currently display links that were removed or gene model changes.
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FB2011_10
References
Chen et al., 2010, J. Biol. Chem. 285(51): 40266--40281
Controlled Vocabulary Terms
day 42 of adulthood
day 41 of adulthood
day 30 of adulthood
day 49 of adulthood
day 17 of adulthood
day 45 of adulthood
day 8 of adulthood
day 26 of adulthood
day 21 of adulthood
day 13 of adulthood
day 25 of adulthood
day 20 of adulthood
day 22 of adulthood
day 39 of adulthood
day 7 of adulthood
day 36 of adulthood
day 11 of adulthood
day 37 of adulthood
day 27 of adulthood
day 18 of adulthood
day 19 of adulthood
day 28 of adulthood
day 9 of adulthood
day 29 of adulthood
adult heart
day 40 of adulthood
day 16 of adulthood
day 24 of adulthood
day 15 of adulthood
day 33 of adulthood
day 43 of adulthood
day 47 of adulthood
day 38 of adulthood
day 32 of adulthood
day 48 of adulthood
day 23 of adulthood
day 35 of adulthood
day 12 of adulthood
day 10 of adulthood
day 31 of adulthood
day 34 of adulthood
day 44 of adulthood
day 14 of adulthood
day 46 of adulthood
FB2012_01
Sequence features
BKN29195
HFA06408
All updates Click here to see a list of all updates to this record from FB2010_08 and on.
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
43D7-43D7  
Limits computationally determined from genome sequence between P{EP}CG1600EP398 and P{PZ}scra03427&P{EP}EP2179  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location
2-[57]
 
Left of (cM)
Right of (cM)
Notes
hide Gene Model & Products
Please see the GBrowse view of Dmel\boca for information on other features
To submit a correction to a gene model please use the Contact FlyBase form
detailed view FBtr0310025 FBtr0088954 FBtr0310026 FBtr0088953 FBtr0088910 FBtr0310024 FBpp0301728 FBpp0088028 FBpp0301729 FBpp0088027 FBpp0087984 FBpp0301727 FBti0066471 FBti0128134 FBti0047586 FBti0051498 FBti0042457 FBti0125011_2 FBti0125011_1 FBti0047466 FBti0100141 FBti0023575 FBti0107720 FBti0107741 FBti0108733 FBti0111570 FBti0056908 FBti0077106 FBti0036836 FBti0038938 FBti0102251 FBti0125012
Comments on Gene Model
Gene model reviewed during 5.42
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
boca-RA
FBtr0088953
 NM_165541
  701
  180
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
boca-PA  
FBpp0088027  
21.0  
180  
4.53  
  NP_724578
  AAF59229
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Mesoderm development candidate 2 (IPR019330)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AE013599
AAF59229
 
AI542360
 
AW944564
 
AY069840
AAL39985
 
BI351827
 
BT044294
 
EL877866
 
EV587414
 
EV591881
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
hide Mapped Features
Mapped Features have been reorganized, please see this article for details.
Additional mapped features and mutations can be found on GBrowse or related reports.
Type
Symbol & Location
Additional Notes
References
hide External Data
Linkouts
Crossreferences
hide Expression Data
hideTranscript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
hidePolypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
day 7 of adulthood -- day 49 of adulthood  
adult heart  
(Cammarato et al., 2011)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
hide High-Throughput Expression Data
or
Untitled Document detailed view CG30499-RB CG30499-RA CG30499-RC boca-RA Vps13-RA Vps13-RB
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
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modENCODE Temporal Expression Data (Graveley et al., 2011)
FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
hide Expression Clusters
A cluster of genes with similar mRNA expression dynamics across development.
(The modENCODE Consortium, 2010)
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
•
hide Alleles & Phenotypes
hide Summary of Allele Phenotypes
Lethality
Allele
lethal
lethal | pupal stage | recessive
viable, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
adult head | dorsal | somatic clone
dorsocentral bristle | somatic clone
eye | ectopic | somatic clone
proboscis
ventral thoracic disc | distal
wing disc
wing margin bristle | cell autonomous | somatic clone
wing margin bristle | cell non-autonomous | ectopic | somatic clone
yolk | germline clone
hide Classical Alleles ( 1 )
For All Classical Alleles Show

