FlyBase Gene Report: Dmel\Ubr1

General Information

Symbol

Dmel\Ubr1

Species

D. melanogaster

Name

Ubr1 ubiquitin ligase

Annotation Symbol

CG9086

Feature Type

protein_coding_gene

FlyBase ID

FBgn0030809

Gene Model Status

Current

Stock Availability

7 publicly available

Enzyme Name (EC)

Gene Summary

E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. (UniProt, Q9VX91)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

15C4-15C6

Sequence location

X:16,956,232..16,968,679 [-]

Recombination map

1-56

RefSeq locus

NC_004354 REGION:16956232..16968679

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 (8 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables ubiquitin protein ligase activity

inferred from biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR039164

(InterPro Project Members, 2004-)

enables ubiquitin-protein transferase activity

inferred from sequence or structural similarity with SGD:S000003416

(Gene Ontology Curators, 2002-)

enables zinc ion binding

inferred from electronic annotation with InterPro:IPR003126

(InterPro Project Members, 2004-)

inferred from sequence model

(Ying et al., 2011)

Biological Process (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

involved_in protein catabolic process

inferred from electronic annotation with InterPro:IPR003769

(InterPro Project Members, 2004-)

involved_in protein ubiquitination

inferred from sequence or structural similarity with SGD:S000003416

(Gene Ontology Curators, 2002-)

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 biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR039164

(InterPro Project Members, 2004-)

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 cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000486924

(GO Reference Genome Project, 2011-)

located_in cytoplasm

inferred from sequence or structural similarity with SGD:S000003416

(Gene Ontology Curators, 2002-)

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

Protein Family (UniProt)

Belongs to the E3 ubiquitin-protein ligase UBR1-like family. (Q9VX91)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

ubiquitin protein ligase activity

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.

Protein Function (UniProtKB)

(UniProt, Q9VX91)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Ubr1 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 Q9VX91)

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 5.51

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

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

Gene model reviewed during 5.40

Gene model reviewed during 5.56

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Ubr1-RA

FBtr0074415

NM_132956

6383

1824

Ubr1-RB

FBtr0308839

NM_001258794

6241

1824

Ubr1-RC

FBtr0346190

NM_001298427

7096

1824

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

Ubr1-PA

FBpp0074189

208.4

1824

6.40

FBpp0300996

208.4

1824

6.40

FBpp0312009

208.4

1824

6.40

Q9VX91

NP_001285356

AHN59826

Polypeptides with Identical Sequences

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

1824 aa isoforms: Ubr1-PA, Ubr1-PB, Ubr1-PC

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Domain

The RING-H2 zinc finger is an atypical RING finger with a His ligand in place of the fourth Cys of the classical motif.

(UniProt, Q9VX91)

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\Ubr1 using the Feature Mapper tool.

External Data

Crossreferences

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

CG9086_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).

-1.33

Transcript Expression

Additional Descriptive Data

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

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ubr1 in JBrowse

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

View exonic expression by developmental stage for Dmel\Ubr1

View exonic expression by tissue for Dmel\Ubr1

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

32687/tissue=All

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

FBgn0030809

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030809

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

FBgn0030809

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

CG9086

Flygut - An atlas of the Drosophila adult midgut

FBgn0030809

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 6 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Ubr1

Transgenic constructs containing regulatory region of Ubr1

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 10 )

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, with Scer\GAL4^Mef2.PR

Ubr1^GD14112

viable, with Scer\GAL4^pnr-MD237

Ubr1^GD14112

viable, with Scer\GAL4^tin.CΔ4

Ubr1^GD14112

Other Phenotypes

Allele

visible, with Scer\GAL4^pnr-MD237

Ubr1^GD14112

Phenotype manifest in

Allele

mesonotum, with Scer\GAL4^pnr-MD237

Ubr1^GD14112

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\UBR2

14 of 14

Yes

Hsap\UBR1

13 of 14

Yes

Hsap\UBR3

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\Ubr2

14 of 14

Yes

Rnor\Ubr1

11 of 14

Yes

Rnor\Ubr3

2 of 14

Mus musculus (laboratory mouse) (3)

Mmus\Ubr2

14 of 14

Yes

Mmus\Ubr1

13 of 14

Yes

Mmus\Ubr3

1 of 14

Xenopus tropicalis (Western clawed frog) (5)

Xtro\ubr2

11 of 13

Yes

Xtro\ubr1

6 of 13

Yes

Xtro\mtm1

5 of 13

Xtro\kdm2a

1 of 13

Xtro\ubr3

1 of 13

Danio rerio (Zebrafish) (3)

Drer\ubr2

14 of 14

Yes

Drer\ubr1

4 of 14

Yes

Drer\ubr3

2 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\ubr-1

14 of 14

Yes

Cele\F10G7.10

2 of 14

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP000171

11 of 12

Yes

Agam\AgaP_AGAP000384

2 of 12

Arabidopsis thaliana (thale-cress) (1)

