A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\l(1)sc

General Information
SymbolDmel\l(1)scSpeciesD. melanogaster
Namelethal of scuteAnnotation symbolCG3839
Feature typeprotein_coding_geneFlyBase IDFBgn0002561
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)XRecombination map1-0.0
Cytogenetic map1B1-1B1Sequence locationX:303,756..304,852 [+]
Map ( GBrowse ) detailed view
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Automatically generated summary

See sections below for more information
The gene lethal of scute is referred to in FlyBase by the symbol l(1)sc (CG3839, FBgn0002561). It has the cytological map location 1B1. Its sequence location is X:303756..304852. Its molecular function is described as: specific RNA polymerase II transcription factor activity; transcription factor activity; DNA binding. It is involved in the biological processes: regulation of transcription from RNA polymerase II promoter; central nervous system development; peripheral nervous system development; neuroblast fate determination; ventral cord development; myoblast cell fate determination. 17 alleles are reported. The phenotypes of these alleles are annotated with 12 unique terms, many of which group under: peripheral nervous system; primordium; nervous system; organ system; germ layer; portion of tissue; adult segment; adult mesothoracic segment; antennal segment; ventral nerve cord primordium. 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
l(1)sc: lethal at scute
Deficiency from which existence of l(1)sc inferred, i.e., In(1)sc4Lsc9R, embryonic lethal. Volume of embryonic ventral nerve cord slightly reduced; posterior commisures thinner than in wild type; longitudinal connectives virtually lacking. Concomitant deletions for scα or scα and ac cause more severe CNS disruptions, although by themselves these deletions have no observable CNS effects; simultaneous deletion of the sc/ region also enchances the CNS disruptions (Jimenez and Campos-Ortega). Transiently expressed at periphery of syncytial blastoderm; late blastoderm shows paired dorsolateral and ventrolateral longitudinal stripes of expression, the latter being coincident with the presumptive neurogenic ectoderm. During germ-band expression, l(1)sc expression seen in many cell clusters over most of the ectoderm; segmental distribution becomes apparent both internally and externally. l(1)sc expression seen in many foci in the head region and in the posterior midgut rudiment (Romani, Campuzano, and Modolell, 1987, EMBO J. 6: 2085-92; Cabrera, Martinez-Arias, and Bate, 1987, Cell 50: 425-33). Little if any expression in later stages, except in the central nervous system (Romani, Campuzano, Macagno, and Modolell, 1989, Genes Dev. 3: 997-1007).
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FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
1B1-1B1  
Limits computationally determined from genome sequence between P{EP}CG17896EP1320&P{EP}EP1398 and P{EP}svrEP356&P{EP}argEP452  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location
1-0.0
 
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
hide Gene Model & Products
Please see the GBrowse view of Dmel\l(1)sc for information on other features
detailed view FBtr0070074 FBtr0273443 FBtr0273442 FBpp0070073 FBti0053791 FBti0078178
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
FBtr0070074
  1097
  257
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
FBpp0070073  
29.0  
257  
6.34  
Additional Polypeptide Data & Comments
Reported size (kD)
258 (aa); 29 (kD)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
  • T00003
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    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
    protein binding site
    l(1)sc-protein_bind-1
    X:303,123..303,143
    bound_moiety=HLHm5-XP
    evidence=experimental
    bound_moiety=E(spl)-XP
    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
     embryonic stage
     embryonic stage
     posterior embryonic/larval midgut
     embryonic stage
     procephalic segment
     embryonic stage
     procephalic neuroblasts
     embryonic stage
     optic lobe
     embryonic stage
     procephalic neurogenic region
     embryonic stage
     embryonic peripheral nervous system
     embryonic stage | early
     embryonic stage
