A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\usp

General Information
SymbolDmel\uspSpeciesD. melanogaster
NameultraspiracleAnnotation symbolCG4380
Feature typeprotein_coding_geneFlyBase IDFBgn0003964
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)XRecombination map
Cytogenetic map2C7-2C7Sequence locationX:1,932,829..1,935,316 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene ultraspiracle is referred to in FlyBase by the symbol usp (CG4380, FBgn0003964). It has the cytological map location 2C7. Its sequence location is X:1932829..1935316. Its molecular function is described as: ecdysteroid hormone receptor activity; ligand-dependent nuclear receptor activity; transcription factor activity; protein binding; DNA binding; juvenile hormone binding; zinc ion binding; sequence-specific DNA binding. It is involved in the biological processes described with 12 unique terms, many of which group under: anatomical structure development; regulation of metabolic process; regulation of developmental process; regulation of biological process; neuron differentiation; transcription, DNA-dependent; neuron maturation; positive regulation of programmed cell death; cell motility; positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process. 21 alleles are reported. The phenotypes of these alleles are annotated with 16 unique terms, many of which group under: organ system; imaginal precursor; anatomical structure; peripheral nervous system; morphogenetic furrow; egg; nervous system; larval imaginal precursor; rhabdomere; vitellarium; spiracle; adult segment. It has one annotated transcript and one annotated polypeptide.

External Summaries

hide Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage
cf1: Chorion factor 1
Encodes a protein that binds the promoter region of Cp15.
usp: ultraspiracle (A. E. Oro)
Mutants are recessive lethals. usp/usp or usp// progeny of usp/+ mothers die during the first larval instar or in the molt to the second instar. Those that die during the molt to the second instar sometimes have incompletely molted the first instar set of larval spiracles and thus have two sets of spiracles (Perrimon et al., 1985; Oro, McKeown and Evans, in prep.). usp/Y embryos derived from usp/usp germ cells die just prior to or just after hatching with an oval scar on the ventral surface of the posterior eighth abdominal or ninth abdominal segment. The spiracles of these animals appear normal as does the rest of the cuticle and the ventral nervous system. Paternally supplied usp+ completely rescues this phenotype and allows survival to adulthood (Perrimon et al., 1985; Oro, McKeown, and Evans, in prep.). Use of a conditional expression system for rescue of the first/second instar lethal phase results in survival into the third instar and early pupal periods, with no animals surviving beyond pupal stage P4 (Oro, Mckeown, and Evans, in prep.). usp/0//usp+ gyandromorphs do not survive suggesting that the gene is required in multiple parts of the body and not just in the terminal regions. γ-ray induced usp/usp clones survive in the female germline, abdomen, thorax and head, showing that usp is not a general cell lethal. Clones in the head are associated with defects in rhabdomere and ommatidial morphology (Oro, McKeown, and Evans, in prep.). Expression of a usp cDNA at high levels throughout development rescues the usp- phenotype and has no deletenous effect on usp+ animals, suggesting that any necessary spatial or temporal regulation of usp action occurs by regulation of some other factor such as a ligand.
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
2C7-2C7  
Limits computationally determined from genome sequence between P{EP}EP427 and P{EP}ActnEP1193&P{EP}CG4322EP1631  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
2C1-2C3
(determined by in situ hybridisation)  
(Henrich et al., 1990)
2C-2C
(determined by in situ hybridisation)  
(Oro et al., 1990)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
Gene Order (overall orientation not stated)
References
Overall orientation not stated: Actn+ usp+ Actn+
(Wahlstrom et al., 2004)
hide Gene Model & Products
Please see the GBrowse view of Dmel\usp for information on other features
detailed view FBtr0070346 FBtr0070344 FBtr0070345 FBtr0070342 FBpp0070332 FBpp0070328 FBti0037354 FBti0039836 FBti0071296 FBti0007384 FBti0037230 FBti0029347 FBti0023555 FBti0029710 FBti0029352 FBti0048814 FBti0048211
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
usp-RA
FBtr0070346
 NM_057433
  2488
  508
Additional Transcript Data & Comments
Reported size (kB)
2.4 (northern blot)
(Oro et al., 1990, Shea et al., 1990)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
usp-PA  
FBpp0070332  
55.2  
508  
8.05  
  NP_476781
  AAF45707
Additional Polypeptide Data & Comments
Reported size (kD)
507 (aa); 55 (kD predicted)
(Henrich et al., 1990)
508 (aa)
(Oro et al., 1990)
55 (kD)
(Christianson et al., 1992)
54, 48 (kD observed)
(Henrich et al., 1994)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
Zinc finger, NHR/GATA-type (IPR013088)
Vitamin D receptor (IPR000324)
Nuclear hormone receptor, ligand-binding, core (IPR000536)
Zinc finger, nuclear hormone receptor-type (IPR001628)
Steroid hormone receptor (IPR001723)
Nuclear hormone receptor, ligand-binding (IPR008946)
PDB - Protein Data Bank. An information portal to biological macromolecular structures
•
TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
•
  • R03988
  • T00117
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA390870
 
