FlyBase Gene Report: Dmel\faf

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).

Protein Function (UniProtKB)

Ubiquitin C-terminal hydrolase involved in development and the imd/NF-kappa-B (IMD) signaling cascade (PubMed:23919485, PubMed:1295747). Required for eye and embryo development, and plays a role in compound eye assembly and oogenesis respectively (PubMed:1295747). In the larval eye disks, cells outside the assembling facets require this protein for short-range cell interactions that prevent the mystery cells from becoming photoreceptors (PubMed:1295747). Also required for nuclear migration and cellularization in early embryogenesis and could play a role in pole cell determination, development or function (PubMed:1295747). Regulates the IMD signaling cascade at later stages of infection (around 6 hours post-infection) by inhibiting the expression of the antimicrobial peptides Dpt and Dro (PubMed:23919485). Acts by modulating the state of imd polyubiquitination and/or stability; a function which appears to be independent of its enzymatic activity (PubMed:23919485). In turn, imd enhances the polyubiquitination and stability of faf suggesting that they may form a regulatory feedback mechanism within the Imd pathway (PubMed:23919485).

(UniProt, P55824)

Summary (Interactive Fly)

conserved Cys and His domains - ubiquitin-specific protease - plays multiple roles in eye and oocyte development - Fat facets and Liquid facets promote Delta endocytosis and Delta signaling

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\faf or the JBrowse view of Dmel\faf 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 5.49

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

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

Gene model reviewed during 5.53

Sequence Ontology: Class of Gene

gene_with_edited_transcript

(Graveley et al., 2011)

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

faf-RA

FBtr0085843

NM_079873

9194

2778

faf-RC

FBtr0085844

NM_170576

8682

2711

faf-RD

FBtr0307547

NM_001260458

9163

2773

faf-RE

FBtr0307548

NM_001260459

9411

2761

faf-RG

FBtr0307550

NM_001260461

9837

2773

faf-RH

FBtr0339188

NM_001300698

9179

2773

faf-RI

FBtr0339189

NM_001260460

9379

2761

Additional Transcript Data and Comments

Reported size (kB)

8.9, 8.5 (compiled cDNA)

(Fischer-Vize et al., 1992)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

faf-PA

FBpp0085202

311.1

2778

5.95

NP_524612

AAF57198

faf-PC

FBpp0085203

304.1

2711

6.02

NP_733455

AAN14291

faf-PD

FBpp0300199

310.6

2773

5.95

NP_001247387

AFH06704

faf-PE

FBpp0300200

309.9

2761

6.22

NP_001247388

AFH06705

faf-PG

FBpp0300202

310.6

2773

5.95

NP_001247390

AFH06707

faf-PH

FBpp0308326

310.6

2773

5.95

NP_001287627

AHN57626

faf-PI

FBpp0308327

309.9

2761

6.22

NP_001247389

AFH06706

Polypeptides with Identical Sequences

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

2773 aa isoforms: faf-PD, faf-PG, faf-PH

2761 aa isoforms: faf-PE, faf-PI

Additional Polypeptide Data and Comments

Reported size (kDa)

2747, 2711 (aa); 300 (kD predicted)

(Fischer-Vize et al., 1992)

Comments

External Data

Subunit Structure (UniProtKB)

Interacts with imd.

(UniProt, P55824)

Post Translational Modification

Ubiquitinated. Ubiquitination is enhanced by the expression of imd.

(UniProt, P55824)

Crossreferences

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

MEROPS - An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

C19.007

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\faf 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 (16 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

protein binding

inferred from physical interaction with UniProtKB:P09052

(assigned by UniProt )

(Liu et al., 2003)

thiol-dependent ubiquitin-specific protease activity

inferred from direct assay

(Chen et al., 2002)

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

traceable author statement

(Wu et al., 1999)

inferred from biological aspect of ancestor with PANTHER:PTN002541993

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (12 terms)

Terms Based on Experimental Evidence (8 terms)