     ventral midline
     embryonic stage
     posterior embryonic/larval midgut
     embryonic stage
     epidermoblast
     embryonic stage
     Malpighian tubule
     embryonic stage
     labral segment
     embryonic stage
     embryonic stomatogastric nervous system
     embryonic stage | stage 11,12
     embryonic ganglion mother cell
     embryonic stage
     neurogenic region
     embryonic stage
     epidermoblast
     embryonic stage
     neuroblast
     embryonic stage
     cephalic furrow
     embryonic stage
     stomodeum
     embryonic stage
     neuroblast
     embryonic stage
     larval optic lobe | presumptive
     embryonic stage
     central nervous system
     embryonic stage
     ectoderm
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
       embryonic stage
       epidermoblast
       embryonic stage | stage 8-11
       procephalic neurectoderm | restricted
       embryonic stage | stage 8-11
       procephalic neuroblast | subset
       embryonic stage
       epidermoblast
       embryonic stage | stage 9-11
       deuterocerebral neuroblast | subset
       embryonic stage | stage >8
       neuroblast
       embryonic stage | stage 9-11
       tritocerebral neuroblast | subset
       embryonic stage | stage 9-11
       protocerebral neuroblast | subset
      Marker for
        Subcellular Localization
        CV Term
        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
        FlyExpress - Embryonic expression images (BDGP data)
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        Other Phenotypes
        Allele
        Phenotype manifest in
        Allele
        macrochaeta & scutellum, with Scer\GAL4455.2
        macrochaeta & abdominal sternite 1, with Scer\GAL4sca-537.4
        macrochaeta & abdominal sternite 2, with Scer\GAL4sca-537.4
        macrochaeta & abdominal sternite 3, with Scer\GAL4sca-537.4
        macrochaeta & abdominal sternite 4, with Scer\GAL4sca-537.4
        macrochaeta & abdominal sternite 5, with Scer\GAL4sca-537.4
        macrochaeta & abdominal sternite 6, with Scer\GAL4sca-537.4
        macrochaeta & pronotum, with Scer\GAL4h-540.3
        macrochaeta & scutum, with Scer\GAL4h-540.3
        macrochaeta & metathoracic laterotergite, with Scer\GAL4h-540.3
        macrochaeta & mesothoracic laterotergite, with Scer\GAL4h-540.3
        microchaeta & pronotum, with Scer\GAL4h-540.3
        microchaeta & scutum, with Scer\GAL4h-540.3
        microchaeta & metathoracic laterotergite, with Scer\GAL4h-540.3
        microchaeta & mesothoracic laterotergite, with Scer\GAL4h-540.3
        macrochaeta & wing, with Scer\GAL4564.2
        scutellum & microchaeta, with Scer\GAL4ptc-559.1
        sensory mother cell & dorsal mesothoracic disc, with Scer\GAL4ap-md544
        hide Classical Alleles ( 1 )
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        Allele of l(1)scClassMutagenStocksKnown lesion
        l(1)scunspecified
          0 --
          hide Alleles Carried on Transgenic Constructs ( 16 )
          For All Alleles Carried on Transgenic Constructs Show

          Allele of l(1)scClassMutagenStocksKnown lesion
          l(1)scAct5C.PO0 Yes
          l(1)scGD162792 Yes
          l(1)scGD43682 Yes
          l(1)scScer\UAS.cBa0 Yes
          l(1)scScer\UAS.cCa0 Yes
          l(1)scScer\UAS.cHa0 Yes
          l(1)scScer\UAS.cHb0 Yes
          l(1)scScer\UAS.cPa0 Yes
          l(1)scYA.Scer\UAS0 Yes
          l(1)schb.PP0 Yes
          l(1)scΔB.Scer\UAS0 Yes
          l(1)scΔC1.Scer\UAS0 Yes
          l(1)scΔC2.Scer\UAS0 Yes
          l(1)scΔHLH.Scer\UAS0 Yes
          l(1)scΔN.Scer\UAS0 Yes
          l(1)scΔNΔC2.Scer\UAS0 Yes
          hide Aneuploid Aberrations
          Useful deficiency
          Disrupted in
          Duplicated in
          Not disrupted in
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          Transgenic Constructs
          Type of construct
          Name
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          characterization construct
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          Type of insertions
          Name
          Expression data
          hide Related Comments
          Please look at the allele reports for the complete phenotype data
