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General Information
Symbol
Dmel\scs
Species
D. melanogaster
Name
special chromatin structure
Annotation Symbol
Feature Type
FlyBase ID
FBgn0015539
Gene Model Status
Stock Availability
Gene Summary
Contribute a Gene Snapshot for this gene.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (0 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Gene Model and Products
    Number of Transcripts
    0
    Number of Unique Polypeptides
    0
    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
    Sequence Ontology: Class of Gene
    Transcript Data
    Annotated Transcripts
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    Polypeptide Data
    Annotated Polypeptides
    Polypeptides with Identical Sequences

     

    Additional Polypeptide Data and Comments
    Reported size (kDa)
    Comments
    External Data
    Crossreferences
    Linkouts
    Sequences Consistent with the Gene Model
    Nucleotide / Polypeptide Records
      Mapped Features

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

      External Data
      Crossreferences
      Linkouts
      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
      Additional Descriptive Data
      Marker for
       
      Subcellular Localization
      CV Term
      Polypeptide Expression
      Additional Descriptive Data
      Marker for
       
      Subcellular Localization
      CV Term
      Evidence
      References
      Expression Deduced from Reporters
      High-Throughput Expression Data
      Associated Tools

      GBrowse - Visual display of RNA-Seq signals

      View Dmel\scs 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
      Alleles, Insertions, Transgenic Constructs, and Aberrations
      Classical and Insertion Alleles ( 0 )
      For All Classical and Insertion Alleles Show
       
      Other relevant insertions
      Transgenic Constructs ( 13 )
      For All Alleles Carried on Transgenic Constructs Show
      Transgenic constructs containing/affecting coding region of scs
      Transgenic constructs containing regulatory region of scs
      Aberrations (Deficiencies and Duplications) ( 0 )
      Inferred from experimentation ( 0 )
      Inferred from location ( 0 )
        Phenotypes
        For more details about a specific phenotype click on the relevant allele symbol.
        Phenotype manifest in
        Allele
        Orthologs
        Human Orthologs (via DIOPT v8.0)
        Homo sapiens (Human) (0)
        No records found.
        Model Organism Orthologs (via DIOPT v8.0)
        Mus musculus (laboratory mouse) (0)
        No records found.
        Rattus norvegicus (Norway rat) (0)
        No records found.
        Xenopus tropicalis (Western clawed frog) (0)
        No records found.
        Danio rerio (Zebrafish) (0)
        No records found.
        Caenorhabditis elegans (Nematode, roundworm) (0)
        No records found.
        Arabidopsis thaliana (thale-cress) (0)
        No records found.
        Saccharomyces cerevisiae (Brewer's yeast) (0)
        No records found.
        Schizosaccharomyces pombe (Fission yeast) (0)
        No records found.
        Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( None identified )
        No orthologies identified
        Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( None identified )
        No non-Drosophilid orthologies identified
        Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( None identified )
        No non-Dipteran orthologies identified
        Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
        No non-Insect Arthropod orthologies identified
        Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
        No non-Arthropod Metazoa orthologies identified
        Paralogs
        Paralogs (via DIOPT v8.0)
        Drosophila melanogaster (Fruit fly) (0)
        No records found.
        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 ( 0 )
          Human Ortholog
          Disease
          Evidence
          References
          Modifiers Based on Experimental Evidence ( 0 )
          Allele
          Disease
          Interaction
          References
          Disease Associations of Human Orthologs (via DIOPT v8.0 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?
          Functional Complementation Data
          Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
          Interactions
          Summary of Physical Interactions
          esyN Network Diagram
          Interactions Browser
          Summary of Genetic Interactions
          esyN Network Diagram
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          External Data
          Linkouts
          Pathways
          Signaling Pathways (FlyBase)
          Metabolic Pathways
          External Data
          Linkouts
          Genomic Location and Detailed Mapping Data
          Chromosome (arm)
          Recombination map
          Cytogenetic map
          Sequence location
          FlyBase Computed Cytological Location
          Cytogenetic map
          Evidence for location
          Experimentally Determined Cytological Location
          Cytogenetic map
          Notes
          References
          Experimentally Determined Recombination Data
          Location
          Left of (cM)
          Right of (cM)
          Notes
          Stocks and Reagents
          Stocks (4)
          Genomic Clones (0)
           
            cDNA Clones (0)
             

