A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\SC35

General Information
SymbolDmel\SC35SpeciesD. melanogaster
NameSC35Annotation symbolCG5442
Feature typeprotein_coding_geneFlyBase IDFBgn0040286
Created / Updated2003-12-22/2003-12-22
Genomic Location
Chromosome (arm)2LRecombination map
Cytogenetic map33E4-33E4Sequence location2L:12,431,856..12,434,665 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
This gene is referred to in FlyBase by the symbol SC35 (CG5442, FBgn0040286). It has the cytological map location 33E4. Its sequence location is 2L:12431856..12434665. Its molecular function is described as: mRNA binding; protein binding; nucleic acid binding; nucleotide binding. It is involved in the biological processes: nuclear mRNA splicing, via spliceosome; mRNA splice site selection; regulation of alternative nuclear mRNA splicing, via spliceosome. 6 alleles are reported. No phenotypic data is available. It has 2 annotated transcripts and 2 annotated polypeptides.

hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
33E4-33E4  
Limits computationally determined from genome sequence between P{PZ}Rab608323 and P{EP}ElfEP476&P{EP}bunEP488  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
33E5-33E7
 
(Bourbon, 2000.2.9)
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\SC35 for information on other features
detailed view FBtr0080367 FBtr0080387 FBtr0089899 FBtr0080369 FBtr0089898 FBpp0079949 FBpp0079968 FBpp0088837 FBpp0088838 FBpp0079951 FBti0075596 FBti0018660 FBti0040072 FBti0029424 FBti0023102 FBti0012448 FBti0057710 FBti0055583 FBti0007606 FBti0026061 FBti0009228 FBti0055965 FBti0099793 FBti0036391 FBti0011014 FBti0045210 FBti0064921 FBti0064897 FBti0029332
Comments on Gene Model
EST data support existence of multiple transcripts due to variable use of 5' exons
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
SC35-RA
FBtr0089898
 NM_205967
  1002
  112
SC35-RB
FBtr0089899
 NM_144355
  1094
  195
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
SC35-PA  
FBpp0088837  
12.1  
112  
12.94  
  NP_995689
  AAS64684
SC35-PB  
FBpp0088838  
21.4  
195  
12.25  
  NP_652612
  AAF53192
Additional Polypeptide Data & Comments
Reported size (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
•
RNA recognition motif, RNP-1 (IPR000504)
Nucleotide-binding, alpha-beta plait (IPR012677)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA438895
 
AA951762
 
AE003636
AAF53192
 
AE003636
AAS64684
 
AF232775
AAF43415
 
AI257126
 
AI533872
 
AI946437
 
AW943136
 
AY069584
AAL39729
 
BF505132
 
BH214628
 
BI163371
 
BI164304
 
BI167083
 
BI228226
 
BI229044
 
BI229085
 
BI229440
 
BI230215
 
BI232441
 
BI235292
 
BI238888
 
BI240004
 
BI355246
 
BI355263
 
BI357192
 
BI370496
 
BI482181
 
BI482250
 
BI485104
 
BI486651
 
BI579224
 
BI580691
 
BI632215
 
BI632446
 
BI632796
 
BI632904
 
BI633676
 
BI635262
 
BI638461
 
BI640670
 
BP553363
 
CK445233
 
CL705934
 
CO155022
 
CO185522
 
CO188566
 
CO264305
 
CO283624
 
CO286531
 
CO344072
 
EC057814
 
EC087296
 
EC195150
 
EC217877
 
EC221280
 
EC221676
 
EC228643
 
EC229684
 
EC232972
 
EC260665
 
EC265636
 
EL871525
 
 
UniProtKB/Swiss-Prot
    UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (Oliver, 2001.8.16)
    (BDGP Project Members, 2000-, Allemand et al., 2001, Allemand et al., 2002)
    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
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      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)
        •
        Show all FlyExpress processed images for SC35
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        viable
        Sterility
        Allele
        fertile
        Phenotype manifest in
        Allele
        hide Classical Alleles ( 2 )
        For All Classical Alleles Show

