FlyBase Gene Report: Dmel\Rpn9

General Information

Symbol

Dmel\Rpn9

Species

D. melanogaster

Name

Regulatory particle non-ATPase 9

Annotation Symbol

CG10230

Feature Type

protein_coding_gene

FlyBase ID

FBgn0028691

Gene Model Status

Current

Stock Availability

9 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

p39A, Rpn4

Key Links

Genomic Location

Cytogenetic map

95B1-95B1

Sequence location

3R:23,731,375..23,733,462 [-]

Recombination map

3-80

RefSeq locus

NT_033777 REGION:23731375..23733462

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 (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables structural molecule activity

inferred from biological aspect of ancestor with PANTHER:PTN000056911

(GO Reference Genome Project, 2011-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in proteasome-mediated ubiquitin-dependent protein catabolic process

inferred by curator from GO:0005838

(Sumegi et al., 2003)

involved_in ubiquitin-dependent protein catabolic process

inferred from biological aspect of ancestor with PANTHER:PTN000056911

(GO Reference Genome Project, 2011-)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

part_of proteasome complex

inferred from direct assay

(Nickell et al., 2009)

part_of proteasome regulatory particle

inferred from direct assay

(Kiss et al., 2005, Sumegi et al., 2003, Holzl et al., 2000)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

is_active_in cytosol

inferred from biological aspect of ancestor with PANTHER:PTN000056911

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000056911

(GO Reference Genome Project, 2011-)

part_of proteasome regulatory particle, lid subcomplex

inferred from biological aspect of ancestor with PANTHER:PTN000056911

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with SGD:S000002835

(Holzl et al., 2000)

part_of proteasome regulatory particle

inferred from sequence or structural similarity with UniProtKB:Q9UNM6

(Holzl et al., 2000)

Gene Group (FlyBase)

PROTEASOME REGULATORY PARTICLE NON-ATPASES

26S PROTEASOME - TESTIS-SPECIFIC VARIANT

26S PROTEASOME

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

PROTEASOME REGULATORY PARTICLE NON-ATPASES -: The 26S proteasome degrades polyubiquitinated proteins in the cytoplasm and nucleus. It is formed from a cylindrical catalytic core 20S proteasome capped at each end by a regulatory 19S particle. The 19S regulatory particle recognizes, unfolds, and translocates ubiquitinated proteins into the catalytic core particle in an ATP-dependent manner. 'Rpn' subunits are non-ATPase subunits located in the base and lid subcomplexes of the regulatory particle (Adapted from FBrf0215459 and PMID:28583440.)
26S PROTEASOME - TESTIS-SPECIFIC VARIANT -: The 26S proteasome degrades polyubiquitinated proteins in the cytoplasm and nucleus. It is formed from a cylindrical catalytic core 20S proteasome capped at each end by a regulatory 19S particle. The 19S regulatory particle recognizes, unfolds, and translocates ubiquitinated proteins into the catalytic core particle in an ATP-dependent manner. (Adapted from FBrf0215459).
26S PROTEASOME -: The 26S proteasome degrades polyubiquitinated proteins in the cytoplasm and nucleus. It is formed from a cylindrical catalytic core 20S proteasome capped at each end by a regulatory 19S particle. The 19S regulatory particle recognizes, unfolds, and translocates ubiquitinated proteins into the catalytic core particle in an ATP-dependent manner. (Adapted from FBrf0215459).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Rpn9 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 Q7KMP8)

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 5.47

Gene model reviewed during 6.02

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Rpn9-RA

FBtr0084470

NM_142920

1340

382

Rpn9-RB

FBtr0084469

NM_170088

1578

382

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

Rpn9-PA

FBpp0083861

43.8

382

4.92

FBpp0083860

43.8

382

4.92

Q7KMP8

NP_732899

AAF56174

Polypeptides with Identical Sequences

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

382 aa isoforms: Rpn9-PA, Rpn9-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q7KMP8

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rpn9 using the Feature Mapper tool.

External Data

Crossreferences

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

Rpn9_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).

1.73

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

anterior endoderm anlage

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

anterior endoderm

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 13 -- 16

gonad

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

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)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

organism

(Lipinszki et al., 2009)

Additional Descriptive Data

Expression of Rpn9 protein is at a fairly constant level throughout development; levels are lower during the second twelve hours of embryogenesis and first and second larval instars than at other stages.

