A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\Ssrp

General Information
SymbolDmel\SsrpSpeciesD. melanogaster
NameStructure specific recognition proteinAnnotation symbolCG4817
Feature typeprotein_coding_geneFlyBase IDFBgn0010278
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)2RRecombination map
Cytogenetic map60A2-60A2Sequence location2R:19,693,884..19,696,518 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene Structure specific recognition protein is referred to in FlyBase by the symbol Ssrp (CG4817, FBgn0010278). It has the cytological map location 60A2. Its sequence location is 2R:19693884..19696518. Its molecular function is described as: single-stranded DNA binding; single-stranded RNA binding; protein binding; DNA secondary structure binding. It is involved in the biological processes: regulation of chromatin assembly or disassembly; regulation of transcription, DNA-dependent. 2 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide.
External Summaries

hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
60A2-60A2  
Limits computationally determined from genome sequence between P{EP}eglEP938 and P{lacW}eIF6k13214  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
60A1-60A4
 
(Bruhn, 1992.9.16)
60A1-60A4
(determined by in situ hybridisation)  
(Hsu et al., 1993)
60A1-60A4
(determined by in situ hybridisation)  
(Bruhn et al., 1993)
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
hide Gene Model & Products
Please see the GBrowse view of Dmel\Ssrp for information on other features
detailed view FBtr0072123 FBtr0072243 FBtr0072242 FBtr0072124 FBpp0072032 FBpp0072152 FBpp0072151 FBpp0072033 FBti0100036
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
Ssrp-RA
FBtr0072242
 NM_079106
  2498
  723
Additional Transcript Data & Comments
Reported size (kB)
2.6 (northern blot)
(Hsu et al., 1993)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
Ssrp-PA  
FBpp0072151  
81.5  
723  
5.31  
  NP_523830
  AAF47064
Additional Polypeptide Data & Comments
Reported size (kD)
723 (aa); 81 (kD)
(Hsu et al., 1993, Bruhn et al., 1993)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
High mobility group box, HMG1/HMG2 (IPR000910)
Structure-specific recognition protein (IPR000969)
High mobility group box, HMG (IPR009071)
TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
•
  • T01848
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA390604
 
AA540678
 
AA696623
 
AA802337
 
AA802829
 
AE003462
AAF47064
 
AI534034
 
AW944457
 
BF490475
 
BF500709
 
BG634972
 
BG640734
 
BI169603
 
BI238760
 
BI351600
 
BI355848
 
BI356671
 
BP544470
 
BP544471
 
BP545863
 
BP558725
 
BP558726
 
BT004831
AAO45187
 
CO181709
 
CO284192
 
CO319705
 
EC198916
 
EC199671
 
EC200207
 
EC204953
 
EC211489
 
EC215867
 
EC222911
 
L08825
AAA28914
 
X68408
CAA48471
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (BDGP Project Members, 2000-)
    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
    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 | female
     ovary
    (Hsu et al., 1993)
     oogenesis stage,adult stage
     nurse cell
    (Hsu et al., 1993)
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        nucleus nucleolus
        (Hsu et al., 1993)
        hide Microarray Data
        Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)
        Untitled Document detailed view FBtr0072123 FBtr0072243 FBtr0072242 FBtr0072124
        AI534034
        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
        Phenotype manifest in
        Allele
        hide Classical Alleles ( 0 )
        For All Classical Alleles Show

        Allele of SsrpClassMutagenStocksKnown lesion
        hide Alleles Carried on Transgenic Constructs ( 2 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of SsrpClassMutagenStocksKnown lesion
        SsrpGD127952 Yes
        SsrpdsRNA.cHa0 Yes
        hide Aneuploid Aberrations
        Useful deficiency
         
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        UAS construct
        P{GD12795}
        NA
        Insertions
        Type of insertions
        Name
        Expression data
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        Drosophila Ssrp identified by sequence similarity to human Ssrp gene.
        (Bruhn et al., 1993)
        cDNA encoding a developmentally regulated high-mobility-group (HMG) box-containing protein was isolated: the encoded protein binds single stranded DNA and RNA, rather than the expected structured DNA.
        (Hsu et al., 1993)
        hide Gene Ontology: Function, Process & Cellular Component ( 9 )
        hide Molecular Function
        CV term
        Evidence
        References
        DNA secondary structure binding
        inferred from sequence or structural similarity with UniProtKB:Q08945
        (FlyBase, 1992-)
        protein binding
        inferred from physical interaction with FLYBASE:Trl; FB:FBgn0013263
        (Shimojima et al., 2003)
        single-stranded DNA binding
        non-traceable author statement
        (Hsu, 1993)
        inferred from sequence or structural similarity with UniProtKB:Q08945
        (FlyBase, 1992-)
        non-traceable author statement
        (Swiss-Prot Project Members, 1994.10.1)
        single-stranded RNA binding
        non-traceable author statement
        (Hsu, 1993)
        non-traceable author statement
        (Swiss-Prot Project Members, 1994.10.1)
        hide Biological Process
        CV term
        Evidence
        References
        regulation of chromatin assembly or disassembly
        inferred from mutant phenotype
        (Shimojima et al., 2003)
        regulation of transcription, DNA-dependent
        inferred from electronic annotation with InterPro:IPR000910
        (FlyBase Curators et al., 2004-)
        hide Cellular Component
        CV term
        Evidence
        References
        FACT complex
        traceable author statement
        (Lehmann, 2004)
        nucleolus
        non-traceable author statement
        (Hsu, 1993)
        non-traceable author statement
        (Swiss-Prot Project Members, 1994.10.1)
        nucleus
        inferred from sequence or structural similarity with UniProtKB:Q08945
        (FlyBase, 1992-)
        non-traceable author statement
        (Swiss-Prot Project Members, 1994.10.1)
        hide Sequence Ontology: Class of Gene
        protein_coding_gene
         