          Deficiency from which existence of l(1)sc inferred, i.e., In(1)sc4Lsc9R, embryonic lethal. Volume of embryonic ventral nerve cord slightly reduced; posterior commissures thinner than in wild type; longitudinal connectives virtually lacking. Concomitant deletions for scα or scα and ac cause more severe CNS disruptions, although by themselves these deletions have no observable CNS effects; simultaneous deletion of the scγ region also enchances the CNS disruptions (Jimenez and Campos-Ortega, 1987). Transiently expressed at periphery of syncytial blastoderm; late blastoderm shows paired dorsolateral and ventrolateral longitudinal stripes of expression, the latter being coincident with the presumptive neurogenic ectoderm. During germ-band expression, l(1)sc expression seen in many cell clusters over most of the ectoderm; segmental distribution becomes apparent both internally and externally. l(1)sc expression seen in many foci in the head region and in the posterior midgut rudiment (Romani, Campuzano and Modolell, 1987; Cabrera, Martinez-Arias and Bate, 1987). Little if any expression in later stages, except in the central nervous system (Romani, Campuzano, Macagno and Modolell, 1989).
           
          Deficiencies for most regions of the achaete-scute complex are hemizygous and homozygous viable; however, deficiency for l(1)sc is lethal.
          Transcripts of ac, sc and l(1)sc accumulate at the blastoderm stage in periodic patterns within the neuroectoderm. Subsequent expression is in partially overlapping patterns that correlate with the segregation of the neuroblasts.
          The patterns of expression of ac, sc and l(1)sc are complex and evolve rapidly, affecting most if not all the known neurogenic regions. Gene expression precedes and is concomitant with the histological appearance of precursors of neural cells. The achaete-scute complex plays a role in determination and early differentiation of embryonic neural cells.
          Sequence analysis reveals that ac, sc and l(1)sc transcription units share highly conserved acidic and basic domains in their protein coding regions. The basic domain of the ac, sc and l(1)sc proteins show similarity to the vertebrate myc and MyoD proteins.
          Ectopic expression of l(1)sc has no effect on sex determination.
          Wild-type embryos show the protein is present in the developing neuroblasts, whereas the corresponding RNA is found in the neural and epidermal lineages. A study of the protein product distribution in mutants and wild type demonstrated that mutants cause neural hyperplasia in embryos.
          A comparison of RNA and protein patterns suggests post-transcriptional regulation of l(1)sc. Protein accumulates in only a subset of the cells that express the RNA and these go on to become neuroblasts. The deployment of l(1)sc protein expression is one of the causal factors that assigns specific fates to the neuroblasts and a basis for the mechanism of lateral inhibition.
          The function of ac, sc and l(1)sc are required for the normal development of the neuroblasts and absence of the genes causes neuroectodermal cells to enter the epidermal pathway of development.
          DNA sequence analysis reveals four E box binding sites, for the binding of hetero-oligomeric complexes composed of da or AS-C proteins, in the first 877 bp of the ac upstream region. Electrophoretic mobility shift assays demonstrate that the emc protein can specifically antagonise DNA binding of the da/AS-C complexes in vitro in a dose-dependent manner, h and E(spl) proteins fail to exhibit this inhibitory effect.
          The expression of l(1)sc protein before and during neuroblast segregation in the embryo has been studied.
          In vitro DNA binding assays using gel retardation to an ac promoter region and hb zygotic promoter region target sequence demonstrates that da protein elicits a weak homodimeric binding and da/ac or da/sc heterodimers bind tightly. Single copy yeast promoters under the control of the GAL4 promoter were used to test whether ac, sc and da proteins could activate transcription of a Ecol\lacZ reporter gene in the yeast assay system, the l(1)sc gene does not induce Ecol\lacZ activity. Results suggest that da/l(1)sc heterodimers can function as transcriptional activators in direct proportion to their DNA-binding affinities.
