FlyBase Gene Report: Dmel\Ubr3

General Information

Symbol

Dmel\Ubr3

Species

D. melanogaster

Name

Ubr3 ubiquitin ligase

Annotation Symbol

CG42593

Feature Type

protein_coding_gene

FlyBase ID

FBgn0260970

Gene Model Status

Current

Stock Availability

16 publicly available

Enzyme Name (EC)

HECT-type E3 ubiquitin transferase (2.3.2.26)

RING-type E3 ubiquitin transferase (2.3.2.27)

RBR-type E3 ubiquitin transferase (2.3.2.31)

RCR-type E3 ubiquitin transferase (2.3.2.33)

RING-type E3 ubiquitin transferase (cysteine targeting) (2.3.2.36)

Gene Summary

E3 ubiquitin-protein ligase which is a component of the N-end rule pathway (PubMed:26383956, PubMed:27195754). Recognizes and binds to proteins bearing specific N-terminal residues, leading to their ubiquitination and subsequent degradation (PubMed:26383956, PubMed:27195754). Binds to the E3 ubiquitin-protein ligase Diap1 and enhances its ubiquitination and anti-apoptotic functions (PubMed:25146930). Essential during trichome development for the ubiquitination of the N-terminus of ovo isoform B (svb), converting it from a transcriptional inhibitor to an activator (PubMed:26383956). Positively regulates a hh-signaling pathway which functions in photoreceptor differentiation (PubMed:27195754). Activation of hh up-regulates transcription of Ubr3, which in turn promotes hh signaling by mediating the ubiquitination and degradation of cos (PubMed:27195754). Necessary for auditory transduction: plays a role in Johnston's organ organization by acting in the regulation of zip and ck function in scolopidial apical attachment (PubMed:27331610). Likely to function by acting in a pathway that negatively regulates the ubiquitination of zip, consequently affecting its interaction with ck (PubMed:27331610). May also negatively regulate a component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex Cul1, which also appears to function in the negative regulation of the zip-ck interaction and scolopidial apical attachment (PubMed:27331610). (UniProt, Q9W3M3)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Pathway
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

7C8-7D1

Sequence location

X:7,935,896..7,953,883 [+]

Recombination map

1-21

RefSeq locus

NC_004354 REGION:7935896..7953883

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 (14 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

enables protein binding

inferred from physical interaction with FLYBASE:cos; FB:FBgn0000352

(Li et al., 2016)

enables ubiquitin protein ligase activity

inferred from direct assay

(Li et al., 2016)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables ubiquitin protein ligase activity

inferred from electronic annotation with InterPro:IPR039164

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

enables zinc ion binding

inferred from sequence model

(Ying et al., 2011)

inferred from electronic annotation with InterPro:IPR003126

(InterPro Project Members, 2004-)

Biological Process (7 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

involved_in negative regulation of apoptotic process

inferred from mutant phenotype

(Huang et al., 2014)

involved_in positive regulation of smoothened signaling pathway

inferred from mutant phenotype

(Li et al., 2016)

involved_in protein autoubiquitination

inferred from direct assay

(Li et al., 2016)

involved_in protein K48-linked ubiquitination

inferred from direct assay

(Li et al., 2016)

involved_in protein ubiquitination

inferred from mutant phenotype

(Huang et al., 2014)

involved_in sensory perception of sound

inferred from mutant phenotype

(Li et al., 2016)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in protein ubiquitination

inferred from biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway

inferred from electronic annotation with InterPro:IPR039164

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Li et al., 2016)

is_active_in neuronal cell body

inferred from mutant phenotype

(Li et al., 2016)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

part_of ubiquitin ligase complex

inferred from biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

UNCLASSIFIED RING DOMAIN UBIQUITIN LIGASES

Pathway (FlyBase)

POSITIVE REGULATORS OF HEDGEHOG SIGNALING PATHWAY

Protein Family (UniProt)

Belongs to the E3 ubiquitin-protein ligase UBR1-like family. (Q9W3M3)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

ubiquitin protein ligase activity

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)- ubiquitinyl-[acceptor protein]-L-lysine (2.3.2.26)

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)- ubiquitinyl-[acceptor protein]-L-lysine (2.3.2.27)

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N(6)-ubiquitinyl-L-lysine (2.3.2.31)

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-threonine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-3-O-ubiquitinyl-L-threonine (2.3.2.33)

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-S-ubiquitinyl-L-cysteine (2.3.2.36)

Summaries

Gene Group (FlyBase)

UNCLASSIFIED RING DOMAIN UBIQUITIN LIGASES -: This group comprises RING domain ubiquitin ligases that do not classify under other groups in FlyBase.