        nuclear_gene
         
        hide Interactions & Pathways
        hide Summary of Genetic Interactions
        Interacts with
        Please look at the allele data for full details of the genetic interactions
        Ssrp allele
        Gene
        References
        hide External Data
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        hide Orthologs
        Genome-wide drosophilid orthologs
        Curated drosophilid orthologs
         
        Linkouts
        InParanoid orthologs - Eukaryotic orthologs
        •
        hide Functional Complementation between Species
        hide Inter-Species Misexpression Data
        Produces phenotype in
        Produces NO phenotype in
        hide Stocks & Reagents
        hide Stocks Listed in FlyBase ( 2 )
        VDRC
        v44343
        w1118; P{GD12795}v44343
        v44344
        w1118; P{GD12795}v44344
        hide Genomic Clones ( 2 )
        hide cDNA Clones ( 18 )
        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
        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        hide RNAi & Array Information
        Affy Oligo
        Linkouts
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
        •
        hide Antibody Information
        polyclonal
        (Hsu et al., 1993)
        hide Other Information
        hide Discoverer
        hide Etymology
        hide Identification
        hide Position Effect Variegation Data
        hide Relationship to Other Genes
        Source for database identity of
        Source for identity of: Ssrp CG4817
        (Zhang, 1999.11)
        Source for database merge of
        Additional comments
        hide Comments About Role
        The FACT complex (FAcilitates Chromatin Transcription) containing dre4 and Ssrp has a crucial role in the modulation of chromatin structure for the regulation of gene expression.
        (Shimojima et al., 2003)
        hide Comments About Molecular Function
        hide Other Comments
        hide External Crossreferences & Linkouts
        Sequence Crossreferences
        RefSeq (Transcripts)
        •
        RefSeq (Proteins)
        •
        DDBJ / EMBL / GenBank
        •
        UniProtKB/Swiss-Prot
        •
        Other Crossreferences
        InterPro domains - A database of protein families, domains, and functional sites
        •
        High mobility group box, HMG1/HMG2 (IPR000910)
        Structure-specific recognition protein (IPR000969)
        High mobility group box, HMG (IPR009071)
        TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles
        •
        • T01848
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        DEDB - Drosophila exon database: splicing graphs
        •
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
        •
        InParanoid orthologs - Eukaryotic orthologs
        •
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        •
        PANTHER - Protein classification by function, families, and pathways
        •
        University of Chicago Dev. Expression
        •
        hide Synonyms & Secondary IDs ( 10 )
        Reported As
        Symbol Synonym
        Cf5
         
        CG4817
         
        dSSRP
        (Wisniewski et al., 1999)
        DssRP
        (Hsu et al., 1993)
        dSSRP1
        (Lehmann, 2004, Shimojima et al., 2003, Nakayama et al., 2007)
        SSRP
        (Hsu, 1993)
        Ssrp
        (Sessa and Bianchi, 2007)
        SSRP1
        (Polo, 2006, Saunders et al., 2003, Bruhn, 1992.9.16, Soullier et al., 1999, Kelley et al., 1999)
        Name Synonym
        Chorion factor
         
        Structure specific recognition protein
         
        Secondary FlyBase IDs
        • FBgn0005644
        hide References ( 23 )
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        List References by type
        hide Recent research papers ( 2 )
        Nakayama et al., 2007, Genes Dev. 21(5): 552--561
        Drosophila GAGA factor directs histone H3.3 replacement that prevents the heterochromatin spreading. [FBrf0195269]
        Sessa and Bianchi, 2007, Gene 387(1-2): 133--140
        The evolution of High Mobility Group Box (HMGB) chromatin proteins in multicellular animals. [FBrf0194706]
        Show all research papers ...
        hide Recent reviews ( 1 )
        Polo, 2006, Curr. Opin. Genet. Dev. 16(2): 104--111
        [title not yet available] [FBrf0191591]
        Show all reviews ...