FlyBase Gene Report: Dmel\scny

Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal) (3.4.19.12)

Predictions / Assertions

Summaries

Gene Group (FlyBase)

UBIQUITIN SPECIFIC PROTEASES (DEUBIQUITINASES) -: The Ubiquitin Specific Proteases (USP) is the largest sub-family of deubiquitinases. They are cysteine proteases and catalyze the removal of ubiquitin from ubiquitin chains and ubiquitinated proteins. (Adapted from PMID:19626045).

Pathway (FlyBase)

Negative Regulators of Imd Signaling Pathway -: Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)

Protein Function (UniProtKB)

Hydrolase that deubiquitinates polyubiquitinated target proteins including imd (PubMed:19837371, PubMed:19039105). Required for preventing the constitutive activation of the imd/NF-kappa-B (Imd) signaling cascade under unchalleneged conditions (PubMed:19837371, PubMed:25027767). Deubiquitinates imd linked 'Lys-63' chains which leads its proteasomal degradation and consequently down-regulation of the Imd signaling cascade (PubMed:19837371). Removal of the activating 'Lys-63'-linked chains is likely to enable their replacement with 'Lys-48'-linked chains which act as 'tags' the for proteosomal degradation of imd (PubMed:19837371). Required for maintaining multiple types of adult stem cells, including male and female germline, epithelial follicle cell and intestinal stem cells (PubMed:19039105). May function as a transcriptional repressor by continually deubiquiting histone H2B at the promoters of genes critical for cellular differentiation, thereby preventing histone H3 'Lys-4' trimethylation (H3K4me3) (PubMed:19039105). Controls selective autophagy activation by ubiquitinated proteins (PubMed:22622177).

(UniProt, Q9VRP5)

Summary (Interactive Fly)

protein deubiquitinase required in germline, epithelial, and intestinal stem cells - acts to repress differentiation genes - deubiquitylates histone H2B and functions in gene silencing - participates in a conserved pathway of chromatin regulation linking H2B ubiquitylation with H3K4me3 methylation

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\scny or the JBrowse view of Dmel\scny for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Comments on Gene Model

Gene model reviewed during 5.55

Gene model reviewed during 5.45

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

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

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene

gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

scny-RB

FBtr0077101

NM_168135

3512

968

scny-RC

FBtr0077103

NM_168134

3637

948

scny-RD

FBtr0077100

NM_168132

4417

1038

scny-RG

FBtr0307975

NM_001259710

4470

976

scny-RH

FBtr0307976

NM_001259711

4303

976

scny-RI

FBtr0330127

NM_168133

3644

886

scny-RJ

FBtr0330128

NM_139729

4538

906

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

RefSeq ID

GenBank

scny-PB

FBpp0076807

107.3

968

9.57

NP_729095

AAN12111

scny-PC

FBpp0076809

105.0

948

9.70

NP_729094

AAN12109

scny-PD

FBpp0076806

114.1

1038

9.53

NP_729092

AAN12107

scny-PG

FBpp0300344

106.0

976

8.12

NP_001246639

AFH04310

scny-PH

FBpp0300345

106.0

976

8.12

NP_001246640

AFH04311

scny-PI

FBpp0303160

96.8

886

8.41

NP_729093

AAN12108

scny-PJ

FBpp0303161

99.1

906

8.19

NP_647986

AAN12110

Polypeptides with Identical Sequences

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

976 aa isoforms: scny-PG, scny-PH

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Interacts with atms/PAF1, but not with CycT (PubMed:19039105). Interacts (via C-terminus) with imd (via N-terminus) (PubMed:19837371).

(UniProt, Q9VRP5)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VRP5

Mapped Features

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

External Data

Crossreferences

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

Linkouts

Gene Ontology (22 terms)

Molecular Function (5 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

Lys63-specific deubiquitinase activity

inferred from direct assay

(Thevenon et al., 2009)

protein binding

inferred from physical interaction with UniProtKB:Q9VN55

(assigned by UniProt )

(Buszczak et al., 2009)

thiol-dependent ubiquitin-specific protease activity

inferred from direct assay

(Buszczak et al., 2009)

thiol-dependent ubiquitinyl hydrolase activity

inferred from mutant phenotype

(assigned by UniProt )

(Buszczak et al., 2009)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

cysteine-type endopeptidase activity

inferred from biological aspect of ancestor with PANTHER:PTN002541993

(assigned by GO_Central )

