FlyBase Gene Report: Dmel\eff

General Information

Symbol

Dmel\eff

Species

D. melanogaster

Name

effete

Annotation Symbol

CG7425

Feature Type

protein_coding_gene

FlyBase ID

FBgn0011217

Gene Model Status

Current

Stock Availability

30 publicly available

Gene Snapshot

Effete (Eff) is a conserved class I E2 ubiquitin-conjugating enzyme that contributes to the protein ubiquitination and degradation pathway. Eff roles include female germline stem cell maintenance, eye development, apoptosis regulation and chromatin organization. [Date last reviewed: 2016-06-23]

Other Summaries

Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

UbcD1, E(Pc)88D, ms(3)88D, UbcD, Ubc-D1

Key Links

Genomic Location

Cytogenetic map

88D2-88D2

Sequence location

3R:14,732,414..14,741,319 [-]

Recombination map

3-56

Sequence

Get Decorated FASTA

Genomic Maps

GBrowse JBrowse

Help me choose

Other Genome Views

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

NCBI Genome Data Viewer

UCSC Genome Browser

Ensembl Genome Browser

PopFly Genome Browser

GO Summary Ribbons

[Detailed GO annotations]

Families, Domains and Molecular Function

Gene Group Membership (FlyBase)

UBIQUITIN CONJUGATING ENZYMES

Negative Regulators of Hedgehog Signaling Pathway

Protein Family (UniProt, Sequence Similarities)

Belongs to the ubiquitin-conjugating enzyme family. (P25867)

Protein Domains/Motifs

InterPro

Ubiquitin-conjugating enzyme E2; Ubiquitin-conjugating enzyme/RWD-like; Ubiquitin-conjugating enzyme, active site

Molecular Function (see GO section for details)

Experimental Evidence

protein binding; ubiquitin conjugating enzyme activity; ubiquitin protein ligase activity; ubiquitin protein ligase binding

Predictions / Assertions

ubiquitin conjugating enzyme activity; ubiquitin protein ligase binding

Summaries

Gene Group Membership

UBIQUITIN CONJUGATING ENZYMES -: Ubiquitin-conjugating (E2) enzymes accept activated ubiquitin (or ubiquitin-like proteins) from ubiquitin-activating (E1) enzymes via thioester bond with a conserved catalytic cysteine. E2s then interact with ubiquitin ligases (E3) to directly or indirectly ubiquitinate target proteins. E2s are characterised by a 200 amino acid ubiquitin-conjugating (UBC) domain which interacts with E1 and E3s and acts catalytically. (Adapted from PMID:1994026).
Negative Regulators of Hedgehog Signaling Pathway -: Negative regulators of hedgehog signaling down-regulation the pathway, resulting in the repression of transcription of hh-responsive genes.

UniProt Contributed Function Data

Catalyzes the covalent attachment of ubiquitin to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. Required for proper telomere behavior during cell divisions and possibly for ubiquitination of proteins involved in postmeiotic stages of spermatogenesis. Deletion mutations are lethal in homozygotes.

(UniProt, P25867)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\eff or the JBrowse view of Dmel\eff 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 5.53

Gene model reviewed during 5.43

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

Gene model reviewed during 5.48

Gene model reviewed during 5.54

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

eff-RA

FBtr0083018

NM_169601

2084

147

eff-RB

FBtr0310554

NM_001275649

1622

147

eff-RC

FBtr0336876

NM_001275650

1913

147

Additional Transcript Data and Comments

Reported size (kB)

2.1, 1.9, 1.7 (northern blot)

(Cenci et al., 1997)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

eff-PA

FBpp0082477

16.7

147

7.38

NP_731941

AAF55093

eff-PB

FBpp0302691

16.7

147

7.38

NP_001262578

AGB95959

eff-PC

FBpp0307824

16.7

147

7.38

NP_001262579

AGB95960

Polypeptides with Identical Sequences

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

147 aa isoforms: eff-PA, eff-PB, eff-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

147 (aa); 17 (kD predicted)

(Treier et al., 1992)

Comments

eff protein can functionally replace yeast UBC4. It rescues growth defects and temperature sensitivity and restores proteolysis proficiency in ubc4 ubc5 double mutants.

