A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\Dcr-1

General Information
SymbolDmel\Dcr-1SpeciesD. melanogaster
NameDicer-1Annotation symbolCG4792
Feature typeprotein_coding_geneFlyBase IDFBgn0039016
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)3RRecombination map
Cytogenetic map94C4-94C4Sequence location3R:18,559,727..18,566,752 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene Dicer-1 is referred to in FlyBase by the symbol Dcr-1 (CG4792, FBgn0039016). It has the cytological map location 94C4. Its sequence location is 3R:18559727..18566752. Its molecular function is described as: double-stranded RNA binding; bidentate ribonuclease III activity; protein binding; ATP binding; helicase activity. It is involved in the biological processes: RNA interference, production of siRNA; RNA interference; gene silencing by miRNA; gene silencing by miRNA, production of miRNAs; germ-line stem cell division; pre-microRNA processing; RNA interference, siRNA loading onto RISC; pole cell formation; mitotic cell cycle, embryonic; segment polarity determination. 16 alleles are reported. The phenotypes of these alleles are annotated with: oocyte; ovariole; germline stem cell; pole cell. It has one annotated transcript and one annotated polypeptide.

External Summaries

hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
94C4-94C4  
Limits computationally determined from genome sequence between P{lacW}GclmL0580 and P{EP}hhEP3521  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
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\Dcr-1 for information on other features
detailed view FBtr0113268 FBtr0113267 FBtr0113328 FBtr0084325 FBtr0084324 FBtr0084308 FBtr0084323 FBpp0083718 FBpp0083717 FBpp0083701 FBti0042953
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
Dcr-1-RA
FBtr0084324
 NM_079729
  6854
  2249
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
Dcr-1-PA  
FBpp0083717  
255.3  
2249  
5.47  
  NP_524453
  AAF56056
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
•
Ribonuclease III (IPR000999)
Double-stranded RNA binding (IPR001159)
DNA/RNA helicase, C-terminal (IPR001650)
Argonaute and Dicer protein, PAZ (IPR003100)
Protein of unknown function DUF283 (IPR005034)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA803140
 
AC009846
 
AE003740
AAF56056
 
AI530872
 
AW944193
 
AX287266
CAD12300
 
AY050230
AAK84929
 
BG637566
 
CO303120
 
CO303631
 
CS456213
CAL91821
 
DQ398885
ABD61601
 
DQ398886
ABD61602
 
DQ398887
ABD61603
 
DQ398888
ABD61604
 
DQ398889
ABD61605
 
DQ398890
ABD61606
 
DQ398891
ABD61607
 
DQ398892
ABD61608
 
EC203082
 
EC248895
 
GM10303
 
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
Maps to
(Bernstein et al., 2001)
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
point mutation
Dcr-1[Q1147X]
3R:18,563,262..18,563,262
comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change.
evidence=experimental
na_change=C18563262T
pr_change=Q1147@|Dcr-1-PA
reported_pr_change=Q1147@
(Lee et al., 2004)
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 Microarray Data
      Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)
      Untitled Document detailed view FBtr0113268 FBtr0113267 FBtr0113328 FBtr0084325 FBtr0084324 FBtr0084308 FBtr0084323
      AI404393
      hide External Data & Images
      Linkouts
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      •
      GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
      •
      hide Alleles & Phenotypes
      hide Summary of Allele Phenotypes
      Lethality
      Allele
      lethal | recessive
      Other Phenotypes
      Allele
      suppressor of variegation, with P{T1}T190-177
      suppressor of variegation, with P{T1(-FRT)}T190-177
      mitotic cell cycle defective | embryonic stage
      Phenotype manifest in
      Allele
      oocyte
      ovariole | germ-line clone
      germline stem cell | germ-line clone
      pole cell | germ-line clone | maternal effect
      hide Classical Alleles ( 2 )
      For All Classical Alleles Show