AA391001
 
AA439415
 
AE003422
AAF45707
 
AI294698
 
AI295311
 
AI404326
 
AL031765
CAA21122
 
AL513225
 
AW942107
 
AY069393
AAL39538
 
BI213172
 
BI228489
 
BI242941
 
BI363855
 
BI365258
 
BI365417
 
BI376191
 
BI376194
 
BI376195
 
BI565858
 
BI577127
 
BI632016
 
BI635419
 
BI638036
 
BI642018
 
CK659237
 
CO275864
 
CO275933
 
CO289648
 
CO300154
 
CO313025
 
CO320273
 
CO321503
 
EC056943
 
EC056945
 
EC059962
 
EC066282
 
EC067154
 
EC087959
 
EC200432
 
EC221627
 
EC230737
 
EC250449
 
X52591
CAA36827
 
X53379
CAA37459
 
X53417
CAA37496
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    (FlyBase, 1992-)
    Does NOT map to
    Identified with
    (BDGP Project Members, 2000-, Benos et al., 2001)
    (BDGP Project Members, 1994-1999)
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    aberration junction
    Tp(3;1)KA21.bk3
    X:1,934,446..1,934,448
    evidence=experimental
    (Oro et al., 1990)
    point mutation
    usp[4]
    X:1,934,559..1,934,559
    evidence=experimental
    pr_change=R130C
    na_change=C1797298T
    (Henrich et al., 1994)
    point mutation
    usp[3]
    X:1,934,468..1,934,468
    evidence=experimental
    pr_change=R160H
    na_change=G1797207A
    (Henrich et al., 1994)
    rescue fragment
    usp[tOa]
    X:1,930,869..1,938,934
    evidence=experimental
    linked_to=EcoRI-EcoRI_rfrag
    (Oro et al., 1990)
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    •
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data     		Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
     oogenesis stage,adult stage
     follicle cell
    (Shea et al., 1990)
     embryonic stage | stage 12
     ventral nerve cord
    (Oro et al., 1992)
     oogenesis stage,adult stage | stage >=S8
     oocyte
    (Oro et al., 1992)
     oogenesis stage,adult stage | stage >=S8
     nurse cell
    (Oro et al., 1992)
     embryonic stage | stage 12
     embryonic/larval midgut
    (Oro et al., 1992)
     embryonic stage | early
     
    (Oro et al., 1992)
     oogenesis stage,adult stage | female
     ovary
    (Shea et al., 1990)
     embryonic stage-adult stage
     
    (Henrich et al., 1994)
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
       larval stage | third instar | late
       larval central nervous system
      (Henrich et al., 1994)
       larval stage | third instar | late
       embryonic/larval fat body
      (Henrich et al., 1994)
       larval stage | third instar | late
       dorsal mesothoracic disc
      (Henrich et al., 1994)
       embryonic stage-pupal stage
       
