FlyBase Gene Report: Dmel\Ubi-p63E

General Information

Symbol

Dmel\Ubi-p63E

Species

D. melanogaster

Name

Ubiquitin-63E

Annotation Symbol

CG11624

Feature Type

protein_coding_gene

FlyBase ID

FBgn0003943

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Ubiquitin-63E (Ubi-p63E) encodes a polyubiquitin precursor: once processed by deubiquitinating enzymes, it produces ten ubiquitin molecules, which are predominantly conjugated to target proteins. Ubiquitin conjugation is involved in a wide range of biological processes, such as protein degradation, endocytosis of plasma membrane proteins, protein trafficking, DNA-damage response and inflammation and immune system response. [Date last reviewed: 2018-09-06] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Also Known As

Ub, ubiquitin, Ubi-p, polyubiquitin, ubi63E

Key Links

Genomic Location

Cytogenetic map

63F5-63F5

Sequence location

3L:3,899,259..3,903,184 [-]

Recombination map

3-9

RefSeq locus

NT_037436 REGION:3899259..3903184

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (7 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables protein tag activity

inferred from biological aspect of ancestor with PANTHER:PTN000071508

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with SGD:S000003962

(Gene Ontology Curators, 2002-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in larval midgut cell programmed cell death

inferred from mutant phenotype

(Chang et al., 2013)

involved_in macroautophagy

inferred from mutant phenotype

(Chang et al., 2013)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in modification-dependent protein catabolic process

inferred from biological aspect of ancestor with PANTHER:PTN000071508

(GO Reference Genome Project, 2011-)

involved_in protein ubiquitination

inferred from biological aspect of ancestor with PANTHER:PTN000071508

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with SGD:S000003962

(Gene Ontology Curators, 2002-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in cytosolic ribosome

inferred from biological aspect of ancestor with PANTHER:PTN000071508

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000071508

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

UBIQUITIN

Protein Family (UniProt)

Belongs to the ubiquitin family. (P0CG69)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

UBIQUITIN -: Ubiquitin is a small (76 amino acid), highly conserved protein found in all eukaryotes. Through its covalent attachment to other proteins, ubiquitin can modify protein activity in numerous ways. The most well known is the targeting of proteins for proteasomal degradation. Ubiquitin is often expressed as a fusion protein, either as polyubiquitin or fused with the ribosomal proteins L40 and S27a. Ubiquitin monomers are generated by post-translational cleavage. (Adapted from PMID:12729753 and PMID:27012465)

Protein Function (UniProtKB)

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).

(UniProt, P0CG69)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

Ubi-p: Ubiquitin-polymeric

Structural gene for ubiquitin (Arribas et al., 1988); structure and expression described by Lee et al. (1988). Threefold increase in level of gene by heat shock. An Ubi-p - lacZ fusion gene introduced by germ line transformation has been expressed at high levels at all life stages tested (embryonic, larval, pupal, and adult).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Ubi-p63E 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry P0CG69)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Apparent introns not annotated: probable artifacts due to repetitive sequence.

Gene model reviewed during 5.46

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Ubi-p63E-RA

FBtr0073177

NM_168043

2521

763

Ubi-p63E-RB

FBtr0073178

NM_079185

2759

763

Ubi-p63E-RC

FBtr0073179

NM_206272

2710

763

Ubi-p63E-RD

FBtr0333142

NM_001274454

2624

763

Additional Transcript Data and Comments

Reported size (kB)

4.4 (northern blot)

(Lee et al., 1988)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Ubi-p63E-PA

FBpp0073034

85.8

763

7.95

FBpp0073035

85.8

763

7.95

FBpp0089269

85.8

763

7.95

FBpp0305348

85.8

763

7.95

P0CG69

NP_001261383

AGB94078

Polypeptides with Identical Sequences

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

763 aa isoforms: Ubi-p63E-PA, Ubi-p63E-PB, Ubi-p63E-PC, Ubi-p63E-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

231 (aa)

(Lee et al., 1988)

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\Ubi-p63E using the Feature Mapper tool.

External Data

Crossreferences

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

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

4.93

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

spermatogenesis & adult stage | male

spermatocyte

(Lu et al., 2013)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage & larval stage & pupal stage

(Lee et al., 1988)

embryonic stage -- adult stage

(Lee et al., 1988)

Additional Descriptive Data

Ubi-p63E transcript is expressed in spermatocytes. Expression is isoform-specific; very little Ubi-p63E-RC transcript is detected in spermatocytes, while Ubi-p63E-RA has higher expression levels than other isoforms.

