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General Information
Symbol
Dmel\faf
Species
D. melanogaster
Name
fat facets
Annotation Symbol
CG1945
Feature Type
FlyBase ID
FBgn0005632
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:31,777,020..31,790,681 [+]
Recombination map
3-102
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the peptidase C19 family. (P55824)
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).
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
Gene Model and Products
Number of Transcripts
7
Number of Unique Polypeptides
4

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
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0085843
9194
2778
FBtr0085844
8682
2711
FBtr0307547
9163
2773
FBtr0307548
9411
2761
FBtr0307550
9837
2773
FBtr0339188
9179
2773
FBtr0339189
9379
2761
Additional Transcript Data and Comments
Reported size (kB)
8.9, 8.5 (compiled cDNA)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0085202
311.1
2778
5.95
FBpp0085203
304.1
2711
6.02
FBpp0300199
310.6
2773
5.95
FBpp0300200
309.9
2761
6.22
FBpp0300202
310.6
2773
5.95
FBpp0308326
310.6
2773
5.95
FBpp0308327
309.9
2761
6.22
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)
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
MEROPS - An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
Linkouts
Sequences Consistent with the Gene Model
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 (15 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from physical interaction with UniProtKB:P09052
(assigned by UniProt )
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002541993
(assigned by GO_Central )
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN002541993
(assigned by GO_Central )
Biological Process (11 terms)
Terms Based on Experimental Evidence (8 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from high throughput mutant phenotype
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:dpp; FB:FBgn0000490
inferred from genetic interaction with FLYBASE:Med; FB:FBgn0011655
inferred from high throughput mutant phenotype
inferred from direct assay
inferred from mutant phenotype
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
non-traceable author statement
traceable author statement
traceable author statement
traceable author statement
inferred from biological aspect of ancestor with PANTHER:PTN002541993
(assigned by GO_Central )
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001163006
(assigned by GO_Central )
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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

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.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
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.
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.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
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
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 4-6
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 32 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 30 )
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 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
adult abdominal sensillum & trichogen cell, with Scer\GAL4sca-537.4
anterior fascicle & bouton, with Scer\GAL4elav-C155
anterior fascicle & synapse, with Scer\GAL4elav-C155
anterior fascicle & synapse | supernumerary, with Scer\GAL4elav-C155
eye photoreceptor cell & ommatidium | ectopic | somatic clone
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
12 of 15
No
Yes
3 of 15
No
Yes
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
14 of 15
Yes
Yes
 
 
12 of 15
No
Yes
3 of 15
No
Yes
1 of 15
No
No
Rattus norvegicus (Norway rat) (3)
9 of 13
Yes
Yes
5 of 13
No
Yes
3 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
5 of 12
Yes
Yes
1 of 12
No
Yes
1 of 12
No
No
Danio rerio (Zebrafish) (2)
14 of 15
Yes
Yes
3 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
4 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (1)
1 of 15
Yes
No
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
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
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
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W005S )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
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
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
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
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (10)
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 )
    Modifiers Based on Experimental Evidence ( 4 )
    Allele
    Disease
    Interaction
    References
    ameliorates  epilepsy
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    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.
    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
    Interactions
    Summary of Physical Interactions
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Interacts with imd.
    (UniProt, P55824 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-102
    Cytogenetic map
    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}pygoEP1076 and P{PZ}ttk02667&P{lacW}ttkj6C7
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    100D1-100D3
    (determined by in situ hybridisation)
    100E-100E
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (19)
    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
    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.

    cDNA Clones, End Sequenced (ESTs)
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    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
    Source for database merge of
    Source for merge of: faf BcDNA:LD22582
    Additional comments
    Source for merge of faf BcDNA:LD22582 was sequence comparison ( date:990717 ).
    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.
    lqf is ubiquitinated in vivo and is deubiquitinated by faf.
    faf de-ubiquitination has a role in controlling the level of activity of critical regulatory molecules at the synapse.
    faf and lqf facilitate endocytosis and antagonise ubiquitination. They function in common cells to generate an inhibitory signal that prevents ectopic photoreceptor cell determination.
    faf gene activity antagonises Ubi-p63E mediated proteolysis.
    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.
    Shows no genetic interaction with sdk.
    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.
    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.
    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.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 81 )
    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.
    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
    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
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    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
    Flygut - An atlas of the Drosophila adult midgut
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    KEGG Genes - Molecular building blocks of life in the genomic space.
    MEROPS - An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyMine - An integrated database for Drosophila genomics
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (13)
    Reported As
    Symbol Synonym
    Secondary FlyBase IDs
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (171)