      (Henrich et al., 1994)
       larval stage | third instar | late
       antennal disc
      (Henrich et al., 1994)
       larval stage | third instar
       eye disc
      (Zelhof et al., 1997)
       larval stage | third instar | late
       ring gland
      (Henrich et al., 1994)
       larval stage | third instar | late
       ventral thoracic disc
      (Henrich et al., 1994)
       oogenesis stage,adult stage
       nurse cell
      (Christianson et al., 1992)
       oogenesis stage,adult stage
       follicle cell
      (Christianson et al., 1992)
       larval stage | third instar | late
       embryonic/larval salivary gland
      (Henrich et al., 1994)
       oogenesis stage,adult stage
       follicle cell
      (Shea et al., 1990)
      Marker for
        Subcellular Localization
        CV Term
        nucleus
        (Henrich et al., 1994)
        hide External Data & Images
        Linkouts
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        lethal
        lethal | recessive
        lethal | germ-line clone | rescuable maternal effect
        lethal | larval stage | maternal effect
        lethal | larval stage | recessive
        lethal | larval stage | partially | conditional - heat sensitive
        Other Phenotypes
        Allele
        wild-type
        hypoactive, with usp2
        hypoactive, with usphs.PO
        touch sensitivity defective, with usp2
        touch sensitivity defective, with usphs.PO
        neuroanatomy defective
        neuroanatomy defective | pupal stage
        Phenotype manifest in
        Allele
        embryonic/larval anterior spiracle, with usphs.PO
        imaginal disc, with usphs.PO
        larval midgut & embryo, with usphs.PO
        midgut imaginal island, with usphs.PO
        larval salivary gland & embryo, with usphs.PO
        dorsal mesothoracic disc & neuron | somatic clone
        egg | germ-line clone | maternal effect
        dorsal appendage | germ-line clone | maternal effect
        terminal filament
        olfactory neuron & axon
        olfactory neuron & dendrite
        antennal lobe & axon
        adult mushroom body & axon
        ommatidial cluster | somatic clone
        morphogenetic furrow | somatic clone
        embryo | germ-line clone | posterior
        dendritic arborising neuron & pupa
        gamma-lobe & neuron | somatic clone
        rhabdomere | somatic clone
        retina | somatic clone
        retina | cell non-autonomous | somatic clone
        gamma-lobe & pupa
        egg chamber | germ-line clone
        embryonic/first instar larval cuticle | germ-line clone
        embryonic/larval anterior spiracle, with usp2
        imaginal disc, with usp2
        larval midgut & embryo, with usp2
        midgut imaginal island, with usp2
        larval salivary gland & embryo, with usp2
        border follicle cell | somatic clone
        triple row | ectopic | precursor | somatic clone
        ommatidium | somatic clone
        hide Classical Alleles ( 8 )
        For All Classical Alleles Show

        Allele of uspClassMutagenStocksKnown lesion
        usp10 --
        usp2amorph, loss of function0 Yes
        usp3hypomorph0 Yes
        usp4hypomorph2 Yes
        usp50 Yes
        uspunspecified
          		0 --
          uspΔ1480 Yes
          uspΔ2080 Yes
          hide Alleles Carried on Transgenic Constructs ( 13 )
          For All Alleles Carried on Transgenic Constructs Show

          Allele of uspClassMutagenStocksKnown lesion
          uspAct5C.PS0 Yes
          uspAct5C.PW0 Yes
          uspGD15541 Yes
          uspGMR.PZ0 Yes
          uspMtnA.PD0 Yes
          uspScer\UAS.cGa0 Yes
          uspcDa0 Yes
          uspdsRNA.cBa0 Yes
          usphs.C.T:Ecol\dam,T:Hsap\MYC0 Yes
          usphs.N.T:Ecol\dam,T:Hsap\MYC0 Yes
          usphs.PO0 Yes
          usphs.T:Scer\GAL41 Yes
          usptOa0 Yes
          hide Aneuploid Aberrations
          Useful deficiency
           
          Useful duplication
           
          Partially disrupted in
          (Wahlstrom et al., 2006)
          (Wahlstrom et al., 2004)
          Duplicated in
          (Perrimon et al., 1985)
          Not disrupted in
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          (Perrimon et al., 1985)
          Not duplicated in
          (Perrimon et al., 1985)
          Disrupted in
          (Oro et al., 1990)
          hide Transgenic Constructs & Insertions
          Transgenic Constructs
          Type of construct
          Name
          Expression data
          UAS construct
          P{GD1554}
          NA
          P{UAS-usp.G}
          NA
          characterization construct
          P{GMR-usp.Z}
          NA
          P{d/cusp}
          NA
          P{usptOa}
          NA
          heat-shock construct
          P{hs-GAL4-usp.LBD}
          NA
          P{hs-usp}
          NA
          Insertions
          Type of insertions
          Name
          Expression data
          insertion of mobile activating element
          P{EP}ActnEP1193
          NA
          hide Related Comments
          Please look at the allele reports for the complete phenotype data
          Mutants are recessive lethals. usp1/usp1 or usp1/γ progeny of usp1/+ mothers die during the first larval instar or in the molt to the second instar. Those that die during the molt to the second instar sometimes have incompletely molted the first instar set of larval spiracles and thus have two sets of spiracles (FBrf0042629; FBrf0055872). usp1/Y embryos derived from usp1/usp1 germ cells die just prior to or just after hatching with an oval scar on the ventral surface of the posterior eighth abdominal or ninth abdominal segment. The spiracles of these animals appear normal as does the rest of the cuticle and the ventral nervous system. Paternally supplied usp+ completely rescues this phenotype and allows survival to adulthood (FBrf0042629; FBrf0055872). Use of a conditional expression system for rescue of the first/second instar lethal phase results in survival into the third instar and early pupal periods, with no animals surviving beyond pupal stage P4 (FBrf0055872). usp1/0//usp+ gynandromorphs do not survive suggesting that the gene is required in multiple parts of the body and not just in the terminal regions. γ-ray induced usp1/usp1 clones survive in the female germ-line, abdomen, thorax and head, showing that usp is not a general cell lethal. Clones in the head are associated with defects in rhabdomere and ommatidial morphology (FBrf0055872). Expression of a usp cDNA at high levels throughout development rescues the usp- phenotype and has no deleterious effect on usp+ animals, suggesting that any necessary spatial or temporal regulation of usp action occurs by regulation of some other factor such as a ligand.
           