(Lu et al., 2013)

Ubi-p63E transcripts are observed in all stages assayed. A reporter construct was used to show that they are expressed in a tissue-general pattern in all life stages assayed.

(Lee et al., 1988)

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ubi-p63E in JBrowse

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

View exonic expression by developmental stage for Dmel\Ubi-p63E

View exonic expression by tissue for Dmel\Ubi-p63E

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

38456/tissue=All

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

FBgn0003943

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003943

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

FBgn0003943

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

CG11624

Flygut - An atlas of the Drosophila adult midgut

FBgn0003943

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 11 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Ubi-p63E

Transgenic constructs containing regulatory region of Ubi-p63E

Aberrations (Deficiencies and Duplications) ( 4 )

Inferred from experimentation ( 4 )

Gene disrupted in

Df(3L)Exel6098

(Lu et al., 2013, Ryder, 2004.4.26)

Gene not disrupted in

Df(3L)ED208

(Lu et al., 2013)

Df(3L)ED4341

(Lu et al., 2013)

Gene partially disrupted in

Df(3L)Ubi-p63E^12c

(Lu et al., 2013)

Inferred from location ( 3 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

viable

viable (with Ubi-p63E^12c)

Ubi-p63E^23b

viable (with Ubi-p63E^23b)

Ubi-p63E^12c

Sterility

Allele

female fertile

Ubi-p63E^12c

female fertile (with Ubi-p63E^12c)

Ubi-p63E^23b

female fertile (with Ubi-p63E^23b)

Ubi-p63E^12c

fertile

Ubi-p63E^EY07341

male sterile

male sterile (with Ubi-p63E^12c)

Ubi-p63E^23b

male sterile (with Ubi-p63E^23b)

Ubi-p63E^12c

Other Phenotypes

Allele

abnormal meiotic cell cycle | cell autonomous | male limited | somatic clone

Ubi-p63E^12c

abnormal meiotic cell cycle | male limited

abnormal meiotic cell cycle | male limited (with Df(3L)Exel6098)

Ubi-p63E^EY07341

abnormal meiotic cell cycle | male limited (with Ubi-p63E^12c)

abnormal meiotic cell cycle | male limited (with Ubi-p63E^23b)

abnormal meiotic cell cycle | male limited (with Ubi-p63E^EY07341)

abnormal meiotic cell cycle | male limited (with Ubi-p63E^Z3-2534)

abnormal meiotic cell cycle | male limited (with Ubi-p63E^Z3-3969)

abnormal meiotic cell cycle | male limited (with Ubi-p63E^Z3-4216)

abnormal meiotic cell cycle | male limited (with Ubi-p63E^Z3-5802)

Phenotype manifest in

Allele

spermatocyte

Ubi-p63E^unspecified

spermatocyte | cell autonomous | somatic clone

Ubi-p63E^12c

testis

Ubi-p63E^12c

testis (with Df(3L)Exel6098)

Ubi-p63E^EY07341

testis (with Ubi-p63E^12c)

testis (with Ubi-p63E^23b)

testis (with Ubi-p63E^EY07341)

testis (with Ubi-p63E^Z3-2534)

testis (with Ubi-p63E^Z3-3969)

testis (with Ubi-p63E^Z3-4216)

testis (with Ubi-p63E^Z3-5802)

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (19)

Hsap\UBC

11 of 14

Yes

Hsap\UBB

6 of 14

Yes

4 of 14

3 of 14

3 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Yes

Hsap\OASL

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (31)

Rnor\Ubc

11 of 14

Yes

Rnor\Ubb

6 of 14

Yes

3 of 14

2 of 14

2 of 14

2 of 14

Yes

Rnor\Fau

1 of 14

Rnor\Isg15

1 of 14

Yes

Rnor\LOC679594

1 of 14

Yes

Rnor\LOC687780

1 of 14

Rnor\LOC100360645

1 of 14

Yes

Rnor\LOC100363494

1 of 14

Yes

Rnor\LOC100910768

1 of 14

Yes

Rnor\Oas1a

1 of 14

Yes

Rnor\Oas1b

1 of 14

Yes

Rnor\Oas1d

1 of 14

Yes

Rnor\Oas1e

1 of 14

Yes

Rnor\Oas1i

1 of 14

Yes

Rnor\Oasl2

1 of 14

Yes

Rnor\Oasl

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (31)