(Treier et al., 1992)

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\eff using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

eff_1

Linkouts

Gene Ontology (20 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

protein binding

inferred from physical interaction with FLYBASE:sina; FB:FBgn0003410

(Tang et al., 1997)

ubiquitin conjugating enzyme activity

inferred from direct assay

(Asaoka et al., 2016, Ryoo et al., 2002)

inferred from genetic interaction with SGD:S000000286 , SGD:S000002466

(Treier et al., 1992)

ubiquitin protein ligase activity

inferred from direct assay

(Herman-Bachinsky et al., 2007)

ubiquitin protein ligase binding

inferred from physical interaction with FLYBASE:Diap1; FB:FBgn0260635

(Ryoo et al., 2002)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

ubiquitin conjugating enzyme activity

inferred from biological aspect of ancestor with PANTHER:PTN002514495

(assigned by GO_Central )

(Gaudet et al., 2011)

ubiquitin protein ligase binding

inferred from biological aspect of ancestor with PANTHER:PTN000630862

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (15 terms)

Terms Based on Experimental Evidence (15 terms)

CV Term

Evidence

References

anaphase-promoting complex-dependent catabolic process

inferred from mutant phenotype

(Chen et al., 2009)

chromosome organization

inferred from mutant phenotype

(Cenci et al., 1997)

compound eye morphogenesis

inferred from mutant phenotype

(Neufeld et al., 1998)

compound eye photoreceptor cell differentiation

inferred from mutant phenotype

(Li et al., 2002)

female germ-line stem cell asymmetric division

inferred from mutant phenotype

(Chen et al., 2009)

germ-line stem cell population maintenance

inferred from mutant phenotype

(Chen et al., 2009)

male meiotic nuclear division

inferred from mutant phenotype

(Cenci et al., 1997)

mitotic cell cycle

inferred from mutant phenotype

(Cenci et al., 1997)

neuron remodeling

inferred from direct assay

(Kuo et al., 2006)

protein linear polyubiquitination

inferred from direct assay

(Asaoka et al., 2016)

protein polyubiquitination

inferred from direct assay

(Herman-Bachinsky et al., 2007)

inferred from mutant phenotype

(Yeh and Bratton, 2013)

protein ubiquitination

inferred from direct assay

(Chen et al., 2009)

regulation of protein stability

inferred from mutant phenotype

(Chen et al., 2009)

regulation of R7 cell differentiation

inferred from genetic interaction with FLYBASE:sina; FB:FBgn0003410

(Li et al., 2002)

ubiquitin-dependent protein catabolic process

inferred from mutant phenotype

(Ryoo et al., 2002)

inferred from genetic interaction with SGD:S000000286 , SGD:S000002466

(Treier et al., 1992)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

protein ubiquitination

inferred from sequence or structural similarity with SGD:S000000286

(Treier et al., 1992)

inferred from sequence or structural similarity with SGD:S000002466

(Treier et al., 1992)

ubiquitin-dependent protein catabolic process

inferred from biological aspect of ancestor with PANTHER:PTN000631055

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

ubiquitin ligase complex

inferred from biological aspect of ancestor with PANTHER:PTN000630862

(assigned by GO_Central )

(Gaudet et al., 2011)

Expression Data

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Cenci et al., 1997)

cleavage stage

organism

(Cenci et al., 1997)

adult stage | male

(Cenci et al., 1997)

Additional Descriptive Data

The 2.1kb eff transcript is male-germ-line specific and initiates upstream of the shorter transcripts.

(Cenci et al., 1997)

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{PZ}eff⁸

Stage

Tissue/Position (including subcellular localization)

Reference

wandering third instar larval stage

embryonic/larval trachea

(Meister and Braun, 1995.10)

imaginal disc

(Meister and Braun, 1995.10)

embryonic/larval brain

(Meister and Braun, 1995.10)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\eff 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\eff

View exonic expression by tissue for Dmel\eff

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0011217

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0011217

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG7425-RA

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

CG7425

Flygut - An atlas of the Drosophila adult midgut

FBgn0011217

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs and Phenotypes

Classical and Insertion Alleles ( 65 )