CV Term

Evidence

References

cellularization

inferred from mutant phenotype

(Fischer-Vize et al., 1992)

defense response to Gram-negative bacterium

inferred from high throughput mutant phenotype

(Cronin et al., 2009)

dorsal/ventral axis specification

inferred from mutant phenotype

(Stinchfield et al., 2012)

inferred from genetic interaction with FLYBASE:dpp; FB:FBgn0000490

(Stinchfield et al., 2012)

inferred from genetic interaction with FLYBASE:Med; FB:FBgn0011655

(Stinchfield et al., 2012)

mystery cell differentiation

inferred from mutant phenotype

(Fischer-Vize et al., 1992)

negative regulation of innate immune response

inferred from high throughput mutant phenotype

(Cronin et al., 2009)

nuclear cortical migration

inferred from mutant phenotype

(Fischer-Vize et al., 1992)

protein deubiquitination

inferred from direct assay

(Huang et al., 1995)

inferred from mutant phenotype

(Chen et al., 2002)

ubiquitin-dependent protein catabolic process

inferred from genetic interaction with FLYBASE:Prosβ6; FB:FBgn0002284

(Huang et al., 1995)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

cell migration

inferred from biological aspect of ancestor with PANTHER:PTN001163006

(assigned by GO_Central )

(Gaudet et al., 2011)

endocytosis

non-traceable author statement

(Narayanan and Ramaswami, 2001)

germ cell migration

traceable author statement

(Coffman, 2003)

mystery cell differentiation

traceable author statement

(Ou et al., 2003)

negative regulation of proteolysis

non-traceable author statement

(Narayanan and Ramaswami, 2001)

protein deubiquitination

traceable author statement

(Ou et al., 2003, Wu et al., 1999)

inferred from biological aspect of ancestor with PANTHER:PTN002541993

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

cytoplasm

inferred from direct assay

(Fischer-Vize et al., 1992)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN001163006

(assigned by GO_Central )

(Gaudet et al., 2011)

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

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage & oogenesis

germarium

(Fischer-Vize et al., 1992)

nurse cell

(Fischer-Vize et al., 1992)

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 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

ventral nerve cord

(Fisher et al., 2012)

Additional Descriptive Data

faf transcripts are detected in the germarium and in the egg chambers at subsequent stages of oogenesis. faf transcripts are observed in nurse cells and unlike faf protein, do not localize to the posterior of the oocyte at stage S10. The probe used does not distinguish between the two faf transcripts.

(Fischer-Vize et al., 1992)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

oogenesis & larval stage

ovary

(Fischer-Vize et al., 1992)

adult stage & oogenesis

nurse cell

(Fischer-Vize et al., 1992)

adult stage & oogenesis stage S10

oocyte | posterior

(Fischer-Vize et al., 1992)

larval stage

eye-antennal disc

(Fischer-Vize et al., 1992)

embryonic/larval fat body

(Fischer-Vize et al., 1992)

embryonic/larval digestive system

(Fischer-Vize et al., 1992)

larval stage & spermatogenesis

testis

(Fischer-Vize et al., 1992)

spermatogenesis & adult stage

testis

(Fischer-Vize et al., 1992)

adult stage oogenesis stage S10 -- S14

oocyte | posterior

(Fischer-Vize et al., 1992)

third instar larval stage

morphogenetic furrow | anterior to

(Fischer-Vize et al., 1992)

oogenesis

egg chamber

(Fischer-Vize et al., 1992)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

faf protein distribution was deduced from the localization of a fafFBtr0091350:pb-XRlacZ fusion protein. faf protein is detected in eye imaginal discs ahead of and behind the morphogenetic furrow but not in the furrow. It is also observed in other imaginal discs, fat body, gut, larval ovary and testis, and adult male sex organs. faf protein is detected in ovaries in the germarium and at all subsequent stages of oogenesis. Staining is restricted to the nurse cells until stage S10 when it becomes apparent at the oocyte posterior pole. Posterior localization of faf is dependent on osk.

(Fischer-Vize et al., 1992)

faf protein distribution was deduced from the localization of a fafFBtr0091350:pb-XRlacZ fusion protein. faf protein is detected in eye imaginal discs ahead of the morphogenetic furrow and at a lower level behind the furrow but not in the furrow. It is also observed in other imaginal discs, fat body, gut, larval ovary and testis, and adult male sex organs. faf protein is detected in ovaries in the germarium and at all subsequent stages of oogenesis. Staining is restricted to the nurse cells until stage S10 when it becomes apparent at the oocyte posterior pole. Posterior localization of faf is dependent on osk.