Mmus\Ubc

12 of 14

Yes

6 of 14

3 of 14

2 of 14

2 of 14

2 of 14

Yes

Mmus\Fau

1 of 14

Mmus\Gm4802

1 of 14

Yes

Mmus\Gm8797

1 of 14

Mmus\Gm11808

1 of 14

Mmus\Isg15

1 of 14

Yes

Mmus\Oas1a

1 of 14

Yes

Mmus\Oas1c

1 of 14

Yes

Mmus\Oas1d

1 of 14

Yes

Mmus\Oas1e

1 of 14

Yes

Mmus\Oas1f

1 of 14

Yes

Mmus\Oas1g

1 of 14

Yes

Mmus\Oas1h

1 of 14

Yes

Mmus\Oasl1

1 of 14

Yes

Mmus\Oasl2

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (11)

Xtro\ubb

7 of 13

Yes

Xtro\ubc

4 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (15)

Drer\ubb

10 of 14

Yes

Drer\ubc

8 of 14

Yes

Drer\si:ch211-202a12.4

6 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (17)

Cele\ubq-1

10 of 14

Yes

Cele\F52C6.2

3 of 14

Yes

Cele\ubq-2

3 of 14

Cele\F52C6.3

2 of 14

Cele\F52C6.4

2 of 14

Yes

Cele\ned-8

2 of 14

Cele\C16C8.4

1 of 14

Cele\C16C8.5

1 of 14

Yes

Cele\C16C8.11

1 of 14

Cele\C16C8.13

1 of 14

Yes

Cele\C16C8.14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (11)

Agam\AgaP_AGAP001971

10 of 12

Yes

Agam\AgaP_AGAP002599

6 of 12

Yes

Agam\AgaP_AGAP001969

4 of 12

Yes

4 of 12

3 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (47)

Atha\UBQ10

10 of 13

Yes

Atha\UBQ14

10 of 13

Yes

Atha\UBQ8

8 of 13

Yes

Atha\UBQ4

7 of 13

Yes

Atha\UBQ3

6 of 13

Yes

Atha\UBQ11

6 of 13

Yes

Atha\UBQ9

5 of 13

Yes

Atha\UBQ12

5 of 13

Yes

Atha\UBQ13

5 of 13

Yes

4 of 13

4 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (8)

Scer\UBI4

9 of 13

Yes

3 of 13

3 of 13

3 of 13

2 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (9)

Spom\ubi4

9 of 12

Yes

3 of 12

3 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Ubi-p63E. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (11)

11 of 13

6 of 13

6 of 13

5 of 13

5 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

congenital heart defect (postulated), UBB-related

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 ( 1 )

Allele

Disease

Interaction

References

Ubi-p63E^unspecified

exacerbates Huntington's disease

modeled by Hsap\HTT^Q93.ex1.UAS

(Steffan et al., 2004)

Disease Associations of Human Orthologs (via DIOPT v9.1 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?

11 of 14

6 of 14

RPS27A; ribosomal protein S27a

4 of 14

191343

NEDD8; NEDD8 ubiquitin like modifier

3 of 14

603171

UBA52; ubiquitin A-52 residue ribosomal protein fusion product 1

3 of 14

191321

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Ubi-p63E - Act88F

ion exchange chromatography, peptide massfingerprinting

(Schmitz et al., 2003)

Ubi-p63E - CG5958

split luciferase complementation, luminiscence technology

(Kolkhof et al., 2017)

Ubi-p63E - CYLD

deubiquitinase assay, anti tag western blot, molecular weight estimation by staining

(Asaoka et al., 2016, Tsichritzis et al., 2007)

Ubi-p63E - Dronc

anti tag coimmunoprecipitation, western blot, anti tag western blot

(Kamber Kaya et al., 2017)

Ubi-p63E - Dscam1

anti tag coimmunoprecipitation, peptide massfingerprinting

(Yang et al., 2012)

Ubi-p63E - Gpat4

split luciferase complementation, luminiscence technology

(Kolkhof et al., 2017)

Ubi-p63E - Graf

pull down, western blot

(Kim et al., 2017)

Ubi-p63E - LUBEL

pull down, western blot, enzymatic study

(Asaoka et al., 2016)

Ubi-p63E - Lsd1

split luciferase complementation, luminiscence technology

(Kolkhof et al., 2017)

Ubi-p63E - Lsd2

split luciferase complementation, luminiscence technology

(Kolkhof et al., 2017)

