FB2020_01, released Feb 12, 2020

Gene: Dmel\be

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General Information
Symbol
Dmel\be
Species
D. melanogaster
Name
ben
Annotation Symbol
CG32594
Feature Type
protein_coding_gene
FlyBase ID
FBgn0052594
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Snapshot
ben (be) encodes a protein involved in neuromuscular synaptic transmission and long-term memory formation. [Date last reviewed: 2019-09-19]
Other Summaries
Also Known As

E protein

Key Links
Genomic Location
Cytogenetic map
13A5-13A5
Sequence location
X:15,024,436..15,042,060 [+]
Recombination map

1-49

RefSeq locus
NC_004354 REGION:15024436..15042060
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
-
Summaries
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\be or the JBrowse view of Dmel\be 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 5.39

Gene model reviewed during 5.42

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

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
be-RB
FBtr0073956
NM_132762
4014
700
be-RC
FBtr0073957
NM_167424
3240
825
be-RF
FBtr0310270
NM_001258745
3069
825
Additional Transcript Data and Comments
Reported size (kB)

4.7, 4 (northern blot)

(Casal and Leptin, 1996)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
be-PB
FBpp0073773
78.1
700
5.75
NP_572990
AAF48412
be-PC
FBpp0073774
91.6
825
6.39
NP_727817
AAF48413
be-PF
FBpp0301953
91.6
825
6.39
NP_001245674
AFH07388
Polypeptides with Identical Sequences

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

825 aa isoforms: be-PC, be-PF
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\be 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 (2 terms)
Molecular Function (0 terms)
There is no information supporting a Molecular Function term for this gene. (Based on a review of available data on: 2013-09-04 )
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
long-term memory
inferred from mutant phenotype
(Zhao et al., 2009)
neuromuscular synaptic transmission
inferred from mutant phenotype
(Zhao et al., 2009)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (0 terms)
There is no information supporting a Cellular Component term for this gene. (Based on a review of available data on: 2013-09-04 )
Terms Based on Experimental Evidence (0 terms)
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
embryonic stage
yolk
(Casal and Leptin, 1996)
embryonic stage 8
head
(Casal and Leptin, 1996)
embryonic stage 5
yolk nucleus
(Casal and Leptin, 1996)
mesoderm anlage
(Casal and Leptin, 1996)
embryonic stage 11
mesectoderm
(Casal and Leptin, 1996)
embryonic stage 6 -- 17
mesoderm
(Casal and Leptin, 1996)
embryonic stage 9 -- 12
midline primordium
(Kearney et al., 2004)
Additional Descriptive Data

Transcripts are expressed in ventral cells of the blastoderm embryo as well as in vitellophages. During germ band extension, expression is strong in the head and much weaker in the invaginated mesoderm. Expression is also observed in the mesectoderm as well as in the periphery of the yolk.

(Casal and Leptin, 1996)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
• membrane
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
Reporter: P{GawB}beNP4013
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
Kenyon cell | subset
(Zhao et al., 2009)
adult brain | restricted
(Zhao et al., 2009)
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\be in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 8 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of be
Transgenic constructs containing regulatory region of be
Deletions and Duplications ( 1 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal | recessive
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
Other Phenotypes
Allele
memory defective (with beEY08069)
memory defective (with beP1)
memory defective | recessive
neurophysiology defective | recessive
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (0)
No records found.
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (0)
No records found.
Rattus norvegicus (Norway rat) (0)
No records found.
Xenopus tropicalis (Western clawed frog) (0)
No records found.
Danio rerio (Zebrafish) (0)
No records found.
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
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) ( EOG091903YR )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\be
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00006261
Drosophila simulans
Dsim\GD17185
Drosophila sechellia
Dsec\GM12051
Drosophila erecta
Dere\GG17856
Drosophila yakuba
Dyak\GE17159
Drosophila ananassae
Dana\GF22074
Drosophila pseudoobscura pseudoobscura
Dpse\GA23053
Drosophila persimilis
Dper\GL26780
Drosophila willistoni
Dwil\GK20121
Drosophila virilis
Dvir\GJ16617
Drosophila mojavensis
Dmoj\GI15207
Drosophila grimshawi
Dgri\GH12762
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091503FD )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17022996
Glossina morsitans
Tsetse fly
Gmor\GMOY007744
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07824
Mayetiola destructor
Hessian fly
Mdes\Mdes003206
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL004074
Anopheles darlingi
American malaria mosquito
Adar\ADAC009029
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ003144
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W07EX )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA012248
Danaus plexippus
Monarch butterfly
Dple\DPOGS203297-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL006373
Apis florea
Little honeybee
Aflo\2628890388
Apis mellifera
Western honey bee
Amel\GB42183
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP13643
Bombus terrestris
Buff-tailed bumblebee
Bter\15209490
Linepithema humile
Argentine ant
Lhum\LH21413
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0019e5
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG007153
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_11101
Tribolium castaneum
Red flour beetle
Tcas\TC004240
Tribolium castaneum
Red flour beetle
Tcas\TC003242
Tribolium castaneum
Red flour beetle
Tcas\TC009457
Pediculus humanus
Human body louse
Phum\PHUM483660
Rhodnius prolixus
Kissing bug
Rpro\RPRC005066
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI47472
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_03199
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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
    Interactions Browser
    Summary of Genetic Interactions
    esyN Network Diagram
    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.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map

    1-49

    Cytogenetic map
    13A5-13A5
    Sequence location
    X:15,024,436..15,042,060 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    13A5-13A5
    Limits computationally determined from genome sequence between P{EP}hiwEP1305 and P{EP}hiwEP1308
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    13A-13A
    (Runde, 2000.3.4)
    Experimentally Determined Recombination Data
    Location

    1-49

    (FlyBase, 2016)

    1-49.7

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (8)
    Genomic Clones (18)
     

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

    cDNA Clones (93)
     

    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
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of

    Source for merge of: CG32594 BEST:LD10566

    (Rana, 2004.7.8)

    Source for merge of: CG5530 anon- EST:CL1a5

    (FlyBase, 1996-)

    Source for merge of: CG15026 CG5530 CG5541

    (FlyBase Genome Annotators, 2002-2003)
    Additional comments

    Annotation CG5541 split out from annotation CG32594 into a distinct annotation in release 3.2 of the genome annotation.

    (FlyBase Genome Annotators, 2004)

    Annotations CG15026, CG5530 and CG5541 merged as CG32594 in release 3 of the genome annotation.

    (FlyBase Genome Annotators, 2002-2003)

    Source for merge of CG5530 anon- EST:CL1a5 was sequence comparison ( date:000423 ).

    (FlyBase, 1996-)
    Other Comments

    Isolated from a subtractive cDNA library enriched in sequences expressed in the mesoderm.

    (Casal and Leptin, 1996)

    A CG32594 cDNA has been cloned and sequenced. CG32594 is expressed in the early mesoderm.

    (Casal and Leptin, 1996)
    Origin and Etymology
    Discoverer
    Etymology

    Named for a memory defective phenotype - 'ben' means stupid in mandarin.

    (Zhao et al., 2009)
    Identification
    External Crossreferences and Linkouts ( 44 )
    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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    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)
    InterPro - A database of protein families, domains and functional sites
    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
    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
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    Synonyms and Secondary IDs (10)
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (41)