Pathway (FlyBase)

POSITIVE REGULATORS OF HEDGEHOG SIGNALING PATHWAY -: Positive regulators of hedgehog signaling up-regulate the pathway, resulting in the activation of transcription of hh-responsive genes.

Protein Function (UniProtKB)

(UniProt, Q9W3M3)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Ubr3 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 Q9W3M3)

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

Gene model reviewed during 5.44

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

Stop-codon suppression (UGA) postulated; FBrf0216884.

Gene model reviewed during 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Ubr3-RA

FBtr0301748

NM_132200

9371

2219

Ubr3-RB

FBtr0331298

NM_001272388

9371

2236

Ubr3-RC

FBtr0331299

NM_001272389

9308

2218

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

UniProt

RefSeq ID

GenBank

Ubr3-PA

FBpp0290962

247.1

2219

5.72

FBpp0303730

249.0

2236

5.66

FBpp0303731

247.0

2218

5.72

M9PGM3

NP_001259318

AGB95163

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Selectively interacts (via UBR-type zinc finger) with the cleaved form of Diap1; this interaction is enhanced by tal (PubMed:25146930, PubMed:26383956). Interacts with tal and Rrp1 (PubMed:26383956). Interacts with ovo isoform B (via N-terminus) (PubMed:26383956). Interacts with Cad99C (via the cytoplasmic domain) (PubMed:27331610). Interacts with ck and Sans (PubMed:27331610). Interacts with cos (via Kinesin motor domain) (PubMed:27195754).

(UniProt, Q9W3M3)

Post Translational Modification

In vitro, self-ubiquitination in the presence of E1, E2 and ubiquitin.

(UniProt, Q9W3M3)

Domain

The UBR-type zinc finger domain is necessary for interaction with Diap1 and anti-apoptotic activity (PubMed:25146930). Domain is also sufficient for interaction with cos (PubMed:27195754).

The RING-type zinc finger domain is not necessary for interaction with Diap1 and anti-apoptotic activity.

(UniProt, Q9W3M3)

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\Ubr3 using the Feature Mapper tool.

External Data

Crossreferences

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

CG42593_1

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).

0.67

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

pupal stage

eye disc morphogenetic furrow

(Li et al., 2016)

eye disc

(Li et al., 2016)

second segment of antenna

(Li et al., 2016)

third segment of antenna

(Li et al., 2016)

Johnston organ neuron

Comment: enriched at apical tip

(Li et al., 2016)

scolopidial cilium

(Li et al., 2016)

scolopale cell of Johnston organ

(Li et al., 2016)

Additional Descriptive Data

Ubr3 is broadly expressed in developing eye discs and is enriched in the morphogenetic furrow.

(Li et al., 2016)

Ubr3 is expressed broadly in the second and third antennalsegments. In Johnston's organ, Ubr3 is enriched in the apical tips of neurons and in scolopale cells.

(Li et al., 2016)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Li et al., 2016)

is_active_in neuronal cell body

inferred from mutant phenotype

(Li et al., 2016)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ubr3 in JBrowse

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

View exonic expression by developmental stage for Dmel\Ubr3

View exonic expression by tissue for Dmel\Ubr3

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

31713/tissue=All

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

FBgn0260970

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

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

FBgn0260970

Flygut - An atlas of the Drosophila adult midgut

FBgn0260970

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 12 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 15 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Ubr3

Transgenic constructs containing regulatory region of Ubr3

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(1)BSC622

(Li et al., 2016)

Inferred from location ( 14 )

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

lethal

lethal | recessive

lethal - all die before end of first instar larval stage

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

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

viable, with Scer\GAL4^Mef2.PR

Ubr3^GD3276

viable, with Scer\GAL4^tin.CΔ4

Other Phenotypes

Allele

abnormal auditory perception | adult stage

abnormal developmental rate | somatic clone

abnormal neurophysiology | adult stage

increased cell death, with Scer\GAL4^en.PU

Ubr3^KK100920

increased cell death, with Scer\GAL4^ey.PU

Ubr3^KK100920

increased cell death, with Scer\GAL4^mirr-DE

Ubr3^KK100920

increased cell death | somatic clone

increased cell death | somatic clone, with Scer\GAL4^Tub.PU, Scer\GAL80^αTub84B.PL