For All Classical and Insertion Alleles Show

Allele of eff

Class

Mutagen

Associated Insertion

Stocks

Known lesion

eff⁸

P-element activity

P{PZ}eff⁸

Yes

eff^s1782

P-element activity

P{lacW}eff^s1782

Yes

eff⁰¹⁴⁶²

P-element activity

P{PZ}eff⁰¹⁴⁶²

Yes

eff^mer4

eff⁰⁶⁵³⁵

P-element activity

P{PZ}eff⁰⁶⁵³⁵

eff^j2C8

P-element activity

P{lacW}eff^j2C8

Yes

eff^unspecified

eff^mer1

P-element activity

P{418}eff^mer1

Yes

eff¹¹

P-element activity

P{PZ}eff¹¹

Yes

eff⁰³⁵²⁷

P-element activity

P{PZ}eff⁰³⁵²⁷

eff^EP674

P-element activity

P{EP}eff^EP674

Yes

eff¹

P-element activity

P{hsneo}eff¹

Yes

eff³

P-element activity

P{hsneo}eff³

Yes

eff⁴

P-element activity

P{ry11}eff⁴

eff⁵

P-element activity

P{ry11}eff⁵

eff⁹

P-element activity

P{PZ}eff⁹

eff¹⁰

P-element activity

P{PZ}eff¹⁰

eff¹²

P-element activity

P{PZ}eff¹²

eff¹³

P-element activity

P{PZ}eff¹³

eff^XS347

eff^e01950

piggyBac activity

Yes

Yes

P-element activity

P{hsneo}eff²

eff⁵⁹⁸

eff^D73

eff^DG04302

P-element activity

P{wHy}eff^DG04302

Yes

eff^EP3627

P-element activity

Yes

Yes

piggyBac activity

PBac{PB}eff^c04358

Yes

eff^c04398

piggyBac activity

Yes

Yes

P-element activity

P{PTT-GC}eff^CC01915

Yes

eff^d00904

P-element activity

P{XP}eff^d00904

Yes

eff^d03427

P-element activity

P{XP}eff^d03427

Yes

eff^e03661

piggyBac activity

PBac{RB}eff^e03661

Yes

eff^EY01601

P-element activity

P{EPgy2}eff^EY01601

Yes

eff^{MI05507-FF.GT-mCh}

loss of function allele

phiC31 integrase

Mi{FlipFlop}eff^{MI05507-FF.GT-mCh}

Yes

Yes

Yes

Yes

Yes

amorphic allele - molecular evidence

P-element activity

Yes

eff⁶

P-element activity

P{A92}eff⁶

eff⁷

P-element activity

P{A92}eff⁷

eff⁵¹⁷⁸²

loss of function allele

eff^D112

eff^d08220

P-element activity

P{XP}eff^d08220

Yes

eff^d10589

P-element activity

Yes

Yes

P-element activity

P{EP}eff^EP384

Yes

eff^EP3100

P-element activity

P{EP}eff^EP3100

Yes

eff^EP3711

P-element activity

Yes

P-element activity

P{lArB}eff^L88D

Yes

eff^L89F

P-element activity

P{lArB}eff^L89F

Yes

eff^mei68

eff^{MI05507-FF.PT-EGFP}

phiC31 integrase

Mi{FlipFlop}eff^{MI05507-FF.PT-EGFP}

Yes

ethyl methanesulfonate

eff^tre1

P-element activity

P{lacW}eff^tre1

Yes

eff^tre2

P-element activity

P{lacW}eff^tre2

Yes

eff^Δ112

P-element activity

Other relevant insertions

insertion of mobile activating element

Name

Expression Data

P{GSV1}EP-536^EP-536

P{Mae-UAS.6.11}B0969^B0969

Transgenic Constructs ( 11 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of eff

Allele of eff

Mutagen

Associated Transgenic Construct

Stocks

in vitro construct - regulatory fusion

P{UAS-eff.N}

eff^+tCa

in vitro construct

P{ro-UbcD1.T:Hsap\MYC}

eff^UASp.cCa

in vitro construct - regulatory fusion

P{UASp-eff.C}

Transgenic constructs containing regulatory region of eff

Deletions and Duplications ( 6 )

Not disrupted in

Df(3R)red1

(Spradling et al., 1999, BDGP Project Members, 1994-1999)

Disrupted in

Df(3R)BSC635

(Cook et al., 2008.12.28)

Df(3R)BSC842

(Cook et al., 2009.11.9)

Df(3R)Exel6275

(Ryder, 2004.4.26)

Df(3R)Exel8160

(Ryder, 2004.4.26)

Df(3R)ry506-85C

(Fauvarque et al., 2001)