Ubi-p63E - Marf

anti bait coimmunoprecipitation, western blot

(Poole et al., 2010)

Ubi-p63E - Rbf

anti tag coimmunoprecipitation, anti tag western blot

(Raj et al., 2012)

Ubi-p63E - Ufl1

split luciferase complementation, luminiscence technology

(Kolkhof et al., 2017)

Ubi-p63E - bam

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, Identification by mass spectrometry

(Ji et al., 2017)

Ubi-p63E - dachs

anti tag coimmunoprecipitation, western blot

(Bosch et al., 2014)

Ubi-p63E - grim

anti tag coimmunoprecipitation, anti tag western blot, pull down, western blot

(Yeh and Bratton, 2013)

Ubi-p63E - lqf

pull down, western blot

(Xie et al., 2012)

Ubi-p63E - lwr

pull down, western blot

(Shih et al., 2002)

Ubi-p63E - morgue

anti tag coimmunoprecipitation, western blot, peptide massfingerprinting, pull down

(Zhou et al., 2013)

Ubi-p63E - rdx

anti tag coimmunoprecipitation, anti tag western blot

(Zhou et al., 2015)

Ubi-p63E - rngo

pull down, anti tag western blot, anti bait coimmunoprecipitation

(Morawe et al., 2011)

Ubi-p63E - smo

anti tag coimmunoprecipitation, covalent binding, anti tag western blot

(Yang et al., 2013)

Ubi-p63E - sturkopf

split luciferase complementation, luminiscence technology

(Kolkhof et al., 2017)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

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

Usp14

enhanceable

Ubi-p63E

(Kovács et al., 2020)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

63944

DroID - A comprehensive database of gene and protein interactions.

FBgn0003943

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

38456

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

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

Regulation of pyruvate metabolism

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

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

Class of Gene

gene_with_edited_transcript

(Graveley et al., 2011)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-9

Cytogenetic map

63F5-63F5

Sequence location

3L:3,899,259..3,903,184 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

63F5-63F5

Limits computationally determined from genome sequence between P{PZ}kst⁰¹³¹⁸ and P{PZ}Sc2⁰⁵⁶³⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

63F2-63F4

(determined by in situ hybridisation)

(Ranz et al., 1997)

63E-63E

(determined by in situ hybridisation)

(Izquierdo, 1994)

63F-63F

(determined by in situ hybridisation)

(Arribas et al., 1986)

Experimentally Determined Recombination Data

Location

3-9

(FlyBase, 2016)

3-8.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Same map position as 63F early ecdysone-induced puff.

Stocks and Reagents

Stocks (5)

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

Bloomington

16814

y¹ w^67c23; P{EPgy2}Ubi-p63E^EY07341

61503

y¹ w^*; Ubi-p63E^23b/TM3, Sb¹

61502

y¹ w^*; Df(3L)Ubi-p63E^12c, Ubi-p63E^12c/TM3, Sb¹

33405

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00284}attP2/TM3, Sb¹

VDRC

v102379

P{KK109327}VIE-260B

Genomic Clones (15)

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

cDNA Clones (49)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

AT20865

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.

FBgn0003943

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0003943

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-DGRC : Stable S2-DGRC cell lines expressing Tag:FLAG-tagged wild-type and mutant versions of IntS8 under the control of the Ubi-p63E promoter were generated.
(Huang et al., 2020)
New stable cell line derived from OSC : Stable OSC lines expressing internally tagged kipf under control of the Ubi-p63E promoter and an SV40 3'UTR were generated by integration into an RMCE landing site.
(Baumgartner et al., 2022)

Other Comments

S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.

(Stroschein-Stevenson et al., 2006)

RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R⁺ cells.

(Boutros et al., 2004)

RNAi screen using dsRNA made from templates generated with primers directed against this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R⁺ cells.

(Boutros et al., 2004)

Area matching Drosophila Ubiquitin gene, Acc. No. M22428.

(Davies, 2001.3.15)

Antibody staining of polytene chromosomes shows that ubiquitin is mainly associated with the compact and stabilized structure that forms the bands rather than with the more decondensed and destabilized protein-DNA structure that forms interbands and puffs.

(Izquierdo, 1994)

Ubi-p63E expression has been studied in heat shocked aging flies.