Allele of bocaClassMutagenStocksKnown lesion
boca12 Yes
hide Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show

Allele of bocaClassMutagenStocksKnown lesion
bocaGD54831 Yes
bocaJF028631 Yes
bocaKK1091951 Yes
bocadsRNA.C0 Yes
bocadsRNA.Scer\UAS0 Yes
bocaMtnA.T:SV5\V5,T:Zzzz\His60 Yes
bocaScer\UAS.cCa0 Yes
hide Aneuploid Aberrations
Disrupted in
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Culi and Mann, 2003, Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Ryder, 2004.4.26)
(Ryder, 2004.4.26)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Eeken et al., 2001)
(Heitzler et al., 1993, Roote, 1996.8)
(Heitzler et al., 1993)
(Eeken et al., 2001)
Not disrupted in
(Heitzler et al., 1993, Roote, 1996.8)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Eeken et al., 2001, Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
(Heitzler et al., 1993)
hide Transgenic Constructs & Insertions
Transgenic Constructs
Type of construct
Name
Expression data
UAS construct
P{GD5483}
NA
P{KK109195}
NA
P{TRiP.JF02863}
NA
P{UAS-boca.C}
NA
P{UAS-boca-RNAi}
NA
Insertions
Type of insertions
Name
Expression data
miscellaneous insertions
P{PTT-GB}CB02070
NA
hide Gene Ontology: Function, Process & Cellular Component ( 9 unique terms )
hide Terms Based on Experimental Evidence ( 9 terms )
Molecular Function ( 0 terms)
Biological Process
CV term
Evidence
References
ER to Golgi vesicle-mediated transport
inferred from expression pattern
(Culi and Mann, 2003)
low-density lipoprotein receptor particle metabolic process
inferred from mutant phenotype
(Culi and Mann, 2003)
oogenesis
inferred from mutant phenotype
(Culi and Mann, 2003)
proboscis development
inferred from mutant phenotype
(Culi and Mann, 2002, Culi and Mann, 2003)
protein targeting to membrane
inferred from mutant phenotype
(Culi and Mann, 2003)
Wnt receptor signaling pathway
inferred from genetic interaction with wg
(Culi and Mann, 2003)
inferred from mutant phenotype
(Culi and Mann, 2003)
Cellular Component
CV term
Evidence
References
apical part of cell
inferred from direct assay
(Culi and Mann, 2003)
cytoplasm
inferred from direct assay
(Culi and Mann, 2003)
endoplasmic reticulum lumen
inferred from direct assay
(Culi and Mann, 2003)
hide Terms Based on Predictions or Assertions ( 0 terms )
hide Sequence Ontology: Class of Gene
nuclear_gene
 
protein_coding_gene
 
hide Interactions & Pathways
hide Summary of Physical Interactions
Protein-protein
Interacting group
Assay
References
hide Summary of Genetic Interactions
Interacts with
Please look at the allele data for full details of the genetic interactions
boca allele
Gene
References
hide 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.
•
hide Orthologs
Genome-wide drosophilid orthologs
Curated drosophilid orthologs
 
Linkouts
InParanoid A subset of ortholog calls from InParanoid.
•
OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs.
•
hide Stocks & Reagents
hide Stocks Listed in FlyBase ( 5 )
Bloomington
28029
y1 v1; P{TRiP.JF02863}attP2
4129
Dp(?;2)bwD, boca1 bwD/CyO
Kyoto
107596
Dp(?;2)bwD, boca1 bwD/CyO
VDRC
v108406
P{KK109195}VIE-260B
v13457
w1118; P{GD5483}v13457
hide Genomic Clones ( 2 )