Summary of Phenotypes

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

Lethality

Allele

lethal

lethal, with Scer\GAL4^GMR.PF

eff^GD10600

lethal (with Df(3R)ry506-85C)

lethal (with eff^mer1)

eff^s1782

lethal (with eff^mer4)

eff^s1782

lethal (with eff^s1782)

lethal | recessive

lethal - all die before end of embryonic stage | recessive

lethal - all die before end of larval stage | recessive

eff^mer1

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

eff^GD10600

lethal - all die before end of pupal stage | recessive

eff^Δ112

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

eff^GD10600

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

eff^GD10600

partially lethal (with eff^D73)

eff^D112

partially lethal (with eff^D112)

eff^D73

partially lethal - majority die

partially lethal - majority die | recessive

eff^tre2

viable

viable, with Scer\GAL4^tin.CΔ4

eff^GD10600

Sterility

Allele

female fertile

female fertile, with Scer\GAL4^nos.PG

female sterile

eff⁸

fertile

eff^EY01601

male sterile

male sterile (with eff⁸)

male sterile (with eff^mer1)

eff⁸

male sterile (with eff^mer4)

eff⁸

male sterile | recessive

Other Phenotypes

Allele

decreased occurrence of cell division | somatic clone

eff⁸

meiotic cell cycle defective

eff^mei68

meiotic cell cycle defective | recessive

mitotic cell cycle defective | recessive

neuroanatomy defective

neuroanatomy defective | larval stage

eff^GD10600

neuroanatomy defective | somatic clone

eff⁸

short lived | heat sensitive, with Scer\GAL4^HCH.Hand

eff^GD10600

short lived | heat sensitive, with Scer\GAL4^tin.CΔ4

eff^GD10600

some die during embryonic stage | recessive

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

eff^GD10600

some die during larval stage | recessive

eff^mer1

some die during pupal stage, with Scer\GAL4^pnr-MD237

eff^GD10600

some die during pupal stage | recessive

eff^Δ112

visible (with eff^D73)

eff^D112

visible (with eff^D112)

eff^D73

visible | dominant

eff^mer4

Phenotype manifest in

Allele

adult heart, with Scer\GAL4^HCH.Hand

eff^GD10600

dendrite

dorsal multidendritic neuron ddaC

eff^mer4

egg chamber & cell

egg chamber & mitotic cell cycle

eye | somatic clone

eff^s81

eye photoreceptor cell | somatic clone

eff^s81

female germline stem cell (with eff⁸)

female germline stem cell (with eff^mer1)

eff⁸

female germline stem cell (with eff^mer4)

eff⁸

female germline stem cell (with eff^s1782)

eff⁸

female germline stem cell | germline clone

ganglion mother cell | larval stage

eff^GD10600

germarium

eff⁸

macrochaeta

macrochaeta | ectopic (with eff^D73)

eff^D112

macrochaeta | ectopic (with eff^D112)

eff^D73

meiosis & chromosome, telomeric region | male

meiosis & nuclear chromosome | male

mesothoracic leg

eff^mer4

mitosis & chromosome, telomeric region

neuroblast | somatic clone

eff⁸

neuron

nuclear chromosome

eff^mei68

nurse cell & nucleus

eff⁸

nurse cell fusome

pigment cell | somatic clone

eff^s81

sex comb | ectopic

eff^mer4

testis

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (10)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\UBE2D3

13 of 15

Yes

Hsap\UBE2D2

12 of 15

Yes

Hsap\UBE2D4

9 of 15

Yes

Hsap\UBE2D1

8 of 15

Yes

2 of 15

2 of 15

2 of 15

1 of 15

1 of 15

1 of 15

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (11)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Ube2d2a

11 of 15

Yes

Mmus\Ube2d3

10 of 15

Yes

Mmus\Ube2d1

7 of 15

Yes

Mmus\Ube2d2b

6 of 15

Yes

Mmus\Ube2dnl1

5 of 15

Yes

Mmus\Ube2dnl2

4 of 15

Yes

2 of 15

2 of 15

2 of 15

1 of 15

1 of 15

Yes

Rattus norvegicus (Norway rat) (7)

Rnor\Ube2d3

8 of 13

Yes

Rnor\Ube2d1

7 of 13

Yes

Rnor\Ube2d4

7 of 13

Yes

Rnor\Ube2d2

5 of 13

Yes

Rnor\Ube2e1

1 of 13

Rnor\Ube2e3

1 of 13

Rnor\Ube2t

1 of 13

Xenopus tropicalis (Western clawed frog) (7)

Xtro\ube2d3

11 of 12

Yes

Xtro\ube2d1

7 of 12

Yes

Xtro\ube2d4

6 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

Danio rerio (Zebrafish) (12)

Drer\ube2d3

11 of 15

Yes

Drer\ube2d2

9 of 15

Yes

Drer\ube2d4

9 of 15

Yes

Drer\ube2d1b

8 of 15

Yes

Drer\ube2d1a

7 of 15

Yes

Drer\ube2d2l

6 of 15

Yes

2 of 15

2 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (4)