(Fischer-Vize et al., 1992)

Marker for

Subcellular Localization

CV Term

Evidence

References

cytoplasm

inferred from direct assay

(Fischer-Vize et al., 1992)

Expression Deduced from Reporters

Reporter: P{faf-lacZ.F}

Stage

Tissue/Position (including subcellular localization)

Reference

third instar larval stage

embryonic/larval fat body

(Fischer-Vize et al., 1992)

embryonic/larval digestive system

(Fischer-Vize et al., 1992)

morphogenetic furrow | anterior to

(Fischer-Vize et al., 1992)

imaginal disc

(Fischer-Vize et al., 1992)

third instar larval stage & spermatogenesis

testis

(Fischer-Vize et al., 1992)

oogenesis & third instar larval stage

ovary

(Fischer-Vize et al., 1992)

spermatogenesis & adult stage

testis

(Fischer-Vize et al., 1992)

oogenesis & adult stage | female

ovary

(Fischer-Vize et al., 1992)

Reporter: P{faf-lacZ.nls}

Stage

Tissue/Position (including subcellular localization)

Reference

third instar larval stage

cone cell

(Fischer-Vize et al., 1992)

eye-antennal disc

(Fischer-Vize et al., 1992)

photoreceptor cell

(Fischer-Vize et al., 1992)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\faf 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\faf

View exonic expression by tissue for Dmel\faf

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

FBgn0005632

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

FBgn0005632

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG1945-RC;CG1945-RC;CG1945-RA

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

CG1945

Flygut - An atlas of the Drosophila adult midgut

FBgn0005632

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\faf

Stages(s) 4-6
Stages(s) 13-16

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 32 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 32 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of faf

Transgenic constructs containing regulatory region of faf

Deletions and Duplications ( 7 )

Disrupted in

Df(3R)E(sina)9

(Wisotzkey et al., 1998, Carthew et al., 1994)

Df(3R)Exel6220

(Ryder, 2004.4.26)

Df(3R)faf-BP

(Fischer-Vize et al., 1992)

Df(3R)ttk-Δ1

(Wisotzkey et al., 1998)

Df(3R)ttk-Δ2

(Wisotzkey et al., 1998)

Df(3R)ttk-Δ3

(Wisotzkey et al., 1998)

In(3R)faf^BX4

(Fischer-Vize et al., 1992)

Phenotypes

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

Lethality

Allele

lethal - all die before end of embryonic stage | maternal effect | recessive

faf^FO8

lethal - all die before end of embryonic stage | non-rescuable maternal effect (with Df(3R)faf-BP)

faf^B6

partially lethal - majority die (with Df(3R)faf-BP)

partially lethal - majority die (with faf^B3)

faf^FO8

partially lethal - majority die (with faf^B4)

faf^B5

partially lethal - majority die (with faf^B5)

faf^B4

partially lethal - majority die (with faf^FO8)

faf^B3

viable

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

faf^GD4722

viable, with Scer\GAL4^Mef2.PR

viable, with Scer\GAL4^pnr-MD237

viable, with Scer\GAL4^tin.CΔ4

Sterility

Allele

female sterile | recessive

Other Phenotypes

Allele

increased cell number | third instar larval stage

faf^FO8

neuroanatomy defective, with Scer\GAL4^elav-C155

neuroanatomy defective, with Scer\GAL4^shot-OK307

faf^EP381

neuroanatomy defective, with Scer\GAL4^Tab2-201Y

faf^EP381

neuroanatomy defective | larval stage, with Scer\GAL4^CCAP.PP

faf^EP3520

neuroanatomy defective | larval stage, with Scer\GAL4^elav-C155

faf^EP381

neuroanatomy defective | pharate adult stage, with Scer\GAL4^CCAP.PP

faf^EP3520

neurophysiology defective, with Scer\GAL4^elav-C155

some die during embryonic stage | non-rescuable maternal effect (with Df(3R)faf-BP)

faf^B6

some die during embryonic stage | recessive | maternal effect | recessive

faf^FO8

visible

faf^BX4

visible, with Scer\GAL4^ap-md544

faf^EP381

visible, with Scer\GAL4^sca-537.4

faf^EP381

visible (with faf^BX4)

faf^FO8

visible (with faf^FO8)