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
hide cDNA Clones ( 6 )

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 Sequenced
BDGP DGC clones
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
hide RNAi & Array Information
Linkouts
DRSC - Results from RNAi screens.
•
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
•
hide Antibody Information
hide Other Information
hide Discoverer
hide Etymology
'boca' means mouth in Catalan.
(Culi and Mann, 2002)
hide Identification
hide Relationship to Other Genes
Source for database identity of
Source for database merge of
Source for merge of: CG30498 l(2)43Ea
(Culi, 2002.3.22)
Additional comments
Annotation CG1364 split into CG30499 and CG30498 (boca) in release 3 of the genome annotation.
(FlyBase Genome Annotators, 2002-2003)
hide Other Comments
boca is an essential component of the wg pathway but is more generally required for the activities of multiple LDL receptor family members.
(Culi and Mann, 2003)
boca is essential for proboscis development, and viability.
(Culi and Mann, 2002)
dsRNA causes embryos to develop into adults with reduced or absent proboscis but other fly body parts are apparently normal.
(Culi and Mann, 2002)
hide External Crossreferences & Linkouts
Sequence Crossreferences
RefSeq (Transcripts)
•
RefSeq (Proteins)
•
DDBJ / EMBL / GenBank
•
Entrez Gene - A searchable database of RefSeq genes.
•
UniProtKB/TrEMBL
•
Other Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Mesoderm development candidate 2 (IPR019330)
Linkouts
DroID - A comprehensive database of gene and protein interactions.
•
DRSC - Results from RNAi screens.
•
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
•
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
•
FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
•
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
•
InParanoid A subset of ortholog calls from InParanoid.
•
InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets.
•
modMine - Data generated by the modENCODE project.
•
OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs.
•
hide Synonyms & Secondary IDs ( 7 )
Reported As
Symbol Synonym
boca
(Buszczak et al., 2007, Culi and Mann, 2003, Khaliullina et al., 2009)
Boca
(Clevers, 2006, Lee and Cooley, 2007, Tien et al., 2008, Kelkar and Dobberstein, 2009, Wakefield and Tear, 2006, Tong et al., 2011, Chen et al., 2010)
CG1364
(Culi, 2002.3.22, Holdener, 2000.7.28, BDGP Project Members, 2000-, )
CG30498
(Keleman et al., 2009.8.5, Perkins et al., 2009, Kondylis et al., 2011, Cammarato et al., 2011)
dmBoca
(Collins and Hendrickson, 2011)
l(2)43Ea
(Eeken et al., 2001, Heitzler et al., 1993, )
Name Synonym
boca
(Culi and Mann, 2002, Schlesinger and Shilo, 2005, Cammarato et al., 2011)
Boca
(Kondylis et al., 2011)
lethal(2)43Ea
 
Secondary FlyBase IDs
  • FBgn0033193
  • FBgn0050498
hide References ( 36 )
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hide Recent research papers ( 4 )
Collins and Hendrickson, 2011, Structure 19(3): 324--336
Structural characterization of the Boca/Mesd maturation factors for LDL-receptor-type β propeller domains. [FBrf0214357]
Kondylis et al., 2011, PLoS ONE 6(2): e17173
Identification of ER Proteins Involved in the Functional Organisation of the Early Secretory Pathway in Drosophila Cells by a Targeted RNAi Screen. [FBrf0213167]
Tong et al., 2011, Neuron 71(3): 447--459
Rich Regulates Target Specificity of Photoreceptor Cells and N-Cadherin Trafficking in the Drosophila Visual System via Rab6. [FBrf0214681]
Chen et al., 2010, J. Biol. Chem. 285(51): 40266--40281
Characterization of the Properties of a Novel Mutation in VAPB in Familial Amyotrophic Lateral Sclerosis. [FBrf0212517]
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