          Ectopic expression shows that l(1)sc displays weak but significant feminizing activity.
          Analysis of deficiencies revealed that l(1)sc affects the level but not the spatial pattern of ac expression.
          The l(1)sc gene has been cloned. A cluster of E boxes, upstream of the transcribed region, suggest regulation by helix-loop-helix gene products.
          The proneural function of l(1)sc is independent of ac, sc and ase. Deletion analysis of l(1)sc demonstrates the basic helix-loop-helix domain is necessary and sufficient to mediate the proneural function of l(1)sc to activate neurogenic genes, E(spl), Dl and HLHm5, and to allow lateral inhibition.
          The gene products of ac, sc and l(1)sc together with vnd act synergistically to specify the neuroectodermal E(spl) and HLHm5 expression.
          vnd controls neuroblast formation, in part, through its regulation of the proneural genes of the ac-sc complex. vnd controls proneural gene expression at two distinct steps during neuroblast formation through separable regulatory regions.
          emc forms heterodimers with the ac, sc, l(1)sc, and da products. emc inhibits DNA-binding of ac, sc and l(1)sc/da heterodimers and da homodimers.
          Neurogenic genes principally regulate l(1)sc expression at the transcriptional level without affecting the domains of proneural gene expression. N and neur are required for the establishment of the mesectodermal fate, Dl and members of the E(spl) complex may be involved in the same process.
          DNaseI footprinting analysis of bacterially expressed da and l(1)sc demonstrates that the gene products can bind as heterodimers to different E-box sequence upstream of the ac gene.
          Proneural gene products (ac, da and l(1)sc) activate transcription of Dl in the neuroectoderm by binding to specific sites within its promoter. This transcriptional activation enhances lateral inhibition and helps ensure that cells in the vicinity of prospective neuroblasts will themselves become epidermoblasts.
          Overexpression of da using the GAL4 system, but not the ectopic expression of the AS-C genes l(1)sc or sc, leads to the formation of ectopic neural cells in embryonic tissue without neural competence. This effect os strongly enhanced by coexpressing l(1)sc or sc. Expression of da and/or l(1)sc is not sufficient to overcome the lateral inhibition in the analgen of the embryonic nervous system.
          Ectopic expression does not affect the viability of either sex, but it does rescue the female lethality caused by ectopic expression of h.
          Giant fibre growth studies in cells where l(1)sc has been ablated suggest l(1)sc is normally required to repel the growth cone of the giant fibre.
          Loss of function and over-expression phenotypes indicate a role for l(1)sc in the segregation of muscle progenitors and the formation of the muscle pattern.
          ac-sc mutants are epistatic over E(spl)-C mutants.
          The expression pattern of proneural genes of the AS-C and neurogenic genes of the E(spl)-C are examined in the procephlon and a map of the cells is constructed.
          The bHLH domains of the gene products encoded by the E(spl)-C and AS-C differ in their ability to form homo- and/or heterodimers. The interactions established through the bHLH link the products of the two complexes in a single interaction network which may function to ensure that a given cell retains the capacity to choose between epidermoblast and neuroblast fates until the cell becomes definitively determined.
          The function of l(1)sc is not interchangable with that of ac or sc within the MP2, specification of MP2 is similar in embryos lacking ac/sc compared with those lacking ac/sc plus ectopic l(1)sc expression.
          All proneural proteins are similarly able to promote the segregation of a neural precursor at the MP2 neuroblast position but show distinct capacities in its specification.
          Analysis of the function of l(1)sc.
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          CV term
          References
          inferred from electronic annotation with InterPro:IPR015660
          inferred from sequence or structural similarity with UniProtKB:P50553
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          inferred from sequence or structural similarity with UniProtKB:P50553
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