faf^BX4

visible | recessive

wild-type

Phenotype manifest in

Allele

adult abdominal sensillum & trichogen cell, with Scer\GAL4^sca-537.4

faf^EP381

adult mushroom body, with Scer\GAL4^Tab2-201Y

faf^EP381

anterior fascicle & bouton, with Scer\GAL4^elav-C155

faf^EP381

anterior fascicle & synapse, with Scer\GAL4^elav-C155

faf^EP381

anterior fascicle & synapse | supernumerary, with Scer\GAL4^elav-C155

faf^EP381

bouton, with Scer\GAL4^elav-C155

faf^EP381

bouton | supernumerary, with Scer\GAL4^elav-C155

cone cell (with faf^BX3)

faf^FO8

cone cell (with faf^FO8)

faf^BX3

denticle (with Df(3R)faf-BP)

denticle (with faf^B3)

faf^FO8

denticle (with faf^FO8)

faf^B3

denticle belt | ectopic (with faf^B3)

faf^FO8

denticle belt | ectopic (with faf^FO8)

faf^B3

denticle belt | ectopic | non-rescuable maternal effect (with faf^B3)

faf^B5

denticle belt | ectopic | non-rescuable maternal effect (with faf^B4)

denticle belt | ectopic | non-rescuable maternal effect (with faf^B5)

faf^B3

denticle belt | ectopic | non-rescuable maternal effect (with faf^BX3)

faf^B4

denticle belt | ectopic | non-rescuable maternal effect (with faf^FO8)

faf^B4

dorsocentral bristle, with Scer\GAL4^sca-537.4

faf^EP381

embryo | embryonic stage 4 | maternal effect (with faf^BX3)

faf^FO8

embryo | embryonic stage 4 | maternal effect (with faf^FO8)

faf^BX3

embryonic/first instar larval cuticle (with Df(3R)faf-BP)

embryonic/first instar larval cuticle (with faf^B3)

faf^FO8

embryonic/first instar larval cuticle (with faf^FO8)

faf^B3

embryonic/first instar larval cuticle | non-rescuable maternal effect (with faf^B3)

faf^B5

embryonic/first instar larval cuticle | non-rescuable maternal effect (with faf^B4)

embryonic/first instar larval cuticle | non-rescuable maternal effect (with faf^B5)

embryonic/first instar larval cuticle | non-rescuable maternal effect (with faf^B6)

faf^B4

embryonic/first instar larval cuticle | non-rescuable maternal effect (with faf^BX3)

faf^B4

embryonic/first instar larval cuticle | non-rescuable maternal effect (with faf^FO8)

faf^B4

embryonic/larval central nervous system, with Scer\GAL4^CCAP.PP

faf^EP3520

embryonic head (with Df(3R)faf-BP)

faf^B3

embryonic head | non-rescuable maternal effect (with faf^B4)

embryonic head | non-rescuable maternal effect (with faf^B5)

faf^B4

embryonic head | non-rescuable maternal effect (with faf^B6)

faf^B4

embryonic head | non-rescuable maternal effect (with faf^BX3)

faf^B4

embryonic head | non-rescuable maternal effect (with faf^FO8)

faf^B4

eye

faf^BX4

eye, with Scer\GAL4^GMR.PF

faf^EP381

eye (with faf^BX4)

faf^FO8

eye (with faf^FO8)

faf^BX4

eye photoreceptor cell

eye photoreceptor cell (with faf^BX4)

faf^FO8

eye photoreceptor cell (with faf^FO8)

faf^BX4

eye photoreceptor cell & ommatidium | ectopic | somatic clone

eye photoreceptor cell | supernumerary

faf^FO8

eye photoreceptor cell | supernumerary (with faf^BX3)

faf^FO8

eye photoreceptor cell | supernumerary (with faf^BX4)

faf^FO8

eye photoreceptor cell | supernumerary (with faf^FO8)

filzkorper (with Df(3R)faf-BP)

filzkorper (with faf^B3)

faf^FO8

filzkorper (with faf^FO8)

faf^B3

filzkorper | non-rescuable maternal effect (with faf^B4)

filzkorper | non-rescuable maternal effect (with faf^B5)

faf^B4

filzkorper | non-rescuable maternal effect (with faf^B6)

faf^B4

filzkorper | non-rescuable maternal effect (with faf^BX3)

faf^B4

filzkorper | non-rescuable maternal effect (with faf^FO8)