Cele\let-70

13 of 15

Yes

Cele\F52C6.12

4 of 15

Yes

Cele\ubc-13

1 of 15

Cele\uev-3

1 of 15

Arabidopsis thaliana (thale-cress) (9)

Atha\UBC8

7 of 9

Yes

Atha\UBC9

7 of 9

Yes

Atha\UBC10

7 of 9

Yes

Atha\UBC11

7 of 9

Yes

Atha\UBC28

7 of 9

Yes

Atha\UBC29

7 of 9

Yes

Atha\UBC30

7 of 9

Yes

Atha\UBC12

2 of 9

Yes

Atha\FUS9

1 of 9

Saccharomyces cerevisiae (Brewer's yeast) (4)

Scer\UBC4

14 of 15

Yes

Scer\UBC5

12 of 15

Yes

Scer\PEX4

1 of 15

Yes

Scer\UBC13

1 of 15

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\ubc4

11 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190HDH )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA26693

Drosophila persimilis

Dper\GL23670

Drosophila willistoni

Dwil\GK11688

Drosophila virilis

Dvir\GJ22971

Drosophila mojavensis

Dmoj\GI10619

Drosophila grimshawi

Dgri\GH14086

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150C03 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17012343

Glossina morsitans

Tsetse fly

Gmor\GMOY009942

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_00722

Mayetiola destructor

Hessian fly

Mdes\Mdes011804

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL003103

Anopheles darlingi

American malaria mosquito

Adar\ADAC000659

Anopheles gambiae

Malaria mosquito

Agam\AGAP000145

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0IP9 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA010541

Bombyx mori

Silkmoth

Bmor\BGIBMGA002918

Danaus plexippus

Monarch butterfly

Dple\DPOGS200166-PA

Danaus plexippus

Monarch butterfly

Dple\DPOGS200498-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL005107

Heliconius melpomene

Postman butterfly

Hmel\HMEL006881

Apis florea

Little honeybee

Aflo\2368864788

Apis florea

Little honeybee

Aflo\3369110196

Apis mellifera

Western honey bee

Amel\LOC724793

Apis mellifera

Western honey bee

Amel\UbcD2

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP10401

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP15298

Bombus terrestris

Buff-tailed bumblebee

Bter\15208574

Bombus terrestris

Buff-tailed bumblebee

Bter\15215993

Linepithema humile

Argentine ant

Lhum\LH13622

Linepithema humile

Argentine ant

Lhum\LH22371

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:00160a

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:00190e

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG007707

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG010264

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_01946

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_02422

Tribolium castaneum

Red flour beetle

Tcas\eff

Tribolium castaneum

Red flour beetle

Tcas\TC012100

Pediculus humanus

Human body louse

Phum\PHUM437950

Pediculus humanus

Human body louse

Phum\PHUM570280

Rhodnius prolixus

Kissing bug

Rpro\RPRC005317

Rhodnius prolixus

Kissing bug

Rpro\RPRC012234

Cimex lectularius

Bed bug

Clec\CLEC001726

Cimex lectularius

Bed bug

Clec\CLEC006604

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI003002

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI000078

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_08928

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_11733

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0DVW )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR008921

Ixodes scapularis

Black-legged tick

Isca\ISCW018551

Ixodes scapularis

Black-legged tick

Isca\ISCW020158

Stegodyphus mimosarum

African social velvet spider

Smim\KFM60987.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM77107.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur348g00010

Tetranychus urticae

Two-spotted spider mite

Turt\tetur07g03260

Tetranychus urticae

Two-spotted spider mite

Turt\tetur11g02420

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_120690

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_230542

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0GF8 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Ube2e

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_008618gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_006199gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_009521gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Ubc

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Ube1

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_027607gn

Ciona intestinalis

Vase tunicate

Cint\LOC100183458

Ciona intestinalis

Vase tunicate

Cint\LOC100185831

Ciona intestinalis

Vase tunicate

Cint\LOC104266887

Ciona intestinalis

Vase tunicate

Cint\LOC100175624

Ciona intestinalis

Vase tunicate

Cint\LOC100185453

Gallus gallus

Domestic chicken

Ggal\UBE2E1

Gallus gallus

Domestic chicken

Ggal\UBE2D1

Gallus gallus

Domestic chicken

Ggal\UBE2E3

Gallus gallus

Domestic chicken

Ggal\UBE2D3

Human Disease Model Data

FlyBase Human Disease Model Reports

Alleles Reported to Model Human Disease (Disease Ontology)