          Molecular cloning and characterization has shown usp to be a novel member of the zinc finger protein superfamily.
          (Shea et al., 1990)
          usp is a Drosophila partner of EcR. Together usp and EcR bind DNA in a highly cooperative pattern. Cotransfection of both usp and EcR is required to render cultured mammalian cells ecdysone responsive.
          (Yao et al., 1992)
          Distribution of usp product during oogenesis, and in vitro binding properties of bacterially produced usp product both to an optimal binding site and to the Cp15 promoter have been studied. USP may operate as a heterodimer in vivo, though identity of the partner remains to be determined.
          (Christianson et al., 1992)
          The equilibrium dissociation constant of the usp protein to its response element on the Cp15 promoter is determined and compared to the binding activities of other nuclear hormone receptors to their cognate elements.
          (Christianson and Kafatos, 1993)
          Transient cotransfection experiments in HeLa cells demonstrated that EcR must heterodimerize with usp (the homolog of the mammalian retinoid X receptor) for DNA binding and transactivation. EcR/usp gene product DNA binding activity is unaffected by ecdysteroid and 9-cis-retinoic acid.
          (Thomas et al., 1993)
          Ecdysteroid-regulated gene.
          (Andres et al., 1993)
          EcR and usp native gene products co-localise on ecdysone-responsive loci. Physical associations in the presence and absence of ecdysone redefine the ecdysone receptor as a dynamic complex whose activity may be altered by combinatorial interactions among subunits and ligand.
          (Yao et al., 1993)
          usp expression undergoes numerous and frequent changes during embryonic, larval and adult development.
          (Henrich et al., 1994)
          The usp product acts as an allosteric effector to enhance steroid binding by the EcR product. Under some conditions, DNA binding by EcR/usp product is highly steroid-dependent.
          (Hu et al., 1995)
          The svp product modulates usp product-based signalling both in vitro and in vivo. Overexpression of usp rescues the larva from the lethal effects of overexpression of svp.
          (Zelhof et al., 1995)
          Testing pairwise combinations of the hormone receptor superfamily demonstrates EcR and usp interact as a dimer.
          (Horner et al., 1995)
          The usp gene is essential for the correct spatial expression of Vm32E.
          (Cavaliere et al., 1995)
          Clonal analysis with usp mutations in adult flies reveals a range of imaginal disc phenotypes.
          (Sutherland and Kafatos, 1995)
          DNA-blotting assay has identified a high affinity ecdysone receptor binding site within the ng1 and ng2 coding sequence. EMSA assay demonstrates the 93bp 'ng element' is able to bind an EcR/usp heterodimer and usp alone.
          (D'Avino et al., 1995)
          dsRNA has been made from templates generated with primers directed against this gene. RNAi of usp reduces the primary dendrite outgrowth of ddaD and ddaE neurons, but causes only modest reduction of lateral branching and lateral branch outgrowth. RNAi also causes defects in muscle, alterations in the number of MD neurons, defects in dendrite morphogenesis and reproducible defects in da dendrite development.
          (Parrish et al., 2006)
          hide Gene Ontology: Function, Process & Cellular Component ( 24 )
          hide Molecular Function
          CV term
          Evidence
          References
          DNA binding
          non-traceable author statement
          (Swiss-Prot Project Members, 1991.2.1)
          ecdysteroid hormone receptor activity
          inferred from direct assay
          (Christianson et al., 1992)