Ubr3^KK100920

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

Ubr3^GD3276

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

Phenotype manifest in

Allele

eye, with Scer\GAL4^ey.PU

eye | somatic clone

Ubr3¹

eye disc, with Scer\GAL4^mirr-DE

Ubr3^KK100920

eye disc | somatic clone

Ubr3¹

Johnston organ | P-stage | somatic clone

Ubr3^B

photoreceptor neuron | somatic clone

scolopidium | P-stage | somatic clone

Ubr3^B

wing disc | somatic clone

Ubr3¹

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) (3)

Hsap\UBR3

13 of 14

Yes

Hsap\UBR1

2 of 14

Hsap\UBR2

2 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) (3)

Rnor\Ubr3

13 of 14

Yes

Rnor\Ubr1

2 of 14

Rnor\Ubr2

2 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Ubr3

13 of 14

Yes

Mmus\Ubr1

2 of 14

Mmus\Ubr2

2 of 14

Xenopus tropicalis (Western clawed frog) (5)

Xtro\ubr3

7 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (3)

Drer\ubr3

13 of 14

Yes

Drer\ubr2

2 of 14

Drer\ubr1

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\F10G7.10

11 of 14

Yes

Cele\ubr-1

2 of 14

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP000384

12 of 12

Yes

Agam\AgaP_AGAP000386

5 of 12

Yes

Agam\AgaP_AGAP000171

2 of 12

Arabidopsis thaliana (thale-cress) (1)

Atha\PRT6

5 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\UBR2

5 of 13

Yes

Scer\UBR1

2 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\ubr1

1 of 12

Yes

Spom\ubr11

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Ubr3. 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) (1)

Ubr1

4 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

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 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?

UBR3; ubiquitin protein ligase E3 component n-recognin 3

13 of 14

613831

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

Ubr3

anti tag coimmunoprecipitation, western blot, enzymatic study, ubiquitinase assay, anti tag western blot

(Li et al., 2016)

Ubr3 - Cad99C

anti tag coimmunoprecipitation, anti tag western blot

(Li et al., 2016)

Ubr3 - Diap1

anti tag coimmunoprecipitation, western blot, anti tag western blot

(Markus et al., 2023, Zanet et al., 2015, Huang et al., 2014, Ditzel et al., 2008)

Ubr3 - Drice

anti tag coimmunoprecipitation, anti tag western blot

(Huang et al., 2014)

Ubr3 - Dronc

anti tag coimmunoprecipitation, anti tag western blot

(Huang et al., 2014)

Ubr3 - Rrp1

anti tag coimmunoprecipitation, anti tag western blot

(Zanet et al., 2015)

Ubr3 - Sans

anti tag coimmunoprecipitation, anti tag western blot

(Li et al., 2016)

Ubr3 - cos

anti tag coimmunoprecipitation, anti tag western blot

(Li et al., 2016)

Ubr3 - ovo

anti tag coimmunoprecipitation, anti tag western blot

(Zanet et al., 2015)

Ubr3 - tal-1A

anti tag coimmunoprecipitation, anti tag western blot

(Zanet et al., 2015)

Ubr3 - tal-2A

anti tag coimmunoprecipitation, anti tag western blot

(Zanet et al., 2015)

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

Ubr3

enhanceable

Cad99C

(Li et al., 2016)

Ubr3

enhanceable

(Li et al., 2016)

suppressible

(Li et al., 2016)

suppressible

(Huang et al., 2014)

Ubr3

enhanceable

Sans

(Li et al., 2016)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

(UniProt, Q9W3M3 )

Linkouts

BioGRID - A database of protein and genetic interactions.

58185

DroID - A comprehensive database of gene and protein interactions.