faf^B4

giant fiber neuron, with Scer\GAL4^shot-OK307

faf^EP381

intersegmental nerve, with Scer\GAL4^elav-C155

faf^EP381

neurite | pharate adult stage, with Scer\GAL4^CCAP.PP

faf^EP3520

neuromuscular junction, with Scer\GAL4^elav-C155

faf^EP381

ommatidium

ommatidium, with Scer\GAL4^GMR.PF

faf^EP381

ommatidium (with faf^BX3)

faf^FO8

ommatidium (with faf^BX4)

faf^FO8

ommatidium (with faf^FO8)

photoreceptor cell R1 | ectopic

faf^BX4

photoreceptor cell R2 | ectopic

faf^BX4

photoreceptor cell R3 | ectopic

faf^BX4

photoreceptor cell R4 | ectopic

faf^BX4

photoreceptor cell R5 | ectopic

faf^BX4

photoreceptor cell R6 | ectopic

faf^BX4

pole cell

faf^B3

rhabdomere R7, with Scer\GAL4^Rh3.PP

faf^GS9924

scutellar bristle, with Scer\GAL4^sca-537.4

faf^EP381

synapse, with Scer\GAL4^elav-C155

faf^EP381

synapse, with Scer\GAL4^shot-OK307

faf^EP381

synapse | supernumerary, with Scer\GAL4^elav-C155

synaptic vesicle, with Scer\GAL4^elav-C155

faf^EP3520

tergotrochanteral muscle motor neuron, with Scer\GAL4^shot-OK307

faf^EP381

trichogen cell, with Scer\GAL4^sca-537.4

faf^EP381

wing sensillum | ectopic, with Scer\GAL4^ap-md544

faf^EP381

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\USP9X

15 of 15

Yes

Hsap\USP9Y

12 of 15

Yes

Hsap\USP24

3 of 15

Yes

Hsap\USP34

1 of 15

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Usp9x

14 of 15

Yes

Mmus\Usp9y

12 of 15

Yes

Mmus\Usp24

3 of 15

Yes

Mmus\Usp34

1 of 15

Rattus norvegicus (Norway rat) (3)

Rnor\Usp9x

9 of 13

Yes

Rnor\Usp9y

5 of 13

Yes

Rnor\Usp24

3 of 13

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\usp9x

5 of 12

Yes

Xtro\usp24

1 of 12

Yes

Xtro\usp34

1 of 12

Danio rerio (Zebrafish) (2)

Drer\usp9

14 of 15

Yes

Drer\usp24

3 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\T24B8.7

4 of 15

Yes

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\UBP15

1 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919003V )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Dmel\faf

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA15146

Drosophila persimilis

Dper\GL23356

Drosophila willistoni

Dwil\GK13174

Drosophila virilis

Dvir\GJ24225

Drosophila mojavensis

Dmoj\GI22109

Drosophila grimshawi

Dgri\GH14199

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150020 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17012005

Glossina morsitans

Tsetse fly

Gmor\GMOY003335

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_02512

Mayetiola destructor

Hessian fly

Mdes\Mdes007273

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL009824

Anopheles darlingi

American malaria mosquito

Adar\ADAC007907

Anopheles gambiae

Malaria mosquito

Agam\GPROP9

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ013863

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W005S )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA007507

Danaus plexippus

Monarch butterfly

Dple\DPOGS204226-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL015148

Apis florea

Little honeybee

Aflo\2250474644

Apis mellifera

Western honey bee

Amel\faf

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP10172

Bombus terrestris

Buff-tailed bumblebee

Bter\15216323

Linepithema humile

Argentine ant

Lhum\LH16594

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:0026ff

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG003610

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_02083

Tribolium castaneum

Red flour beetle

Tcas\TC010455

Pediculus humanus

Human body louse

Phum\PHUM076540

Rhodnius prolixus

Kissing bug

Rpro\RPRC007692

Cimex lectularius

Bed bug

Clec\CLEC001917

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI008226

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_09944

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X005M )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR006759

Ixodes scapularis

Black-legged tick

Isca\ISCW009097

Stegodyphus mimosarum

African social velvet spider

Smim\KFM62543.1

Stegodyphus mimosarum

African social velvet spider

Smim\KFM62549.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur06g04700

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_306876

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0069 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Usp9Y

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000021573

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000011983

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000002637

Gallus gallus

Domestic chicken

Ggal\USP9X

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (10)