(Gaudet et al., 2011)

thiol-dependent ubiquitin-specific protease activity

inferred from biological aspect of ancestor with PANTHER:PTN002541993

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (14 terms)

Terms Based on Experimental Evidence (13 terms)

CV Term

Evidence

References

germ-line stem cell population maintenance

inferred from mutant phenotype

(assigned by UniProt )

(Buszczak et al., 2009)

histone H2B conserved C-terminal lysine deubiquitination

inferred from direct assay

(Buszczak et al., 2009)

inferred from mutant phenotype

(Buszczak et al., 2009)

negative regulation of antimicrobial peptide production

inferred from mutant phenotype

(Engel et al., 2014)

negative regulation of innate immune response

inferred from mutant phenotype

(Engel et al., 2014)

negative regulation of macroautophagy

inferred from mutant phenotype

(assigned by UniProt )

(Taillebourg et al., 2012)

negative regulation of peptidoglycan recognition protein signaling pathway

inferred from mutant phenotype

(Engel et al., 2014, Thevenon et al., 2009)

positive regulation of chromatin silencing

inferred from mutant phenotype

(Buszczak et al., 2009)

positive regulation of proteasomal protein catabolic process

inferred from mutant phenotype

(Thevenon et al., 2009)

positive regulation of stem cell population maintenance

inferred from mutant phenotype

(Buszczak et al., 2009)

protein deubiquitination

inferred from mutant phenotype

(assigned by UniProt )

(Buszczak et al., 2009)

protein K63-linked deubiquitination

inferred from direct assay

(Thevenon et al., 2009)

regulation of apoptotic process

inferred from mutant phenotype

(Ribaya et al., 2009)

somatic stem cell population maintenance

inferred from mutant phenotype

(assigned by UniProt )

(Buszczak et al., 2009)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

protein deubiquitination

inferred from biological aspect of ancestor with PANTHER:PTN002541993

(assigned by GO_Central )

(Gaudet et al., 2011)

ubiquitin-dependent protein catabolic process

inferred from electronic annotation with InterPro:IPR018200

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

nucleolus

inferred from direct assay

(Buszczak et al., 2009)

inferred from high throughput direct assay

(Lye et al., 2014)

nucleoplasm

inferred from high throughput direct assay

(Lye et al., 2014)

nucleus

inferred from direct assay

(Buszczak et al., 2009)

Terms Based on Predictions or Assertions (0 terms)

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

expression microarray

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult fat body

Comment: cyclical, peak ZT21-0

(Xu et al., 2011)

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

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | ubiquitous

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

pupal stage

salivary gland

(Lee et al., 2003)

Additional Descriptive Data

Expressed cyclically in the adult fat body.

(Xu et al., 2011)

The expression of this gene along with several others is induced in salivary glands in pupae at the time of head eversion. This stage is characterized by an increase in the ecdysone titer as well as large amounts of cell death in this tissue.

(Lee et al., 2003)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

female germline stem cell

(Buszczak et al., 2009)

adult stage | male

male germline stem cell

(Buszczak et al., 2009)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

nucleolus

inferred from direct assay

(Buszczak et al., 2009)

inferred from high throughput direct assay

(Lye et al., 2014)

nucleoplasm

inferred from high throughput direct assay

(Lye et al., 2014)

nucleus

inferred from direct assay

(Buszczak et al., 2009)

Expression Deduced from Reporters

Reporter: P{PTT-GA}scny^CA06690

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

female germline stem cell

(Buszczak et al., 2009)

adult stage | male

male germline stem cell

(Buszczak et al., 2009)

Reporter: PBac{681.P.FSVS-1}scny^CPTI001323

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

ellipsoid body

(Knowles-Barley, 2011.8.24)

fan-shaped body

(Knowles-Barley, 2011.8.24)

adult brain cell body rind

(Knowles-Barley, 2011.8.24)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\scny in GBrowse 2

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

View exonic expression by developmental stage for Dmel\scny

View exonic expression by tissue for Dmel\scny

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

FBgn0260936

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

FBgn0260936

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

CG5505

Flygut - An atlas of the Drosophila adult midgut

FBgn0260936

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 17 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 13 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of scny

Transgenic constructs containing regulatory region of scny

Deletions and Duplications ( 3 )

Disrupted in

Df(3L)BSC884

(Cook and Cook, 2010.5.7)