(Lipinszki et al., 2009)

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of proteasome complex

inferred from direct assay

(Nickell et al., 2009)

part_of proteasome regulatory particle

inferred from direct assay

(Kiss et al., 2005, Sumegi et al., 2003, Holzl et al., 2000)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Rpn9 in JBrowse

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

View exonic expression by developmental stage for Dmel\Rpn9

View exonic expression by tissue for Dmel\Rpn9

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

FBgn0028691

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

42802/tissue=All

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

FBgn0028691

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0028691

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

FBgn0028691

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

CG10230

Flygut - An atlas of the Drosophila adult midgut

FBgn0028691

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Rpn9

Stages(s) 1-3
Stages(s) 4-6
Stages(s) 7-8
Stages(s) 9-10
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 4 )

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 Rpn9

Transgenic constructs containing regulatory region of Rpn9

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3R)Exel9013

(Ryder, 2004.4.26)

Df(3R)mbc-R1

(Szeged Stock Center, 1998-)

Inferred from location ( 6 )

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 | recessive

Rpn9^S071806b

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

Rpn9^GD6909

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

Rpn9^GD6909

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

Rpn9^GD6909

partially lethal - majority die | recessive

Rpn9^S071806b

viable, with Scer\GAL4^tin.CΔ4

Rpn9^GD6909

Other Phenotypes

Allele

abnormal body color | adult stage, with Scer\GAL4^pnr-MD237

Rpn9^HMS05753

abnormal neuroanatomy, with Scer\GAL4^GMR.PU

Rpn9^NIG.10230R

abnormal size | third instar larval stage, with Scer\GAL4^Cg.PA

Rpn9^HMS01007

increased mortality during development, with Scer\GAL4^pnr-MD237

Rpn9^HMS05753

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

Rpn9^GD6909

Phenotype manifest in

Allele

adult external thorax, with Scer\GAL4^pnr-MD237

Rpn9^HMS05753

embryonic/larval fat body | third instar larval stage, with Scer\GAL4^Cg.PA

Rpn9^HMS01007

mitochondrion | third instar larval stage, with Scer\GAL4^Cg.PA

Rpn9^HMS01007

rhabdomere of eye photoreceptor cell, with Scer\GAL4^GMR.PU

Rpn9^NIG.10230R

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) (5)

Hsap\PSMD13

14 of 14

Yes

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) (5)

Rnor\Psmd13

14 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (5)

Mmus\Psmd13

13 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (5)

Xtro\psmd13

8 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (4)

Drer\psmd13

14 of 14

Yes

Drer\cops2

1 of 14

Drer\cops7a

1 of 14

Drer\eif3m

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\rpn-9

14 of 14

Yes

Cele\cif-1

1 of 14

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP001651

12 of 12

Yes

Agam\AgaP_AGAP012398

1 of 12

Agam\EIF3M_ANOGA

1 of 12

Arabidopsis thaliana (thale-cress) (5)

Atha\AT4G19006

13 of 13

Yes

Atha\AT5G45620

13 of 13

Yes

Atha\AT3G02200

1 of 13

Atha\AT5G15610

1 of 13

Atha\FUS5

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\RPN9

13 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\rpn9

12 of 12

Yes

Spom\csn71

1 of 12

Spom\SPAC1751.03

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Rpn9. 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) (3)

alien

1 of 13

CSN7

1 of 13

eIF3m

1 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 ( 2 )

Allele

Disease

Interaction

References

Rpn9^HMS01007

exacerbates cancer

modeled by Rbf^HMS03004

(Parkhitko et al., 2021)

Rpn9^GD6909

exacerbates Machado-Joseph disease

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

(Voßfeldt et al., 2012)

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?

PSMD13; proteasome 26S subunit, non-ATPase 13

14 of 14

603481

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

RNA-protein

Physical Interaction

Assay

References

Rpn9 - orb2

pull down, western blot

(Mastushita-Sakai et al., 2010)

protein-protein

Physical Interaction

Assay

References

Rpn9 - Akt

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Rpn9 - PSMG1

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosα3

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosα4

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosα5

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosα6

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosα7

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosβ1

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosβ2

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosβ3

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosβ4

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosβ5

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosβ6

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Prosβ7

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rad23

affinity chromatography technology, molecular sieving, western blot

(Lipinszki et al., 2012)

Rpn9 - Rpn1

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn10

molecular sieving, western blot

(Lipinszki et al., 2012, Lipinszki et al., 2009)

Rpn9 - Rpn11

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn12

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn13

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn2

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn3

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn5

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn6

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn7

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpn8

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpt1

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpt2

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpt3

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpt4

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpt5

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Rpt6

experimental knowledge based

(Guruharsha et al., 2011)

Rpn9 - Ubqn

affinity chromatography technology, molecular sieving, western blot

(Lipinszki et al., 2012)

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

Rpn9

suppressible

Ddc

(Zhang et al., 2021)

Rpn9

suppressible

ple

(Zhang et al., 2021)

Rpn9

suppressible

sima

(Zhang et al., 2021)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

67740

DroID - A comprehensive database of gene and protein interactions.