Gene Symbol

Score

Source

Alignment

puf

3 of 10

2 of 10

2 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 ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 2 )

Human Ortholog

Disease

Evidence

References

USP9X; ubiquitin specific peptidase 9 X-linked

model of non-syndromic X-linked intellectual disability

IEA

(FlyBase, 2019-)

USP9Y; ubiquitin specific peptidase 9 Y-linked

model of Y-linked spermatogenic failure 2

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 4 )

Allele

Disease

Interaction

References

faf^B3

ameliorates epilepsy

modeled by pk^sple-1

(Paemka et al., 2015)

faf^BX3

ameliorates epilepsy

modeled by pk^sple-1

(Paemka et al., 2015)

faf^BX4

exacerbates Huntington's disease

modeled by Hsap\HTT^{128Q.1-336.UAS}

(Kaltenbach et al., 2007)

ameliorates epilepsy

modeled by pk^sple-1

(Paemka et al., 2015)

faf^EP381

ameliorates Huntington's disease

modeled by Hsap\HTT^{128Q.1-336.UAS}

(Kaltenbach et al., 2007)

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?

USP9X; ubiquitin specific peptidase 9 X-linked

15 of 15

300072

non-syndromic X-linked intellectual disability

USP9Y; ubiquitin specific peptidase 9 Y-linked

12 of 15

400005

SPERMATOGENIC FAILURE, Y-LINKED, 2; SPGFY2

Y-linked spermatogenic failure 2

USP24; ubiquitin specific peptidase 24

3 of 15

610569

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.

Dmel gene

Ortholog showing functional complementation

Supporting References

faf

Mmus\Usp9x

(Chen et al., 2000)

Interactions

Summary of Physical Interactions

esyN Network Diagram

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

faf - Lkb1

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

faf - Pten

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

faf - Rab26

pull down, peptide massfingerprinting

(Gillingham et al., 2014)

faf - Rab6

pull down, peptide massfingerprinting

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

faf - gig

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

faf - imd

anti tag coimmunoprecipitation, anti tag western blot

(Yagi et al., 2013)

faf - par-1

enzymatic study, western blot

(Lee et al., 2012)

faf - rictor

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

faf - sstn

anti tag coimmunoprecipitation, peptide massfingerprinting

(Liu et al., 2015)

faf - vas

anti bait coimmunoprecipitation, protein cross-linking with a bifunctional reagent, peptide massfingerprinting

(Liu et al., 2003)

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

faf

suppressible

14-3-3ζ

(Isaksson et al., 1997)

faf

enhanceable

aop

(Isaksson et al., 1997)

faf|lqf

enhanceable

Chc

(Cadavid et al., 2000)

faf

enhanceable

Chc

(Cadavid et al., 2000)

faf

suppressible

DNApol-α60

(Chen et al., 2000)

faf

enhanceable

E(faf)bE160

(Fischer et al., 1997)

faf

enhanceable

E(faf)bE184

(Fischer et al., 1997)

faf

enhanceable

E(faf)bE365

(Fischer et al., 1997)

faf|lqf

suppressible

eff

(Cadavid et al., 2000)

faf

suppressible

eff

(Chen et al., 2000, Wu et al., 1999)

faf

suppressible

Jra

(Isaksson et al., 1997)

faf

enhanceable

lqf

(Cadavid et al., 2000, Fischer et al., 1997)

faf

suppressible

lqf

(Cadavid et al., 2000)

dpp|faf

suppressible

Med

(Stinchfield et al., 2012)

faf

enhanceable

pbl

(Reiter et al., 2006)

faf

suppressible

pnt

(Isaksson et al., 1997)

faf|lqf

suppressible

Prosβ6

(Cadavid et al., 2000)

faf

suppressible

Prosβ6

(Huang et al., 1995)

faf

enhanceable

Ras85D

(Fischer et al., 1997)

faf

suppressible

S(faf)86

(Chen et al., 2000)

faf

suppressible

S(faf)196

(Chen et al., 2000)

faf

suppressible

S(faf)244

(Chen et al., 2000)

faf

enhanceable

shi

(Cadavid et al., 2000)

SkpA|faf

suppressible

wnd

(Brace et al., 2014)

faf

suppressible

wnd

(Collins et al., 2006)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

(Kim et al., 2010)

suppressible

(Neuert et al., 2017)

hiw

suppressible

faf

(DiAntonio et al., 2001)

suppressible

faf

(Paemka et al., 2015)

Ppt1

enhanceable

faf

(Buff et al., 2007)

enhanceable

(Li et al., 1997)

suppressible

(Stinchfield et al., 2012)

External Data

Subunit Structure (UniProtKB)

Interacts with imd.