Atha\PRT6

8 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\UBR1

10 of 13

Yes

Scer\UBR2

8 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\ubr1

11 of 12

Yes

Spom\ubr11

11 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Ubr1. 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)

Ubr3

4 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

metabolic dysfunction-associated steatotic liver disease

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 4 )

Allele

Disease

Evidence

References

Ubr1^JF01341

model of metabolic dysfunction-associated steatotic liver disease

CEA

(Zhao et al., 2023, Zhang et al., 2022)

Ubr1^KO

model of metabolic dysfunction-associated steatotic liver disease

CEA

(Zhang et al., 2022)

Ubr1^{CD.UAS.Tag:FLAG}

model of metabolic dysfunction-associated steatotic liver disease

CEA

(Zhang et al., 2022)

Ubr1^CD-KI

model of metabolic dysfunction-associated steatotic liver disease

CEA

(Zhang et al., 2022)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

UBR1; ubiquitin protein ligase E3 component n-recognin 1

model of Johanson-Blizzard syndrome

IEA

(FlyBase, 2019-)

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?

UBR2; ubiquitin protein ligase E3 component n-recognin 2

14 of 14

609134

UBR1; ubiquitin protein ligase E3 component n-recognin 1

13 of 14

605981

JOHANSON-BLIZZARD SYNDROME; JBS

Johanson-Blizzard syndrome

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

Ubr1

anti tag coimmunoprecipitation, anti tag western blot

(Zhao et al., 2023, Zhang et al., 2022)

Ubr1 - Diap1

anti tag coimmunoprecipitation, anti tag western blot

(Ditzel et al., 2008)

Ubr1 - Lsd-2

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

(Zhao et al., 2023, Zhang et al., 2022)

Ubr1 - Rab5

pull down, peptide massfingerprinting

(Gillingham et al., 2014, Gillingham et al., 2014)

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

Naa20A

suppressible

Ubr1

(François et al., 2023)

psidin

suppressible

Ubr1

(François et al., 2023)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

59018

DroID - A comprehensive database of gene and protein interactions.

FBgn0030809

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

32687

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

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

Antigen processing: Ubiquitination & Proteasome degradation

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-56

Cytogenetic map

15C4-15C6

Sequence location

X:16,956,232..16,968,679 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

15C4-15C6

; Limits computationally determined from genome sequence between P{EP}EP1337 and P{EP}baz^EP1446

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-56

(FlyBase, 2016)

1-57.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (7)

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

Bloomington

12537

w¹¹¹⁸ P{GT1}Ubr1^BG01122

31374

y¹ v¹; P{TRiP.JF01341}attP2

11640

9086R-2

9086R-3

v108902

v29775

w¹¹¹⁸ P{GD14112}v29775

Genomic Clones (13)

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

cDNA Clones (56)

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

LD31957

Other clones

FI05389

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.

FBgn0030809

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0030809

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Zhao et al., 2023, Zhang et al., 2022, 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

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Ubr1 CG9086

(Huang et al., 2014)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG9086

(Ibaraki et al., 2021, Van Bortle et al., 2015, Huang et al., 2014, Kwon et al., 2013, McPhee et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Du et al., 2011, Ying et al., 2011, Ellis and Carney, 2009, Keleman et al., 2009.8.5, Ditzel et al., 2008, Ni et al., 2008, Ranade et al., 2008, Morozova et al., 2006)

UBR1

(Eikenes et al., 2015)

UBR1/2

(Ashton-Beaucage et al., 2016)

Ubr1

(Ibaraki et al., 2021, Pang et al., 2021, Sheng and Du, 2020, Gene Disruption Project members, 2018-, Ketosugbo et al., 2017, Huang et al., 2014, Haddad et al., 2013, Speese et al., 2003)

dUBR1

(François et al., 2023)

ubr1

(Huang et al., 2014)

Name Synonyms

Ubr1 ubiquitin ligase

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 ( 46 )

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.

32687

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.

Q9VX91

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

Q9VX91

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

M9NFA7

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.

Q9VX91

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

32687/tissue=All

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

FBgn0030809

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

FBgn0030809

FlyMine - An integrated database for Drosophila genomics

FBgn0030809

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

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

dme:Dmel_CG9086

MARRVEL_MODEL - MARRVEL (model organism gene)

32687

Linkouts

BioGRID - A database of protein and genetic interactions.

59018

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

FBgn0030809

DroID - A comprehensive database of gene and protein interactions.

FBgn0030809

DRSC - Results frm RNAi screens

FBgn0030809

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

CG9086_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030809

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0030809

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

CG9086

Flygut - An atlas of the Drosophila adult midgut

FBgn0030809

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0030809

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

TC007434

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

32687

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

Antigen processing: Ubiquitination & Proteasome degradation

References (52)

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

-1.33

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