            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 sequenced
            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)
                  BDGP DGC clones
                    Other clones
                      RNAi and Array Information
                      Linkouts
                      Antibody Information
                      Laboratory Generated Antibodies
                       
                      Commercially Available Antibodies
                       
                      Other Information
                      Relationship to Other Genes
                      Source for database identify of
                      Source for database merge of
                      Additional comments
                      Other Comments

                      scs shows enhancer blocking activity. scs does not define the borders of a heat shock puff and does not block the propagation of altered chromatin states associated with puffing.

                      Pairs of scs insulators are able to block enhancer function.

                      The dwg gene product is a component of the scs chromatin domain boundary and can block enhancer-promoter interactions.

                      The long distance regulatory activity of the Mcp element can be enhanced by placing it in a mini-w transgene which is flanked by scs and scs'.

                      Xenopus oocyte assay demonstrates the scs and scs' insulator elements do not require chromosomal context to block enhancer-activated transcription. A single insulator element partially blocks enhancer-activated transcription indicating that each element operates independently rather than as a pair. Deletion analysis identifies a 220bp fragment that has full enhancer blocking activity. A time course of transcription shows the scs element blocks enhancer-activated transcription prior to complete chromatin assembly. The scs and scs' elements do not block site-specific recombination by Scer\FLP1. These data are most consistent with a model for insulator action in which direct interaction between the insulator and either the enhancer or promoter confers directionality to enhancer-activated transcription.

                      The full length and 0.9kb fragment of scs can block the interaction of defined eve stripe enhancers when positioned between the enhancer and target promoter.

                      Results suggest that scs may act as flexible regulatory element that modulates enhancer-promoter interactions within complex promoters and complex genetic loci. The insulator does not propagate changes in chromatin structure and may not be restricted to the functional isolation of neighbouring genetic loci.

                      The full length or 0.9kb fragment of scs is a chromatin insulator that prevents an enhancer located on one side of a boundary from acting on promoters of neighbouring genes located in the adjacent domain.

                      The scs and scs' boundary elements do not facilitate expression in a heterologous system, unlike SARs.

                      The 87A7 Hsp70B region is bordered on the proximal and distal sides by two special chromatin structures, scs and scs'. An enhancer blocking assay based on the w gene demonstrates that the two nuclease hypersensitive regions that define part of the special chromatin structure are essential for the blocking activity. The DNA sequence spanning the nuclease resistant core located between the two hypersensitive regions is dispensable.

                      Heat shock alters the distribution of Top2 in the 87A7 heat shock locus. scs and scs' are targets for Top2 localisation. A return to normal temperatures relocalises Top2.

                      The Hsp70Aa and Hsp70Ab loci are flanked by special chromatin structures, scs and scs'. Each structure is defined by a pair of nuclease hypersensitivity sites bordering a nuclease resistant core of 250-350bp in length. Both scs and scs' have properties that suggest they may correspond to the boundaries of the 87A7 chromomere.

                      scs and scs' are capable of establishing a domain of independent gene activity: w gene flanked by scs and scs' inserted into the genome by P element mediated transformation is isolated against both positive and negative position effects at most insertion sites. scs and scs' also have enhancer blocking activities: when inserted between a Yp1 enhancer and a heat shock promoter-Ecol\lacZ fusion little or no Ecol\lacZ expression is detected even though the promoter is fully heat shock inducible.

                      Origin and Etymology
                      Discoverer
                      Etymology
                      Identification
                      External Crossreferences and Linkouts ( 0 )
                      Synonyms and Secondary IDs (4)
                      Datasets (0)
                      Study focus (0)
                      Experimental Role
                      Project
                      Project Type
                      Title
                      References (99)