(UniProt, P55824 )

Linkouts

BioGRID - A database of protein and genetic interactions.

68590

DroID - A comprehensive database of gene and protein interactions.

FBgn0005632

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

43749

MIST (genetic) - An integrated Molecular Interaction Database

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

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

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

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-102

Cytogenetic map

100D2-100D2

Sequence location

3R:31,777,020..31,790,681 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

100D2-100D2

Limits computationally determined from genome sequence between P{EP}pygo^EP1076 and P{PZ}ttk⁰²⁶⁶⁷&P{lacW}ttk^j6C7

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

100D1-100D3

(determined by in situ hybridisation)

(Abdelilah-Seyfried et al., 2000)

100E-100E

(Fischer-Vize, 1993.1.22, Fischer-Vize, 1993.1.22)

100E-100E

(determined by in situ hybridisation)

(Fischer-Vize et al., 1992)

Experimentally Determined Recombination Data

Location

3-102

(FlyBase, 2016)

3-99.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (17)

Bloomington

4921

P{faf-lacZ.F}JF1

25100

st¹ faf^B3/TM6B, Tb¹

15390

y¹ w^67c23; P{EPgy2}faf^EY02018

25101

w^*; st¹ faf^BX3/TM6B, Tb¹

25107

w^*; st¹ faf^BX4/TM6B, Tb¹

25108

w^*; st¹ faf^FO8/TM6C, Sb¹

65538

w¹¹¹⁸; PBac{IT.GAL4}faf^1281-G4/TM6B, Tb¹

VDRC

v107716

P{KK100775}VIE-260B

v2955

w¹¹¹⁸; P{GD1444}v2955

v2956

w¹¹¹⁸; P{GD1444}v2956

v30679

w¹¹¹⁸; P{GD4722}v30679

v30680

w¹¹¹⁸; P{GD4722}v30680/TM3

More stocks available...

Genomic Clones (12)

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

cDNA clones, fully sequences

BDGP DGC clones

Other clones

MIP20638

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.

FBgn0005632

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0005632

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

43749

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: faf CG1945

(Zhao, 1999.11)

Source for database merge of

Source for merge of: faf BcDNA:LD22582

(FlyBase, 1996-)

Additional comments

Source for merge of faf BcDNA:LD22582 was sequence comparison ( date:990717 ).

(FlyBase, 1996-)

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)

lqf is ubiquitinated in vivo and is deubiquitinated by faf.

(Chen et al., 2002)

faf de-ubiquitination has a role in controlling the level of activity of critical regulatory molecules at the synapse.

(DiAntonio et al., 2001)

faf and lqf facilitate endocytosis and antagonise ubiquitination. They function in common cells to generate an inhibitory signal that prevents ectopic photoreceptor cell determination.

(Cadavid et al., 2000)

faf gene activity antagonises Ubi-p63E mediated proteolysis.

(Wu et al., 1999)

Analysis of genetic interactions among faf and R and Ras85D reveals that in addition to its critical role anterior to the morphogenetic furrow, faf has a function in undifferentiated cells alter in eye development that involves, probably indirectly, Ras85D and R. These results suggest that cells outside the facet influence cell fates within the facet.

(Li et al., 1997)

Shows no genetic interaction with sdk.

(Nguyen et al., 1997)

faf is essential only early in eye development and only outside of the 7-cell precluster and cone cell precursors. The critical role of faf in eye development is not in the regulation of argos, aop or Gap1 activities, nor in the regulation of any other protein that functions within cells of the developing facets. Undifferentiated cells outside the facet precluster direct ommatidial assembly by sending to the mystery cells and other cells an inhibitory signal, regulated by faf protein.

(Huang and Fischer-Vize, 1996)

The faf protein acts as a regulatory Ubiquitin-specific protease that prevents degradation of its substrate by the proteasome. The faf Ubiquitin-specific protease is cell type- and substrate-specific and regulates cell fate decisions.