Download

Models ( 0 )

Allele

Disease

Evidence

References

Interactions ( 3 )

Allele

Disease

Interaction

References

eff⁸

exacerbates autosomal dominant cerebellar ataxia

modeled by Hsap\ATXN1^30Q.UAS

(Fernandez-Funez et al., 2000)

modeled by Hsap\ATXN1^82Q.UAS

(Fernandez-Funez et al., 2000)

exacerbates Huntington's disease

modeled by Hsap\HTT^{128Q.1-336.UAS}

(Branco et al., 2008)

exacerbates olivopontocerebellar atrophy

modeled by Hsap\ATXN1^82Q.UAS

(Branco et al., 2008)

eff^EP674

exacerbates autosomal dominant cerebellar ataxia

modeled by Hsap\ATXN1^30Q.UAS

(Fernandez-Funez et al., 2000)

modeled by Hsap\ATXN1^82Q.UAS

(Fernandez-Funez et al., 2000)

eff^HM05268

ameliorates Machado-Joseph disease

modeled by Hsap\ATXN3^{tr.Q78.UAS.Tag:HA}

(Tsou et al., 2015)

Comments ( 0 )

Human Orthologs (via DIOPT v7.1)

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

Complementation?

Transgene?

UBE2D3; ubiquitin conjugating enzyme E2 D3

13 of 15

602963

UBE2D2; ubiquitin conjugating enzyme E2 D2

12 of 15

602962

UBE2D4; ubiquitin conjugating enzyme E2 D4 (putative)

9 of 15

UBE2D1; ubiquitin conjugating enzyme E2 D1

8 of 15

602961

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

View in Interactions Browser

Please look at the Interaction Group reports for full details of the physical interactions

protein-protein

Interacting group

Assay

References

eff - CG11982

two hybrid

(Hu et al., 2017.6.13)

eff - Diap1

pull down, autoradiography

(Ryoo et al., 2002)

eff - LUBEL

enzymatic study, western blot

(Asaoka et al., 2016)

eff - ci

enzymatic study, western blot

(Pan et al., 2017)

eff - mr

anti tag coimmunoprecipitation, anti tag western blot, two hybrid, western blot

(Chen et al., 2009)

eff - sina

two hybrid

(Tang et al., 1997)

eff - sinah

two hybrid

(Hu et al., 2017.6.13)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

eff

suppressible

CycA

(Lilly et al., 2000)

eff

enhanceable

CycA

(Chen et al., 2009)

eff

enhanceable

(Chen et al., 2009)

eff

enhanceable

Ube3a

(Lu et al., 2009)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

bchs

enhanceable

eff

(Simonsen et al., 2007)

suppressible

(Kim et al., 2010)

suppressible

(Ryoo et al., 2002)

Dronc

enhanceable

eff

(Ryoo et al., 2002)

suppressible

(Ji et al., 2012)

enhanceable

(Caldwell et al., 2008)

enc

enhanceable

eff

(Ohlmeyer and Schupbach, 2003)

faf

suppressible

eff

(Chen et al., 2000, Wu et al., 1999)

faf|lqf

suppressible

eff

(Cadavid et al., 2000)

hid

suppressible

eff

(Ryoo et al., 2002)

Iswi

suppressible

eff

(Arancio et al., 2010)

neur

suppressible

eff

(Lai et al., 2001)

enhanceable

eff

(Fauvarque et al., 2001, Fauvarque and Dura, 1993)

ph-p

enhanceable

eff

(Fauvarque et al., 2001, Fauvarque and Dura, 1993)

ph-p|Pc

enhanceable

eff

(Fauvarque and Dura, 1993)

rpr

suppressible

eff

(Ryoo et al., 2002)

sina

suppressible

eff

(Neufeld et al., 1998)

Ube3a

enhanceable

eff

(Lu et al., 2009)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

66859

DroID - A comprehensive database of gene and protein interactions.

FBgn0011217

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

41785

Pathways

Gene Group - Pathway Membership (FlyBase)

Negative Regulators of Hedgehog Signaling Pathway -: Negative regulators of hedgehog signaling down-regulation the pathway, resulting in the repression of transcription of hh-responsive genes.