Df(3L)Exel6107

(Ribaya et al., 2009, Ryder, 2004.4.26)

Df(3L)ZN47

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

Phenotypes

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

Lethality

Allele

cell lethal | recessive | somatic clone

scny^GS13655

lethal, with Scer\GAL4^sqh.PW

scny^KK102113

lethal (with Df(3L)ZN47)

lethal (with scny⁰²³³¹)

scny^e00340

lethal (with scny^e00340)

scny⁰²³³¹

lethal | first instar larval stage, with Scer\GAL4^GMR.PF

scny^C.UAS

lethal | heat sensitive, with Scer\GAL4^GMR.PF

scny^GS13668

lethal | recessive

lethal | second instar larval stage, with Scer\GAL4^GMR.PF

scny^C.UAS

lethal - all die before end of embryonic stage, with Scer\GAL4^Act.PU

scny^GS13668

lethal - all die before end of first instar larval stage | recessive

scny^Df

lethal - all die before end of larval stage

scny^Δ43

lethal - all die before end of larval stage, with Scer\GAL4^da.G32

scny^dsRNA.UAS

lethal - all die before end of larval stage, with Scer\GAL4^sqh.PW

scny^KK102113

lethal - all die before end of larval stage | recessive

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

scny^GD2319

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

scny^GD2319

partially lethal - majority die (with scny⁰²³³¹)

scny^f01742

partially lethal - majority die (with scny^f01742)

scny⁰²³³¹

partially lethal - majority die | recessive

scny^f01742

viable

viable, with Scer\GAL4^pnr-MD237

scny^GD2319

viable, with Scer\GAL4^tin.CΔ4

scny^GD2319

viable (with scny^d06513)

viable (with scny^e00340)

viable (with scny^f01742)

Sterility

Allele

female sterile

scny^roo

female sterile (with Df(3L)ZN47)

scny^d06513

female sterile (with scny⁰²³³¹)

female sterile (with scny^e00340)

scny^roo

female sterile (with scny^EY08858)

scny^roo

female sterile (with scny^f01742)

scny⁰²³³¹

female sterile (with scny^GS13655)

scny^roo

female sterile (with scny^roo)

female sterile | recessive

scny^d06513

fertile

male sterile

scny^roo

male sterile (with Df(3L)ZN47)

scny^d06513

male sterile (with scny⁰²³³¹)

scny^roo

male sterile (with scny^e00340)

scny^roo

male sterile (with scny^EY08858)

scny^roo

male sterile (with scny^GS13655)

scny^roo

male sterile (with scny^roo)

male sterile | recessive

scny^d06513

semi-fertile (with scny⁰²³³¹)

scny^d06513

semi-fertile (with scny^d06513)

scny⁰²³³¹

sterile

Other Phenotypes

Allele

immune response defective

scny^UY1507

immune response defective, with Scer\GAL4^hs.PB

scny^UAS.RB

locomotor behavior defective | adult stage, with Scer\GAL4^elav.PU

scny^KK102113

short lived, with Scer\GAL4^elav.PU

scny^KK102113

small body | adult stage, with Scer\GAL4^GMR.PF

scny^GS13668

some die during embryonic stage, with Scer\GAL4^Act.PU

scny^GS13668

some die during first instar larval stage | recessive

scny^Df

some die during larval stage

scny^Δ43

some die during larval stage, with Scer\GAL4^da.G32

scny^dsRNA.UAS

some die during larval stage, with Scer\GAL4^sqh.PW

scny^KK102113

some die during larval stage | recessive

visible, with Scer\GAL4^dpp.PU

scny^KK102113

visible, with Scer\GAL4^GMR.PF

visible, with Scer\GAL4^pnr-MD237

scny^GD2319

visible | heat sensitive, with Scer\GAL4^GMR.PF

scny^GS13668

Phenotype manifest in

Allele

eye, with Scer\GAL4^GMR.PF

eye | heat sensitive, with Scer\GAL4^GMR.PF

scny^GS13668

eye | somatic clone

scny^GS13655

female germline cell

scny^roo

female germline stem cell (with scny⁰²³³¹)

scny^d06513

female germline stem cell (with scny^d06513)

scny⁰²³³¹

female germline stem cell | somatic clone

follicle stem cell | somatic clone

gonad (with scny⁰²³³¹)

scny^roo

gonad (with scny^roo)

scny⁰²³³¹

intestinal stem cell (with scny⁰²³³¹)

scny^f01742

intestinal stem cell (with scny^f01742)

scny⁰²³³¹

intestinal stem cell & adult midgut

scny^f01742

male germline cell

scny^roo

male germline stem cell

scny^d06513

ommatidium, with Scer\GAL4^GMR.PF

scny^D.UAS

ommatidium | somatic clone

scny^GS13655

ovary

scny^roo

scutellar bristle, with Scer\GAL4^dpp.PU

scny^KK102113

testis

scny^roo

trichogen cell, with Scer\GAL4^pnr-MD237

scny^GD2319

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (30)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\USP36