(Huang et al., 1995)

faf is required for cell interactions that prevent particular cells in the developing eye from becoming photoreceptors. Mosaic analysis indicates that faf is required in cells close to, but outside the normal developing photoreceptors and also outside the ectopic photoreceptors in mutant facets. The faf product is also required during oogenesis (embryos from faf mutant mothers never cellularize, except for the pole cells), but is not required for nos localization or function. The faf gene has been cloned, and all regions essential for its function identified by transformation rescue of the mutant phenotypes. faf-Ecol\lacZ chimeric proteins become posteriorly localized in oocytes, and the first 392 amino acids of faf protein is sufficient for this localization.

(Fischer-Vize et al., 1992)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 82 )

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.

43749

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

P55824

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

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0005632

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

FBgn0005632

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

CG1945

Flygut - An atlas of the Drosophila adult midgut

FBgn0005632

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

43749

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

TC010455

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

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

Dmel_CG1945

MEROPS - An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

C19.007

modMine - A data warehouse for the modENCODE project

FBgn0005632

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

Linkouts

BioGRID - A database of protein and genetic interactions.

68590

DroID - A comprehensive database of gene and protein interactions.

FBgn0005632

DRSC - Results frm RNAi screens

FBgn0005632

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

FBgn0005632

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG1945-RC;CG1945-RC;CG1945-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0005632

FlyMine - An integrated database for Drosophila genomics

FBgn0005632

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.

43749

MIST (genetic) - An integrated Molecular Interaction Database

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

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

Synonyms and Secondary IDs (13)

Reported As

Symbol Synonym

BcDNA.LD22582

(Rubin, 1999.4.23)

BcDNA:LD22582

CG1945

(Neuert et al., 2017, Çiçek et al., 2016, Zhou et al., 2015, Engel et al., 2014, Christis and Munro, 2012, Tsou et al., 2012, Zhang et al., 2012, Ni et al., 2011.7.19, Klement et al., 2010, Keleman et al., 2009.8.5, Molnar et al., 2006, Kanuka et al., 2005, Hernandez et al., 2004, Kraut et al., 2001, Kraut et al., 2001)

Faf

(Ge et al., 2019, Bandyopadhyay et al., 2016, Zhou et al., 2015, Xia et al., 2012, Cronin et al., 2009, Murphey and Godenschwege, 2002)

Fat

(Klement et al., 2010)

P55824

(Clague et al., 2013)

USPX

(Murtaza et al., 2015)

faf

(Ly et al., 2018, Neuert et al., 2017, Seugnet et al., 2017, Sinenko, 2017, Clandinin and Owens, 2016-, Hsu et al., 2015, Liu et al., 2015, Murtaza et al., 2015, Paemka et al., 2015, Ashwal-Fluss et al., 2014, Kwon et al., 2013, Kwon et al., 2013, Strutt et al., 2013, Yagi et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Lee et al., 2012, Senthilan et al., 2012, Stinchfield et al., 2012, Tsou et al., 2012, Zhang et al., 2012, Zhang et al., 2012, Cho and Fischer, 2011, Friedman et al., 2011, Kim et al., 2010, Hazelett et al., 2009, Tripodi et al., 2008, Uthaman et al., 2008, Zhao et al., 2008, Buff et al., 2007, Horiuchi et al., 2007, Kaltenbach et al., 2007, Minidorff et al., 2007, Minidorff et al., 2007, Collins et al., 2006, Millard and Wood, 2006, Molnar et al., 2006, Reiter et al., 2006, Viquez et al., 2006, Kanuka et al., 2005, Murphey and Godenschwege, 2002)

Name Synonyms

Fat Facets

(Brace et al., 2014)

Fat facets

(Ly et al., 2018, Buff et al., 2007, Murphey and Godenschwege, 2002)

Fat-Facets

(Bandyopadhyay et al., 2016)

fat facets

(Paemka et al., 2015, Engel et al., 2014, Yagi et al., 2013, Klement et al., 2010, Uthaman et al., 2008, Zhao et al., 2008, Horiuchi et al., 2007, Kaltenbach et al., 2007, Collins et al., 2006, Millard and Wood, 2006, Reiter et al., 2006, Viquez et al., 2006, Kraut et al., 2001, Kraut et al., 2001)

fat-facets

(Tripodi et al., 2008)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (171)

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