FlyBase Gene Report: Dmel\ebo

General Information

Symbol

Dmel\ebo

Species

D. melanogaster

Name

ellipsoid body open

Annotation Symbol

CG3923

Feature Type

protein_coding_gene

FlyBase ID

FBgn0266572

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

ellipsoid body open (ebo) encodes a protein that complexes with actin, the product of chic, and Ran-GTPase to mediate actin nuclear export. Loss of ebo during development results in defects in the ellipsoid body of the central complex. In the adult brain, accumulation of nuclear actin results in the inhibition of the product of bs and subsequent loss of visual orientation memory. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Red Book
Interactive Fly

Also Known As

Exp6, EG:165H7.3 , Exportin 6

Key Links

Genomic Location

Cytogenetic map

1B4-1B4

Sequence location

X:471,019..476,579 [-]

Recombination map

1-0

RefSeq locus

NC_004354 REGION:471019..476579

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (8 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables nuclear export signal receptor activity

inferred from electronic annotation with InterPro:IPR040016

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

enables small GTPase binding

inferred from electronic annotation with InterPro:IPR001494

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in central complex development

inferred from mutant phenotype

(Renn et al., 1999)

involved_in flight behavior

inferred from mutant phenotype

(Ilius et al., 1994)

involved_in mushroom body development

inferred from mutant phenotype

(de Belle and Heisenberg, 1996)

involved_in short-term memory

inferred from mutant phenotype

(Thran et al., 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in adult walking behavior

traceable author statement

(Ilius et al., 1994)

involved_in protein export from nucleus

inferred from biological aspect of ancestor with PANTHER:PTN001087101

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

l(1)1Bb

Homozygous clones in eyes display swelling and vacuolization of pigment cells (alleles designated MM2 and TE10). Deletion for l(1)1Bb enhances central-nervous-system and eye effects of ASC deficiencies (Jimenez and Campos-Ortega, 1987, J. Neurogenet. 4: 179-200; Gonzalez, Romani, Cubas, Modolell, and Campuzano, 1989, EMBO J. 8: 3553-62).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\ebo 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

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry X2J9Y4)

If you don't see the viewer to the right, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.49

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

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

Sequence Ontology: Class of Gene

gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

ebo-RA

FBtr0070098

NM_080140

4142

1047

ebo-RB

FBtr0339442

NM_001297809

4160

1053

ebo-RC

FBtr0339443

NM_001297810

4163

1054

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

ebo-PA

FBpp0070093

117.8

1047

5.86

NP_524879

AAF45504

ebo-PB

FBpp0308528

118.6

1053

5.86

NP_001284738

AHN59209

ebo-PC

FBpp0308529

118.6

1054

5.86

NP_001284739

AHN59210

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\ebo using the Feature Mapper tool.

External Data

Crossreferences

Linkouts

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

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\ebo in GBrowse 2

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\ebo

View exonic expression by tissue for Dmel\ebo

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

47141/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0266572

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0001337

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0266572

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG3923

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 8 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of ebo

Transgenic constructs containing regulatory region of ebo

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(1)Exel6221

(Ryder, 2004.4.26)

Inferred from location ( 0 )

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

partially lethal, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

ebo^GD11110

viable

ebo^EY06510

viable, with Scer\GAL4^Mef2.PR

ebo^GD11110

viable, with Scer\GAL4^pnr-MD237

ebo^GD11110

viable, with Scer\GAL4^tin.CΔ4

ebo^GD11110

Sterility

Allele

fertile

ebo^EY06510

Other Phenotypes

Allele

abnormal behavior | larval stage | recessive

ebo^ebo-KS263

abnormal flight

abnormal memory

abnormal memory | adult stage | recessive

ebo⁶⁷⁸

abnormal neuroanatomy | adult stage, with ebo⁶⁷⁸, Scer\GAL4^lilli-189Y

ebo^UAS.cTa

abnormal neuroanatomy | adult stage, with ebo^UAS.cTa, Scer\GAL4^lilli-189Y

ebo⁶⁷⁸

abnormal optomotor response

flightless

ebo⁶⁷⁸

some die during pupal stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

ebo^GD11110

Phenotype manifest in

Allele

adult mushroom body

ebo¹⁰⁴¹

adult optic lobe

ebo^KS234

calyx of adult mushroom body

ebo⁶⁷⁸

ellipsoid body

ellipsoid body | adult stage, with ebo⁶⁷⁸, Scer\GAL4^lilli-189Y

ebo^UAS.cTa

ellipsoid body | adult stage, with ebo^UAS.cTa, Scer\GAL4^lilli-189Y

ebo⁶⁷⁸

fan-shaped body

lobe system of adult mushroom body

ebo⁶⁷⁸

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (3)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\XPO6