(Niedzwiecki and Fleming, 1993)

Structural gene for ubiquitin (Arribas, Sampedro and Izquierdo, 1988); structure and expression described by Lee, Simon and Lis (1988). Threefold increase in level of gene by heat shock. A Ubi-p63E-lacZ fusion gene introduced by germ line transformation has been expressed at high levels at all life stages tested (embryonic, larval, pupal and adult).

Relationship to Other Genes

Source for database merge of

Additional comments

The Ubi-p5E and Ubi-p63E genes share at least 50% identity.

(Langille and Clark, 2007)

The insertion in the "l(3)05634" line is within the Sc2 gene, rather than affecting Ubi-p63E as stated in FBrf0111489.

(Vaskova et al., 2000)

The insertion in the "l(3)05634" line is stated to affect Ubi-p63E in this paper. A subsequent publication suggests that this is incorrect and the insertion is in fact in Sc2 (see FBrf0130136).

(Spradling et al., 1999)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Named 'magellan' because mutant spermatocytes arrest development with abnormal structures that resemble Magellanic clouds.

(Lu et al., 2013)

Synonyms and Secondary IDs (28)

Reported As

Symbol Synonym

CG11624

(Ristic et al., 2016, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Hughes et al., 2008, Qin et al., 2005, Ramet et al., 2002, Fulton et al., 2001)

DmUb

(Shih et al., 2002)

DmUbi-p63E

(Hoe et al., 2011)

(Chi et al., 2016, Poole et al., 2010)

(Nagy et al., 2018, Ji et al., 2017, Kim et al., 2017, Zhou et al., 2015, Bosch et al., 2014, Chang et al., 2013, Yang et al., 2013, Yeh and Bratton, 2013, Zhou et al., 2013, Raj et al., 2012, Tsichritzis et al., 2007, Koh et al., 2006, Koh et al., 2006, Moberg et al., 2005, Kanuka et al., 2003, Huang et al., 1995)

Ub-p63E

(Kanoh et al., 2015)

Ubi-P63e

(Qin et al., 2005)

Ubi-p

(Vaskova et al., 2000, Lindsley and Zimm, 1992)

Ubi63E

(Bernards and Hariharan, 2001, Fernandez-Funez et al., 2000)

Ubi63p

(Stielow et al., 2008)

Ubip

(Maroni, 1994)

Ubip63E

(Munoz-Soriano et al., 2012)

Ubiq

(Wesley and Mok, 2003)

Ubp

(Fischer-Vize et al., 1997)

magn

(Lu et al., 2013)

ubi

(Witzberger et al., 2008)

ubi-p63E

(Zhou et al., 2008)

ubi63E

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

Name Synonyms

Ubiquitin

(Kolkhof et al., 2017, Herz et al., 2006, Wesley and Mok, 2003, Zoghbi and Botas, 2002, Noll et al., 2000, Pham and Sauer, 2000)

Ubiquitin 63E

(Bardet et al., 2013)

Ubiquitin-63-E

(Yang et al., 2012)

Ubiquitin-63E

(Urban et al., 2017, Nybakken et al., 2005, Qin et al., 2005, Gim et al., 2001)

Ubiquitin-polymeric

(Lindsley and Zimm, 1992)

magellan

(Lu et al., 2013)

polyubiquitin

(Lu et al., 2013, Niedzwiecki and Fleming, 1993)

ubiquitin

(Xu et al., 2017, Chang et al., 2013, Morawe et al., 2011, Simonsen et al., 2007, Lu and Bilder, 2005, Moberg et al., 2005, Park et al., 2005, Sakata et al., 2004, Finley et al., 2003, Schmitz et al., 2003, Auluck et al., 2002, Murphey and Godenschwege, 2002)

ubiquitin-63E

(Geronikolou et al., 2018)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 218 )

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.

38456

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.

P0CG69

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

P0CG69

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.

P0CG69

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

38456/tissue=All

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

FBgn0003943

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

FBgn0003943

FlyMine - An integrated database for Drosophila genomics

FBgn0003943

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

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

dme:Dmel_CG11624

MARRVEL_MODEL - MARRVEL (model organism gene)

38456

Linkouts

BioGRID - A database of protein and genetic interactions.

63944

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

FBgn0003943

DroID - A comprehensive database of gene and protein interactions.

FBgn0003943

DRSC - Results frm RNAi screens

FBgn0003943

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0003943

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0003943

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

CG11624

Flygut - An atlas of the Drosophila adult midgut

FBgn0003943

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

TC009978

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

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

38456

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

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

Regulation of pyruvate metabolism

References (374)

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

4.93

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