11 of 15

Yes

Hsap\USP42

10 of 15

Yes

Hsap\USP17L2

7 of 15

Yes

Hsap\USP17L3

6 of 15

Yes

Hsap\USP17L5

6 of 15

Yes

Hsap\USP17L7

6 of 15

Yes

Hsap\USP17L12

6 of 15

Yes

Hsap\USP17L1

5 of 15

Yes

Hsap\USP17L4

5 of 15

Yes

Hsap\USP17L8

5 of 15

Yes

Hsap\USP17L10

5 of 15

Yes

Hsap\USP17L11

5 of 15

Yes

Hsap\USP17L15

5 of 15

Yes

Hsap\USP17L17

5 of 15

Yes

Hsap\USP17L18

5 of 15

Yes

Hsap\USP17L19

5 of 15

Yes

Hsap\USP17L20

5 of 15

Yes

Hsap\USP17L21

5 of 15

Yes

Hsap\USP17L22

5 of 15

Yes

Hsap\USP17L30

5 of 15

Yes

Hsap\USP17L13

4 of 15

Yes

Hsap\USP17L25

4 of 15

Yes

Hsap\USP17L24

3 of 15

Yes

Hsap\USP17L26

3 of 15

Yes

Hsap\USP17L27

3 of 15

Yes

Hsap\USP17L28

3 of 15

Yes

Hsap\USP17L29

3 of 15

Yes

Hsap\USP3

1 of 15

Hsap\USP44

1 of 15

Yes

Hsap\USP49

1 of 15

Yes

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (9)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Usp36

10 of 15

Yes

Mmus\Usp42

10 of 15

Yes

Mmus\Usp17ld

7 of 15

Yes

Mmus\Usp17la

6 of 15

Yes

Mmus\Usp17lb

6 of 15

Yes

Mmus\Usp17lc

6 of 15

Yes

Mmus\Usp17le

6 of 15

Yes

Mmus\Usp3

1 of 15

Mmus\Usp49

1 of 15

Rattus norvegicus (Norway rat) (5)

Rnor\Usp42

10 of 13

Yes

Rnor\Usp36

9 of 13

Yes

Rnor\LOC689730

4 of 13

Yes

Rnor\LOC100910107

4 of 13

Yes

Rnor\Usp49

1 of 13

Yes

Xenopus tropicalis (Western clawed frog) (6)

Xtro\usp36

5 of 12

Yes

Xtro\usp42

4 of 12

Yes

Xtro\LOC101735032

1 of 12

Yes

Xtro\usp3

1 of 12

Yes

Xtro\usp44

1 of 12

Yes

Xtro\usp49

1 of 12

Yes

Danio rerio (Zebrafish) (4)

Drer\usp36

11 of 15

Yes

Drer\usp42

6 of 15

Yes

Drer\usp44

1 of 15

Yes

Drer\usp49

1 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (6)

Cele\T22F3.2

3 of 15

Yes

Cele\usp-33

3 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

Yes

Arabidopsis thaliana (thale-cress) (11)

Atha\UBP23

5 of 9

Yes

Atha\UBP25

5 of 9

Yes

Atha\UBP15

4 of 9

Yes

Atha\UBP16

4 of 9

Yes

Atha\UBP17

4 of 9

Yes

Atha\UBP18

4 of 9

Yes

Atha\UBP19

4 of 9

Yes

Atha\UBP21

2 of 9

Yes

Atha\AT1G65150

1 of 9

Yes

Atha\AT3G22085

1 of 9

Yes

Atha\UBP20

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\UBP10

4 of 15

Yes

Scer\UBP1

2 of 15

Yes

Scer\UBP16

2 of 15

Scer\UBP3

1 of 15

Scer\UBP8

1 of 15

Schizosaccharomyces pombe (Fission yeast) (5)