12 of 15

Yes

Hsap\XPO1

1 of 15

Hsap\XPO5

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (3)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Xpo6

11 of 15

Yes

Mmus\Xpo1

1 of 15

Mmus\Xpo5

1 of 15

Rattus norvegicus (Norway rat) (3)

Rnor\Xpo6

11 of 13

Yes

Rnor\Xpo1

1 of 13

Rnor\Xpo5

1 of 13

Xenopus tropicalis (Western clawed frog) (4)

Xtro\xpo6

7 of 12

Yes

Xtro\exd3

1 of 12

Xtro\xpo1

1 of 12

Xtro\xpo5

1 of 12

Danio rerio (Zebrafish) (4)

Drer\xpo6

12 of 15

Yes

Drer\xpo1a

1 of 15

Drer\xpo1b

1 of 15

Drer\xpo5

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (0)

No records found.

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\CRM1

1 of 15

Yes

Scer\MSN5

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Other Organism Orthologs (via OrthoDB)

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (2)

Gene Symbol

Score

Source

Alignment

emb

1 of 10

Ranbp21

1 of 10

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 v8.0 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?

XPO6; exportin 6

12 of 15

608411

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

MIST (protein-protein) - An integrated Molecular Interaction Database

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-0

Cytogenetic map

1B4-1B4

Sequence location

X:471,019..476,579 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

1B4-1B4

Limits computationally determined from genome sequence between P{EP}CG17896^EP1320&P{EP}EP1398 and P{EP}svr^EP356&P{EP}arg^EP452

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-0

(FlyBase, 2016)

1-0.0

(Comeron et al., 2012)

1-3.8

(Varnam et al., 1996)

Left of (cM)

Right of (cM)

(Ilius et al., 1993)

Notes

Stocks and Reagents

Stocks (5)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

35829

ebo¹⁰⁴¹

16733

y¹ P{EPgy2}ebo^EY06510 w^67c23

83494

y¹ sc^* v¹ sev²¹; P{TKO.GS04203}attP40

32347

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00338}attP2

VDRC

v34737

w¹¹¹⁸; P{GD11110}v34737

Genomic Clones (8)

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

cDNA Clones (245)

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

SD03282

Other clones

FI17502

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.

FBgn0266572

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

47141

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: Exp6 ebo

(Thran et al., 2013)

Additional comments

l(1)1Bb¹⁹ complements ebo⁶⁷⁸, indicating that l(1)1Bb and ebo are not members of the same complementation group.

(Poeck, 2014.3.8)

The l(1)1Bb complementation group was previously merged with the ebo gene in FlyBase, based on information in FBrf0125093 (which provided molecular map information for the region including ebo and information about changes in the restriction enzyme map of this region in l(1)1Bb mutants). However, FBrf0224496 shows that the l(1)1Bb¹⁹ allele complements ebo mutant alleles. Thus l(1)1Bb and ebo have been split back out into separate gene records in FlyBase.

(FlyBase, 1992-)

Other Comments

ebo is required for central complex formation.

(Fleischmann et al., 1995)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 45 )

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.

47141

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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

X2J9Y4

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

X2J9Y4

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0266572

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

47141/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0266572

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0001337

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0266572

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG3923

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

47141

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC006436

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG3923

MARRVEL_MODEL - MARRVEL (model organism gene)

47141

Linkouts

MIST (protein-protein) - An integrated Molecular Interaction Database

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

CG3923

(Ni et al., 2010.12.1, Stueven et al., 2003)

EBO

(Thran et al., 2013)

EG:165H7.3

(Benos et al., 2001, Takano-Shimizu, 2001, Benos, 2000.12.13)

Exp1

Exp6

(Demakova et al., 2020, Okamoto et al., 2018, Malone et al., 2012, Rohn et al., 2011, Gutierrez et al., 2007)

ebo

(Transgenic RNAi Project members, 2017-, Thran et al., 2013, Hong et al., 2008, Neckameyer and Matsuo, 2008, Neuser et al., 2008, Xi et al., 2008, Ilius et al., 2007, de Belle and Heisenberg, 1996)

Name Synonyms

Exportin 6

(Thran et al., 2013, Ko et al., 2006, Stueven et al., 2003)

Exportin-6

(Chan et al., 2011)

ellipsoid body open

(Neckameyer and Matsuo, 2008, Neuser et al., 2008, Ilius et al., 2007)

ellipsoid-body-open

(Buchanan et al., 2015)

Secondary FlyBase IDs