FBgn0028691

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

42802

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 ornithine decarboxylase (ODC)

External Data

Linkouts

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

Proteasome

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

3-80

Cytogenetic map

95B1-95B1

Sequence location

3R:23,731,375..23,733,462 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

95B1-95B1

Limits computationally determined from genome sequence between P{PZ}l(3)06906⁰⁶⁹⁰⁶ and P{PZ}l(3)04684⁰⁴⁶⁸⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-80

(FlyBase, 2016)

3-81.9

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (9)

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

Bloomington

34034

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01007}attP2

67915

y¹ sc^* v¹ sev²¹; P{TRiP.HMS05753}attP40

15642

y¹ w^67c23; P{EPgy2}Rpn9^EY03352/TM3, Sb¹ Ser¹

FlyORF

F001557

M{UAS-Rpn9.ORF}ZH-86Fb

F000756

M{UAS-Rpn9.ORF.3xHA}ZH-86Fb

NIG-Fly

10230R-1

P{NIG.10230R}1

HMS01007

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01007}attP2/TM3, Sb¹

VDRC

v103733

P{KK102254}VIE-260B

v31206

w¹¹¹⁸; P{GD6909}v31206

Genomic Clones (22)

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

cDNA Clones (79)

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

DPiM_LD17530

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.

FBgn0028691

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0028691

Antibody Information

Laboratory Generated Antibodies

monoclonal

(Lipinszki et al., 2009)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Source for merge of: Rpn9 l(3)S071806b

(Faria et al., 2003)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

The nomenclature of genes encoding subunits of the 26S proteasome of D. melanogaster have been standardized according to FBrf0215459. These symbols/names largely follow those used already in FlyBase, and largely mirror fly community usage. HOWEVER, note that at least one other nomenclature system exists that is followed by the HUGO Gene Nomenclature Committee (HGNC), for example, with the unfortunate result that several D. melanogaster genes have shared synonyms.

(FlyBase, 2009-)

Etymology

The gene is named "Nobody" after the mutant phenotype; mutant third instar larval brain neuroblasts show no apparent mid-body formation.

(Faria et al., 2003)

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

0718/06

(Deak et al., 1997)

718/06

(Faria et al., 2003)

CG10230

(Kolkhof et al., 2017, Hosono et al., 2015, Rosa-Ferreira et al., 2015, Wang et al., 2014, Schertel et al., 2013, Voßfeldt et al., 2012, Yano et al., 2012, Cammarato et al., 2011, Ni et al., 2010.12.1, Belote and Zhong, 2009, Keleman et al., 2009.8.5, Perkins et al., 2009, Chen et al., 2008, Barbash and Lorigan, 2007, Gandhi et al., 2007, Li et al., 2007, Lundgren et al., 2005, Ma et al., 2002)

CT28749

(Ceriani et al., 2002)

PSMD13

(Gieger et al., 2011)

Rpn4

(Nickell et al., 2009, Barbash and Lorigan, 2007)

Rpn94

(Hölzl, 1999.4.23)

S11

(Lundgren et al., 2005)

l(3)S071806

l(3)S071806b

p39A

(Lipinszki et al., 2013, Lipinszki et al., 2012, Lipinszki et al., 2011, Lipinszki et al., 2009, Szabó et al., 2007, Kiss et al., 2005, Lundgren et al., 2005, Faria et al., 2003, Sumegi et al., 2003, Kurucz et al., 2002, Ma et al., 2002, Holzl et al., 2000)

rpn9

(Gieger et al., 2011, Tonoki et al., 2009, Ceriani et al., 2002, Jasper et al., 2002)

Name Synonyms

Nobody

(Faria et al., 2003)

Regulatory particle non-ATPase 9

Rpn9

(Cammarato et al., 2011)

p39A

(Fredriksson et al., 2012)

Secondary FlyBase IDs

FBgn0028103

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 94 )

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.

42802

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.

Q7KMP8

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

Q7KMP8

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.

Q7KMP8

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0028691

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

42802/tissue=All

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

FBgn0028691

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

FBgn0028691

FlyMine - An integrated database for Drosophila genomics

FBgn0028691

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

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

dme:Dmel_CG10230

MARRVEL_MODEL - MARRVEL (model organism gene)

42802

Linkouts

BioGRID - A database of protein and genetic interactions.

67740

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

FBgn0028691

DroID - A comprehensive database of gene and protein interactions.

FBgn0028691

DRSC - Results frm RNAi screens

FBgn0028691

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

Rpn9_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0028691

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0028691

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

CG10230

Flygut - An atlas of the Drosophila adult midgut

FBgn0028691

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

TC015728

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

Proteasome

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

42802

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 ornithine decarboxylase (ODC)

References (102)

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

1.73

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