Spom\ubp16

7 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091902J6 )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\scny

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA18934

Drosophila persimilis

Dper\GL16307

Drosophila willistoni

Dwil\GK17299

Drosophila virilis

Dvir\GJ13192

Drosophila mojavensis

Dmoj\GI13361

Drosophila grimshawi

Dgri\GH16215

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504G2 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17009216

Glossina morsitans

Tsetse fly

Gmor\GMOY007731

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_01167

Mayetiola destructor

Hessian fly

Mdes\Mdes001461

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL002698

Anopheles darlingi

American malaria mosquito

Adar\ADAC005703

Anopheles gambiae

Malaria mosquito

Agam\AGAP007521

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ007009

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W049R )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA011805

Danaus plexippus

Monarch butterfly

Dple\DPOGS213523-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL013680

Apis florea

Little honeybee

Aflo\2581680036

Apis mellifera

Western honey bee

Amel\GB47732

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP14667

Bombus terrestris

Buff-tailed bumblebee

Bter\15209758

Linepithema humile

Argentine ant

Lhum\LH15238

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:002fbf

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG007690

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_11110

Tribolium castaneum

Red flour beetle

Tcas\TC002978

Pediculus humanus

Human body louse

Phum\PHUM042200

Rhodnius prolixus

Kissing bug

Rpro\RPRC001267

Cimex lectularius

Bed bug

Clec\CLEC004383

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI009445

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI007349

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_15037

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_09993

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_06519

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_15038

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X046B )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR003566

Ixodes scapularis

Black-legged tick

Isca\ISCW018973

Stegodyphus mimosarum

African social velvet spider

Smim\KFM56762.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur09g02360

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_16988

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_39928

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )

No non-Arthropod Metazoa orthologies identified

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (11)

Gene Symbol

Score

Source

Alignment

1 of 10

faf

1 of 10

not

1 of 10

puf

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

scny^HMS02044

model of congenital heart disease

CEA

(Zhu et al., 2017)

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 v7.1 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?

USP36; ubiquitin specific peptidase 36

11 of 15

612543

USP42; ubiquitin specific peptidase 42

10 of 15

USP17L2; ubiquitin specific peptidase 17 like family member 2

7 of 15

610186

USP17L3; ubiquitin specific peptidase 17 like family member 3

6 of 15

USP17L5; ubiquitin specific peptidase 17 like family member 5

6 of 15

USP17L7; ubiquitin specific peptidase 17 like family member 7

6 of 15

USP17L12; ubiquitin specific peptidase 17 like family member 12

6 of 15

USP17L1; ubiquitin specific peptidase 17 like family member 1

5 of 15

USP17L4; ubiquitin specific peptidase 17 like family member 4

5 of 15

USP17L8; ubiquitin specific peptidase 17 like family member 8

5 of 15

USP17L10; ubiquitin specific peptidase 17 like family member 10

5 of 15

USP17L11; ubiquitin specific peptidase 17 like family member 11

5 of 15

USP17L15; ubiquitin specific peptidase 17 like family member 15

5 of 15

USP17L17; ubiquitin specific peptidase 17 like family member 17

5 of 15

USP17L18; ubiquitin specific peptidase 17 like family member 18

5 of 15

USP17L19; ubiquitin specific peptidase 17 like family member 19

5 of 15

USP17L20; ubiquitin specific peptidase 17 like family member 20

5 of 15

USP17L21; ubiquitin specific peptidase 17 like family member 21

5 of 15

USP17L22; ubiquitin specific peptidase 17 like family member 22

5 of 15

USP17L30; ubiquitin specific peptidase 17 like family member 30

5 of 15

USP17L13; ubiquitin specific peptidase 17 like family member 13

4 of 15

USP17L25; ubiquitin specific peptidase 17 like family member 25

4 of 15

USP17L24; ubiquitin specific peptidase 17 like family member 24

3 of 15

USP17L26; ubiquitin specific peptidase 17 like family member 26

3 of 15

USP17L27; ubiquitin specific peptidase 17 like family member 27

3 of 15

USP17L28; ubiquitin specific peptidase 17 like family member 28

3 of 15

USP17L29; ubiquitin specific peptidase 17 like family member 29

3 of 15

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

esyN Network Diagram

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

RNA-protein

Physical Interaction

Assay

References

scny - aub

iclip, partial RNA sequence identification

(Ma et al., 2017)

