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General Information
Symbol
Dmel\cora
Species
D. melanogaster
Name
coracle
Annotation Symbol
CG11949
Feature Type
FlyBase ID
FBgn0010434
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As
Cor, D4.1, l(2)k08713
Key Links
Genomic Location
Cytogenetic map
Sequence location
2R:19,229,063..19,243,751 [+]
Recombination map
2-88
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]
Experimental Evidence
-
Predictions / Assertions
Summaries
Protein Function (UniProtKB)
An integral component of the septate junction. May play a role in cell-cell interactions that are necessary for proper development. Vital for embryonic development.
(UniProt, Q9V8R9)
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
6
Number of Unique Polypeptides
6

Please see the GBrowse view of Dmel\cora or the JBrowse view of Dmel\cora 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
Low-frequency RNA-Seq exon junction(s) not annotated.
Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.
Gene model reviewed during 5.50
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0086509
5899
1698
FBtr0086508
3472
889
FBtr0086506
2914
703
FBtr0301279
2902
699
FBtr0340468
5605
1600
FBtr0340469
5893
1696
Additional Transcript Data and Comments
Reported size (kB)
6.3, 3.6, 2.9 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0085697
184.2
1698
9.17
FBpp0085696
98.0
889
6.81
FBpp0085694
78.2
703
7.99
FBpp0290494
77.8
699
8.74
FBpp0309410
173.9
1600
9.27
FBpp0309411
183.9
1696
9.17
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
Antibodies were prepared against sequences from the 5' end of the coding sequence that are shared by all of the cora cDNAs as well as to a region specific to the 1698aa species. The staining pattern obtained with both antisera are not noticably different.
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\cora 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 (20 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 electronic annotation with InterPro:IPR008379
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR008379
(assigned by InterPro )
Biological Process (12 terms)
Terms Based on Experimental Evidence (8 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001150527
(assigned by GO_Central )
traceable author statement
non-traceable author statement
traceable author statement
Cellular Component (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
NOT fusome
inferred from direct assay
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR000299, InterPro:IPR008379
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000589691
(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
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference

Comment: reference states 4-20 hr AEL

Comment: reference states 8-20 hr AEL

Additional Descriptive Data
cora mRNA localizes in a rim around the boutons of the neuromuscular junction.
The 6.3kb cora transcript is first detected in 4-8hr embryos, is much more abundant in 8-12hr embyros and remains prevalent through embryonic and larval stages.
The 3.6kb cora transcript is first detected in 8-12hr embryos and is detected through the remaining embryonic and early larval stages.
The 2.9kb cora transcript is first detected in 8-12hr embryos and is detected through the remaining embryonic and early larval stages.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
cora protein appears to be associated with the cytoplasmic face of septate junctions in epithelial cells. It does not appear to co-localize to a great extent with either filamentous actin or spectrin in the apical-basal axis of the cell.
cora protein is expressed in a short apical stretch of the basolateral membrane of embryonic septate junctions in the embryonic hindgut.
cora protein is first observed at the onset of germ band retraction in the epidermis, the hindgut, and the foregut. As the germ band retracts, expression increases in these tissues and appears in the tracheal branches and in the salivary glands. It is not expressed in the CNS but is observed in some sensory neural cells such as the scolopidia of the pentascolopidial chordotonal organ.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
NOT fusome
inferred from direct assay
inferred from direct assay
inferred from direct assay
(assigned by UniProt )
inferred from direct assay
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\cora 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) 4-6
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 23 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 21 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of cora
Transgenic constructs containing regulatory region of cora
Deletions and Duplications ( 9 )
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
embryonic ganglionic branch & embryonic tracheole (with cora4)
embryonic ganglionic branch & embryonic tracheole (with cora5)
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
8 of 15
Yes
Yes
8 of 15
Yes
Yes
8 of 15
Yes
Yes
6 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
8 of 15
Yes
Yes
7 of 15
No
Yes
7 of 15
No
Yes
6 of 15
No
Yes
Rattus norvegicus (Norway rat) (5)
7 of 13
Yes
Yes
5 of 13
No
Yes
4 of 13
No
Yes
2 of 13
No
Yes
2 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
7 of 12
Yes
Yes
4 of 12
No
Yes
3 of 12
No
Yes
2 of 12
No
Yes
Danio rerio (Zebrafish) (6)
5 of 15
Yes
Yes
5 of 15
Yes
Yes
4 of 15
No
Yes
4 of 15
No
Yes
2 of 15
No
Yes
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
3 of 15
Yes
Yes
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) ( EOG091900GY )
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) ( EOG091500FU )
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
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W01ZH )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman 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
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X01X1 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
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) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (5)
2 of 10
2 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 ( 1 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 2 )
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.
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
RNA-RNA
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
Gene Group - Pathway Membership (FlyBase)
External Data
Linkouts
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2R
Recombination map
2-88
Cytogenetic map
Sequence location
2R:19,229,063..19,243,751 [+]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
56C4-56C4
Limits computationally determined from genome sequence between P{PZ}ena02029&P{lacW}corak08713 and P{lacW}htsk06121
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
56C1-56C2
(determined by in situ hybridisation)
56C-56C
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Right of (cM)
Notes
Stocks and Reagents
Stocks (16)
Genomic Clones (20)
cDNA Clones (80)
 

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
DRSC - Results frm RNAi screens
GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
Antibody Information
Laboratory Generated Antibodies
 
monoclonal, polyclonal
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 identity of: cora CG11949
Source for database merge of
Source for merge of: cora l(2)k08713
Additional comments
Other Comments
Appears to function to stabilize and align prehairs relative to anterior-posterior cell boundaries during pupal wing development.
Proper targetting of pck gene product to the pleated septate junctions in the tracheal system depends on Nrx-IV and cora but not Fas3.
dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.
dsRNA made from templates generated with primers directed against this gene is tested in an RNAi screen for effects on actin-based lamella formation.
cora is a necessary component of the septate junction required for the maintenance of the transepithelial barrier.
The amino-terminal 383 amino acids of cora define a functional domain that is both necessary and sufficient for proper septate junction localisation of the protein. This domain and the cytoplasmic domain of Nrx-IV interact directly.
Some of the proteins of apico-lateral junctions are required both for apico-basal cell polarity and for the signalling mechanisms controlling cell proliferation, whereas others are required more specifically in cell-cell signalling.
The cora gene product is a component of neither fusomes nor spectrosomes.
cora mutants die early in embryogenesis as they fail to complete dorsal closure. cora interacts genetically with EgfrE1 and Ras85DV12.
The cora product is associated with a septate junction and may play a role in cell-cell interactions essential for normal development.
Origin and Etymology
Discoverer
Etymology
Identification
External Crossreferences and Linkouts ( 73 )
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
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
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Linkouts
ApoDroso - Functional genomic database for photoreceptor development, survival and function
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
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
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Synonyms and Secondary IDs (12)
Reported As
Symbol Synonym
Name Synonyms
Secondary FlyBase IDs
  • FBgn0005646
  • FBgn0022032
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
References (353)