FBgn0260970

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

31713

Pathways

Signaling Pathways (FlyBase)

POSITIVE REGULATORS OF HEDGEHOG SIGNALING PATHWAY

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_stop_codon_read_through

(Jungreis et al., 2011)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-21

Cytogenetic map

7C8-7D1

Sequence location

X:7,935,896..7,953,883 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

7C8-7D1

Limits computationally determined from genome sequence between P{EP}EP1243 and P{EP}sn^EP1217

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

7C7-7C9

(determined by in situ hybridisation)

(Peter et al., 2002)

Experimentally Determined Recombination Data

Location

1-21

(FlyBase, 2016)

1-22.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (16)

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

Bloomington

67191

y¹ w^*; PBac{UAS-Ubr3.L}VK00033

37703

y¹ w^* Mi{MIC}Ubr3^MI04537

605400

y¹ w^*; PBac{UAS-Ubr3.EGFP}VK00037

67195

y¹ w^*; PBac{Ubr3.18.3.EGFP}VK00033

67190

y¹ w^*; PBac{UAS-Ubr3.L}VK00037/SM6a

67193

y¹ w^*; PBac{UAS-Ubr3.RINGmut.FLAG}VK00033

67189

y¹ w^*; PBac{Ubr3.18.3}VK00033/TM6B, Tb¹

86477

y¹ w^* TI{CRIMIC.TG4.1}Ubr3^{CR01645-TG4.1}

67192

y¹ w^*; PBac{UAS-Ubr3.L.FLAG}VK00033/TM6B, Tb¹

Kyoto

103736

y^* w^* P{GawB}Ubr3^NP0739 / FM7c

VDRC

v106993

P{KK100920}VIE-260B

v22901

w¹¹¹⁸; P{GD12698}v22901

More stocks available...

Genomic Clones (21)

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

cDNA Clones (9)

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

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.

FBgn0260970

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260970

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Li et al., 2016, Huang et al., 2014)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG1531 CG1530

(FlyBase Genome Annotators, 2009)

Additional comments

Annotations CG1531 and CG1530 merged as CG42593 in release 5.18 of the genome annotation.

(FlyBase Genome Annotators, 2009)

Original annotation in this location (CG1531) utilized wrong ORF; current ORF (CG34339) supported by conservation across Drosophila species.

(FlyBase Genome Annotators, 2007)

Nomenclature History

Source for database identify of

Source for identity of: Ubr3 CG42593

(Huang et al., 2014)

Nomenclature comments

Etymology

Named 'Ubr3' after its mammalian homolog.

(Huang et al., 2014)

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG1530

(Ashwal-Fluss et al., 2014, Ditzel et al., 2008)

CG1531

(Jungreis et al., 2011, Keleman et al., 2009.8.5)

CG42593

(Li et al., 2016, Hosono et al., 2015, Kanoh et al., 2015, Huang et al., 2014, White-Grindley et al., 2014, Du et al., 2011, Ying et al., 2011, FlyBase Genome Annotators, 2009)

UBR3

(Ashton-Beaucage et al., 2016)

Ubr3

(Kashio and Miura, 2025, Markus et al., 2023, Al Hayek et al., 2021, Bordet et al., 2021, Piedade and Famulski, 2021, Graves et al., 2020, Ray et al., 2019, Bohère et al., 2018, Gene Disruption Project members, 2018-, Li et al., 2018, Bellen, 2017.1.20, Zanet et al., 2016, Kanoh et al., 2015, Zanet et al., 2015)

ubr3

(Zhang and Jiang, 2021, Li et al., 2016, Huang et al., 2014)

Name Synonyms

CG1530

CG1531

Ubr3 ubiquitin ligase

(Graves et al., 2020)

Secondary FlyBase IDs

FBgn0029985
FBgn0029983

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 38 )

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.

31713

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.

Q9W3M3

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

Q9W3M3

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

M9PDZ8

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.

Q9W3M3

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

31713/tissue=All

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

FBgn0260970

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

FBgn0260970

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

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

dme:Dmel_CG42593

MARRVEL_MODEL - MARRVEL (model organism gene)

31713

Linkouts

BioGRID - A database of protein and genetic interactions.

58185

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

FBgn0260970

DroID - A comprehensive database of gene and protein interactions.

FBgn0260970

DRSC - Results frm RNAi screens

FBgn0260970

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

CG42593_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0260970

Flygut - An atlas of the Drosophila adult midgut

FBgn0260970

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

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

31713

References (56)

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

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