protein-protein

Physical Interaction

Assay

References

scny - Dsor1

anti tag coimmunoprecipitation, peptide massfingerprinting

(Friedman et al., 2011)

scny - His2B

anti bait coimmunoprecipitation, western blot

(Buszczak et al., 2009)

scny - atms

anti tag coimmunoprecipitation, anti tag western blot

(Buszczak et al., 2009)

scny - imd

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

(Thevenon et al., 2009)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

scny

enhanceable

Diap1

(Ribaya et al., 2009)

scny

suppressible

Diap1

(Ribaya et al., 2009)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

(Sinenko, 2017)

suppressible

(Ribaya et al., 2009)

rpr

suppressible

scny

(Ribaya et al., 2009)

External Data

Subunit Structure (UniProtKB)

Interacts with atms/PAF1, but not with CycT (PubMed:19039105). Interacts (via C-terminus) with imd (via N-terminus) (PubMed:19837371).

(UniProt, Q9VRP5 )

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0260936

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

38648

MIST (genetic) - An integrated Molecular Interaction Database

scny

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

scny

Pathways

Signaling Pathways (FlyBase)

Negative Regulators of Imd Signaling Pathway -: Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)

Metabolic Pathways

External Data

Linkouts

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

Ub-specific processing proteases

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-15

Cytogenetic map

64E8-64E7

Sequence location

3L:5,769,002..5,776,271 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

64E8-64E7

Left limit from in situ hybridisation (FBrf0067338) Right limit from in situ hybridisation (FBrf0067338); Limits computationally determined from genome sequence between P{PZ}sinu⁰⁶⁵²⁴ and P{PZ}Bre1⁰¹⁶⁴⁰

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

64E8-64E12

(determined by in situ hybridisation)

(Spradling et al., 1999)

64E8-64E12

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

3-15

(FlyBase, 2016)

3-13.8

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (12)

Bloomington

27558

y¹ v¹; P{TRiP.JF02712}attP2

40865

y¹ v¹; P{TRiP.HMS02032}attP40

21775

y¹ w^67c23; P{wHy}scny^DG39208

33406

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00285}attP2

40877

y¹ sc^* v¹ sev²¹; P{TRiP.HMS02044}attP2

11565

P{PZ}scny⁰²³³¹ ry⁵⁰⁶/TM3, ry^RK Sb¹ Ser¹

Kyoto

115520

w¹¹¹⁸; PBac{681.P.FSVS-1}scny^CPTI001752

115150

w¹¹¹⁸; PBac{681.P.FSVS-1}scny^CPTI001323

204856

y¹ w^67c23; P{GSV6}scny^GS13655/TM3, Sb¹ Ser¹

204865

y¹ w^67c23; P{GSV6}scny^GS13668/TM3, Sb¹ Ser¹

VDRC

v105989

P{KK102113}VIE-260B

v11152

w¹¹¹⁸; P{GD2319}v11152

Genomic Clones (21)

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

cDNA Clones (125)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequences

BDGP DGC clones

Other clones

FI06147

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.

FBgn0260936

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260936

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

38648

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Buszczak et al., 2009)

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: mule CG5505

(Ribaya, 2005.3.12)

Source for identity of: Usp36 mule

(Taillebourg, 2007.2.26)

Source for identity of: scny Usp36

(Buszczak et al., 2009)

Source for database merge of

Source for merge of: Usp36 l(3)02331

(Buszczak et al., 2009)

Source for merge of: mule anon-WO0118547.247

(FlyBase, 1996-)

Additional comments

FlyBase curator comment: Correspondence with author Buszczak revealed that 'scny' = 'CG5505'.

(Buszczak et al., 2008)

Source for merge of mule anon-WO0118547.247 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Other Comments

scny negatively regulates the IMD pathway and suppresses fly immunity through its catalytic activity.

(Thevenon et al., 2009)

Usp36 encodes a deubiquitinating enzyme homologous to the human USP36 protein.

(Taillebourg and Fauvarque, 2007)

Usp36 mutant larvae are severely impaired in growth and die during the larval stages. They undergo the first larval moult more slowly than wild-type larvae and only a fraction of them undergo the second larval moult. The delayed first larval moult can be partially rescued by feeding ecdysone to the mutant larvae.