        Allele of SC35ClassMutagenStocksKnown lesion
        SC35EY073911 --
        SC35KG029861 --
        hide Alleles Carried on Transgenic Constructs ( 4 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of SC35ClassMutagenStocksKnown lesion
        SC35GD116541 Yes
        SC35T:Avic\GFP-EGFP0 Yes
        SC35ΔRRM.T:Avic\GFP-EGFP0 Yes
        SC35ΔRS.T:Avic\GFP-EGFP0 Yes
        hide Aneuploid Aberrations
        Useful deficiency
         
        Useful duplication
         
        Disrupted in
        (Ryder, 2004.4.26)
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        UAS construct
        P{GD11654}
        NA
        Insertions
        Type of insertions
        Name
        Expression data
        miscellaneous insertions
        P{SUPor-P}SC35KG02986
        NA
        insertion of mobile activating element
        P{EPgy2}SC35EY07391
        NA
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        hide Gene Ontology: Function, Process & Cellular Component ( 12 )
        hide Molecular Function
        CV term
        Evidence
        References
        mRNA binding
        inferred from sequence or structural similarity
        (Lasko, 2000)
        nucleic acid binding
        inferred from electronic annotation with InterPro:IPR000504
        (FlyBase Curators et al., 2004-)
        nucleotide binding
        inferred from electronic annotation with InterPro:IPR012677
        (FlyBase Curators et al., 2004-)
        protein binding
        inferred from physical interaction with FLYBASE:Trn-SR; FB:FBgn0031456
        (Allemand et al., 2002)
        hide Biological Process
        CV term
        Evidence
        References
        mRNA splice site selection
        inferred from sequence or structural similarity with NCBI_NP:035488
        (Mount and Salz, 2000)
        nuclear mRNA splicing, via spliceosome
        non-traceable author statement
        (Bourbon, 2000.2.9)
        inferred from sequence or structural similarity with NCBI_NP:035488
        (Mount and Salz, 2000)
        regulation of alternative nuclear mRNA splicing, via spliceosome
        inferred from mutant phenotype
        (Park et al., 2004)
        hide Cellular Component
        CV term
        Evidence
        References
        chromatin
        inferred from direct assay
        (Prasanth et al., 2000)
        nuclear speck
        inferred from direct assay
        (Prasanth et al., 2000)
        nucleus
        inferred from direct assay
        (Allemand et al., 2002)
        inferred by curator from GO:0000381
        (Park et al., 2004)
        NOT
        omega speckle
        inferred from direct assay
        (Prasanth et al., 2000)
        spliceosome
        non-traceable author statement
        (Bourbon, 2000.2.9)
        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
        SC35 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 ( 3 )
        VDRC
        v40590
        w1118; P{GD11654}v40590
        Bloomington
        20169
        y1 w67c23; P{EPgy2}SC35EY07391
        12904
        y1 w67c23; P{SUPor-P}SC35KG02986
        hide Genomic Clones ( 2 )
        hide cDNA Clones ( 45 )
        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
        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 database merge of
        Source for merge of: SC35 CG5442
        (Whitfield, 2000.5.9)
        Additional comments
        hide Comments About Role
        hide Comments About Molecular Function
        hide Other Comments
        hide External Crossreferences & Linkouts
        Sequence Crossreferences
        RefSeq (Transcripts)
        •
        RefSeq (Proteins)
        •
        DDBJ / EMBL / GenBank
        •
        UniProtKB/TrEMBL
        •
        Other Crossreferences
        InterPro domains - A database of protein families, domains, and functional sites
        •
        RNA recognition motif, RNP-1 (IPR000504)
        Nucleotide-binding, alpha-beta plait (IPR012677)
        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
        •
        FlyExpress - Embryonic expression images (BDGP data)
        •
        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
        •