External Data

Linkouts

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P25867

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-56

Cytogenetic map

88D2-88D2

Sequence location

3R:14,732,414..14,741,319 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

88D2-88D2

Limits computationally determined from genome sequence between P{EP}CG33967^EP666 and P{lacW}Hsc70-4^L3929

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

88D5-88D6

(determined by in situ hybridisation)

(Spradling et al., 1999)

88D-88D

(determined by in situ hybridisation)

(Cenci et al., 1997, Matuschewski et al., 1996, Fauvarque and Dura, 1993, Treier et al., 1992)

88D1-88D10

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

3-56

(FlyBase, 2016)

3-54.5

(Comeron et al., 2012)

(Neufeld et al., 1998)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (30)

Bloomington

26691

w^*; P{UAS-eff.HA}1.4

56495

w^*; P{UAS-eff.N}GH-3/CyO

d00904

d03427

c04358

c04398

e01950

e03661

v105731

v110767

v26011

w¹¹¹⁸; P{GD10600}v26011

v26012

w¹¹¹⁸; P{GD10600}v26012

More stocks available...

Genomic Clones (20)

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

cDNA Clones (196)

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.

FBgn0011217

cDNA Clones, End Sequenced (ESTs)

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0011217

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

41785

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Pan et al., 2017, Cipressa et al., 2013)

monoclonal

(Chen et al., 2009)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: eff CG7425

(Zheng, 1999.11)

Source for database merge of

Source for merge of: eff mei68

(Gatti, 1998.8.3)

Source for merge of: eff E(Pc)88D

(Fauvarque et al., 2001)

Source for merge of: eff anon-WO0118547.343

(FlyBase, 1996-)

Additional comments

Source for merge of eff anon-WO0118547.343 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Other Comments

DNA-protein interactions: genome-wide binding profile assayed for eff protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).

(Filion et al., 2010)

Area matching Drosophila EST AI297203. This EST forms a 1122bp contig with AI455195 and AA438815.

(Davies, 2001.3.15)

Identification: Enhancer trap expression pattern survey for loci expressed in the ring gland.

(Harvie et al., 1998)

14 "SS3-3" alleles of eff have been isolated in a screen for dominant modifiers of the sina^GMR.PN eye phenotype.

(Neufeld et al., 1998)

eff encodes a class I ubiquitin-conjugating enzyme required for proper telomere behaviour.

(Cenci et al., 1997)

An eff cDNA has been cloned.

(Matuschewski et al., 1996)

Mutants affect telomere behavior during mitosis and male meiosis. Some form of ubiquitin-mediated proteolysis must occur in wild type cells to resolve the adhesion of telomeres prior to chromosome separation.

(Cenci et al., 1995)

Postmeiotic differentiation defect.

(Castrillon et al., 1993)

Isolated by PCR using primers specific for yeast UBC1, UBC4, UBC5 ubiquitin-conjugating enzyme subfamily.

(Treier et al., 1992)

eff has been cloned and functionally analysed.

(Treier et al., 1992)

Origin and Etymology

Discoverer

Etymology

Named 'UbcD1' for 'ubiquitin-conjugating enzyme from Drosophila 1 (the numbering reflects the order of identification).

(Matuschewski et al., 1996)

Named 'UbcD1' for 'ubiquitin-conjugating enzyme from Drosophila melanogaster 1'. (The numbering reflects the order of gene identification and does NOT follow the numbering of yeast UBC genes).

(Treier et al., 1992)

Identification

External Crossreferences and Linkouts ( 83 )

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.

41785

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

P25867

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

A0A0B4KHJ1

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0011217

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

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Linkouts

BioGRID - A database of protein and genetic interactions.

66859

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones

FBgn0011217

DroID - A comprehensive database of gene and protein interactions.

FBgn0011217

DRSC - Results frm RNAi screens

FBgn0011217

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

eff_1

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0011217

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG7425-RA

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

CG7425

Flygut - An atlas of the Drosophila adult midgut

FBgn0011217

FlyMine - An integrated database for Drosophila genomics

FBgn0011217

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

104199

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

41785

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

41785

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

Dmel_CG7425

modMine - A data warehouse for the modENCODE project

FBgn0011217

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P25867

Synonyms and Secondary IDs (36)

Reported As

Symbol Synonym

3527

(Harvie et al., 1998)

6535

(Harvie et al., 1998)

CG7425

(Hosono et al., 2015, Roussel et al., 2013, Ni et al., 2011.7.19, Ying et al., 2011, Keleman et al., 2009.8.5, Perkins et al., 2009, Hughes et al., 2008, Grieder et al., 2007, Molnar et al., 2006, Norga et al., 2003)