(Taillebourg and Fauvarque, 2007)

dsRNA made from templates generated with primers directed against mule that is transfected into S2 treated with Listeria monocytogenes reveals mule to be involved in Listeria monocytogenes intracellular growth, with increased intracellular growth observed in mule-treated cells.

(Cheng et al., 2005)

mule encodes a deubiquitinating enzyme.

(Ribaya and Laski, 2005)

Most loss of function mutants of mule have a lethal phenotype, however the authors original mule allele is viable, with only germline defects. mule mutant ovaries are very small and consist mostly of somatic tissue, however germline stem cells are still present.

(Ribaya and Laski, 2005)

Area matching Drosophila ESTs AA246386 and AA541060.

(Davies, 2001.3.15)

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

(Harvie et al., 1998)

Origin and Etymology

Discoverer

Etymology

Overexpression of a long form of the gene inhibit apoptosis, whereas overexpression of the short form has a proapoptotic effect. The gene is thus named "emperor's thumb" for this ability to regulate both life (thumbs up) and death (thumbs down).

(Ribaya et al., 2009)

Identification

External Crossreferences and Linkouts ( 69 )

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.

38648

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

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

Q9VRP5

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0260936

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

FBgn0260936

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

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

CG5505

Flygut - An atlas of the Drosophila adult midgut

FBgn0260936

FlyMine - An integrated database for Drosophila genomics

FBgn0260936

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

38648

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

TC002978

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

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

Dmel_CG5505

modMine - A data warehouse for the modENCODE project

FBgn0260936

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

Ub-specific processing proteases

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0260936

DRSC - Results frm RNAi screens

FBgn0260936

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

FBgn0260936

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

Interactive Fly

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

38648

MIST (genetic) - An integrated Molecular Interaction Database

scny

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

scny

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

Ub-specific processing proteases

Synonyms and Secondary IDs (22)

Reported As

Symbol Synonym

2331

(Harvie et al., 1998)

Q9VRP5

(Clague et al., 2013)

Scny

(Zhu et al., 2017, Mao et al., 2016, Engel et al., 2014, Lim et al., 2012)

USP36

(Ayyaz and Jasper, 2013, Vandenabeele and Bertrand, 2012, Xia et al., 2012)

Usp36

(Zhou et al., 2015, Ashwal-Fluss et al., 2014, Engel et al., 2014, Engel et al., 2014, Mulakkal et al., 2014, Xu et al., 2011)

anon-WO0118547.247

dUSP36

(Zhai et al., 2018, Kleino and Silverman, 2014, Kounatidis and Ligoxygakis, 2012, Thevenon et al., 2009, Taillebourg, 2007.2.26, Taillebourg and Fauvarque, 2007)

dUsp36

(Engel et al., 2014, Mulakkal et al., 2014, Taillebourg et al., 2014, Taillebourg et al., 2012)

(Ribaya et al., 2009)

l(3)02331

(Buszczak et al., 2009)

mule

(Vaque et al., 2013, Zhou et al., 2008, Taillebourg, 2007.2.26)

scny

(Meltzer et al., 2019, Lee et al., 2017, Ma et al., 2017, Kang et al., 2016, Choi and Aquadro, 2015, Kavi et al., 2015, Kwong et al., 2015, Yan et al., 2014, Yang et al., 2014, Morillo Prado et al., 2013, Lim et al., 2012, Tsou et al., 2012, Zhang et al., 2012, Friedman et al., 2011, Cook and Cook, 2010.5.7, Buszczak et al., 2009, Buszczak et al., 2009, Buszczak et al., 2008)

usp36

(Fan et al., 2015)

Name Synonyms

Scrawny

(Mehrotra and Deshpande, 2018, Buszczak et al., 2009)

Ubiquitin specific protease 36

Ubiquitin-specific protease 36

emperor's thumb

(Taillebourg et al., 2012, Ribaya et al., 2009)

lethal (3) 02331

mule

scrawny

(Lye et al., 2014, Lim et al., 2012, Taillebourg et al., 2012, Winbush et al., 2012, Buszczak et al., 2009, Buszczak et al., 2008)

ubiquitin C-terminal hydrolase 36

(Vandenabeele and Bertrand, 2012)

ubiquitin-specific protease 36

(Kounatidis and Ligoxygakis, 2012, Thevenon et al., 2009)

Secondary FlyBase IDs

FBgn0035633
FBgn0062147
FBgn0010777

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (93)

Report Sections

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