      Allele of Dcr-1ClassMutagenStocksKnown lesion
      Dcr-1Q1147X0 Yes
      Dcr-1d102
        		0 --
        hide Alleles Carried on Transgenic Constructs ( 14 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of Dcr-1ClassMutagenStocksKnown lesion
        Dcr-1GD114292 Yes
        Dcr-1MtnA.T:Zzzz\FLAG0 Yes
        Dcr-1Scer\UAS.cDa0 Yes
        Dcr-1T:Uuuu\T70 Yes
        Dcr-1dsRNA.5912-67370 Yes
        Dcr-1dsRNA.cBa0 Yes
        Dcr-1dsRNA.cDa0 Yes
        Dcr-1dsRNA.cFa0 Yes
        Dcr-1dsRNA.cJa0 Yes
        Dcr-1dsRNA.cJb0 Yes
        Dcr-1dsRNA.cLa0 Yes
        Dcr-1dsRNA.cOa0 Yes
        Dcr-1dsRNA.cRa0 Yes
        Dcr-1dsRNA.cSa0 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{GD11429}
        NA
        P{UAS-Dcr-1.D}
        NA
        Insertions
        Type of insertions
        Name
        Expression data
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        hide Gene Ontology: Function, Process & Cellular Component ( 18 )
        hide Molecular Function
        CV term
        Evidence
        References
        ATP binding
        inferred from electronic annotation with InterPro:IPR001650
        (FlyBase Curators et al., 2004-)
        bidentate ribonuclease III activity
        inferred from direct assay
        (Bernstein et al., 2001)
        double-stranded RNA binding
        inferred from sequence or structural similarity
        (Lasko, 2000)
        inferred from electronic annotation with InterPro:IPR001159
        (FlyBase Curators et al., 2004-)
        helicase activity
        inferred from electronic annotation with InterPro:IPR001650
        (FlyBase Curators et al., 2004-)
        protein binding
        inferred from physical interaction with FLYBASE:AGO2; FB:FBgn0046812
        (Hammond et al., 2001)
        inferred from physical interaction with FLYBASE:Fmr1; FB:FBgn0028734
        (Ishizuka et al., 2002)
        inferred from physical interaction with FLYBASE:AGO1; FB:FBgn0026611
        (Okamura et al., 2004)
        inferred from physical interaction with FLYBASE:piwi; FB:FBgn0004872 inferred from physical interaction with FLYBASE:vas; FB:FBgn0003970
        (Megosh et al., 2006)
        inferred from physical interaction with FLYBASE:loqs; FB:FBgn0032515
        (Ye et al., 2007)
        hide Biological Process
        CV term
        Evidence
        References
        RNA interference
        traceable author statement
        (Hammond et al., 2001)
        traceable author statement
        (Cerutti, 2003)
        inferred from direct assay
        (Pham et al., 2004)
        traceable author statement
        (Heinrichs, 2004)
        inferred from mutant phenotype
        (Lee et al., 2004)
        RNA interference, production of siRNA
        inferred from direct assay
        (Bernstein et al., 2001)
        inferred from direct assay
        (Ishizuka et al., 2002)
        RNA interference, siRNA loading onto RISC
        inferred from mutant phenotype
        (Lee et al., 2004)
        gene silencing by miRNA
        traceable author statement
        (Heinrichs, 2004)
        gene silencing by miRNA, production of miRNAs
        traceable author statement
        (Heinrichs, 2004)
        inferred from mutant phenotype
        (Lee et al., 2004)
        traceable author statement
        (Skipper, 2004)
        germ-line stem cell division
        inferred from mutant phenotype
        (Hatfield et al., 2005)
        mitotic cell cycle, embryonic
        inferred from mutant phenotype
        (Megosh et al., 2006)
        pole cell formation
        inferred from mutant phenotype
        (Megosh et al., 2006)
        pre-microRNA processing
        inferred from mutant phenotype
        (Jiang et al., 2005)
        inferred from mutant phenotype
        (Forstemann et al., 2005)
        inferred from mutant phenotype
        (Saito et al., 2005)
        traceable author statement
        (He and Hannon, 2004)
        inferred from direct assay
        (Ye et al., 2007)
        segment polarity determination
        inferred from genetic interaction with FLYBASE:AGO1; FB:FBgn0026611
        (Meyer et al., 2006)
        hide Cellular Component
        CV term
        Evidence
        References
        RNA-induced silencing complex
        inferred from direct assay
        (Pham et al., 2004)
        cytoplasm
        inferred from direct assay
        (Saito et al., 2005)
        inferred from direct assay
        (Grimaud et al., 2006)
        colocalizes_with
        nucleus
        inferred from direct assay
        (Grimaud et al., 2006)
        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
        Dcr-1 allele
        Gene
        References
        Dcr-1Q1147X
        dap
        (Hatfield et al., 2005)
        hide External Data
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        Drosophila PIMRider - The Drosophila Protein Interaction map
        •
        hide Orthologs
        Genome-wide drosophilid orthologs
        Curated drosophilid orthologs
         
        (Obbard et al., 2006.2.10)
        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
        v24666
        w1118; P{GD11429}v24666
        v24667
        w1118; P{GD11429}v24667
        hide Genomic Clones ( 1 )
        hide cDNA Clones ( 4 )
        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 identity of: Dcr-1 CG4792
        (Bernstein et al., 2001)
        Source for database merge of
        Additional comments
        hide Comments About Role
        loqs is required together with Dcr-1 for normal pre-miRNA processing.
        (Forstemann et al., 2005)
        Dcr-1 is not required for repeat-associated small interfering RNA (rasiRNA) production
        (Vagin et al., 2006)
        hide Comments About Molecular Function
        loqs protein alone is not capable of converting pre-miRNAs into mature miRNAs. However, the loqs and Dcr-1 proteins form a complex that converts pre-miRNAs into mature miRNAs, and the loqs protein stimulates and directs the specific pre-miRNA processing activity of Dcr-1 protein.
        (Saito et al., 2005)
        hide Other Comments
        Expression is not enriched in embryonic gonads.
        (Shigenobu et al., 2006)
        hide External Crossreferences & Linkouts
        Sequence Crossreferences
        RefSeq (Transcripts)
        •
        RefSeq (Proteins)
        •
        DDBJ / EMBL / GenBank
        •
        UniProtKB/Swiss-Prot
        •
        UniProtKB/TrEMBL
        •
        Other Crossreferences
        InterPro domains - A database of protein families, domains, and functional sites
        •
        Ribonuclease III (IPR000999)
        Double-stranded RNA binding (IPR001159)
        DNA/RNA helicase, C-terminal (IPR001650)
        Argonaute and Dicer protein, PAZ (IPR003100)
        Protein of unknown function DUF283 (IPR005034)
        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
        •
        Drosophila PIMRider - The Drosophila Protein Interaction map
        •
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        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