E(Pc)88D

(Mollaaghababa et al., 2001, Fauvarque and Dura, 1993)

EFF

(Filion et al., 2010)

Eff

(Cipressa et al., 2016, Kleino and Silverman, 2014, Raffa et al., 2013, Ying et al., 2011, Paquette et al., 2010)

SS3-3

(Neufeld et al., 1998)

UBC4

(Neely et al., 2010, Oh et al., 1994)

UBCD-1

(Brachmann and Cagan, 2003)

UBCD1

(Danial and Korsmeyer, 2004, Ou et al., 2003, Palaga and Osborne, 2002, Philp, 1998)

Ubc-D1

(Lilly et al., 1997, Tang et al., 1997)

Ubc5

(Chen et al., 2017)

UbcD

(Kim et al., 2010, Lai et al., 2001)

UbcD1

(Pan et al., 2017, Asaoka et al., 2016, Hans et al., 2014, Raffa et al., 2013, Velentzas et al., 2013, Yeh and Bratton, 2013, Raffa et al., 2011, Sandu et al., 2010, Michelle et al., 2009, Michelle et al., 2009, Xu et al., 2009, Doheny et al., 2008, Herman-Bachinsky et al., 2007, Kuranaga and Miura, 2007, Rathke et al., 2007, Cenci et al., 2005, Brumby et al., 2004, Cenci et al., 2004, D'Amours and Amon, 2004, Biessmann and Mason, 2003, Cenci et al., 2003, Claveria and Torres, 2003, Shulman and Feany, 2003, Gozani et al., 2002, Li et al., 2002, Zoghbi and Botas, 2002, Bocca et al., 2001, Deng and Lin, 2001, Kramer, 2001, Lai et al., 2001, Lai et al., 2001, Muzzopappa et al., 2001, Cadavid et al., 2000, Carthew and Xu, 2000, Cenci et al., 2000, Chen et al., 2000, Fernandez-Funez et al., 2000, Gonzalez and Bornens, 2000, Lilly et al., 2000, Raabe, 2000, Robertson et al., 2000, Thomas and Wassarman, 1999, Wu et al., 1999, Cenci et al., 1998, Gatti, 1998.8.3, Neufeld et al., 1998, Anonymous, 1997, Cenci et al., 1997, Cenci et al., 1997, Hawley, 1997, Matuschewski et al., 1996, Rawson, 1996.8.28, Treier et al., 1992)

UbcH5

(Tsou et al., 2015)

anon-WO0118547.343

effete

(Tsou et al., 2015, Staudt et al., 2005)

fs(3)01295

(Lilly and Spradling, 1996)

l(3)01462

l(3)j2C8

l(3)s1782

mei68

ms(3)01295

ms(3)1

ms(3)3

ms(3)88D

(Castrillon et al., 1993, Berg and Spradling, 1991)

ms(3)neo2

ms(3)ry1

(Bloomington Drosophila Stock Center, 1998.9.14)

ms(3)ry3

(Bloomington Drosophila Stock Center, 1998.9.14)

ubcD1

(Rumpf et al., 2014, Caldwell et al., 2008, Caldwell and Eberl, 2007, Kuo et al., 2006, Yoo, 2005, Bergmann et al., 2003, Martin, 2002, Ryoo et al., 2002, Ryoo et al., 2002)

Name Synonyms

Effete

(Asaoka et al., 2016, Raffa et al., 2013, Vandenabeele and Bertrand, 2012, Valanne et al., 2011, Chen et al., 2009, Ditzel et al., 2008, Hossain et al., 2008, Nybakken et al., 2005)

Suppressor of GMR-sina 3-3

(Neufeld et al., 1998)

Ubiquitin conjugating enzyme 1

(Matuschewski et al., 1996)

effete

(Park et al., 2016, Kim et al., 2010, Paquette et al., 2010, Hoopfer et al., 2008, Musarò et al., 2008, Simonsen et al., 2007, Kuo et al., 2006, Mukai et al., 2006, Birch-Machin et al., 2005, Staudt et al., 2005)

effette

(Rathke et al., 2007)

meiotic 68

Secondary FlyBase IDs

FBgn0004831
FBgn0011011
FBgn0011333
FBgn0011657
FBgn0013661
FBgn0013663
FBgn0013935
FBgn0062081

Datasets (1)

Study focus (1)

Experimental Role

Project

Project Type

Title

transgene_used

FBGSE22069

genome binding

Protein profiling reveals five principal chromatin types in Drosophila cells.

References (191)

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

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