A Database of Drosophila Genes & Genomes

FB2008_06, released July 3, 2008
 

Gene Dmel\knrl

General Information
SymbolDmel\knrlSpeciesD. melanogaster
Nameknirps-likeAnnotation symbolCG4761
Feature typeprotein_coding_geneFlyBase IDFBgn0001323
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)3LRecombination map
Cytogenetic map 77D4-77E1 Sequence location3L:20,590,241..20,613,636 [-]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
The gene knirps-like is referred to in FlyBase by the symbol knrl (CG4761, FBgn0001323). It has the cytological map location 77D4-77E1. Its sequence location is 3L:20590241..20613636. Its molecular function is described as: ligand-dependent nuclear receptor activity; transcription factor activity; zinc ion binding; sequence-specific DNA binding. It is involved in the biological processes: regulation of mitosis; epithelial cell migration, open tracheal system; branched duct epithelial cell fate determination, open tracheal system; regulation of tube size, open tracheal system; open tracheal system development; regulation of transcription, DNA-dependent. 6 alleles are reported. The phenotypes of these alleles are annotated with: dorsal closure embryo; embryonic dorsal epidermis; metathoracic femur. It has one annotated transcript and one annotated polypeptide.

hide Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage
knrl: knirps-related
Expressed maternally at low levels in very early stages; expression increases during early embryogenesis and continues in larvae and adults (in contrast to kni, which is first expressed zygotically and does not continue beyond embryonic stages) (Oro et al., 1988; Rothe et al., 1989).
hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
77D4-77E1  
Limits computationally determined from genome sequence between P{EP}trblEP3519 and P{EP}fngEP3082&P{lacW}skdL7062  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
77E1-77E2
(determined by in situ hybridisation)  
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\knrl for information on other features
detailed view FBtr0078212 FBpp0077870 FBti0078468 FBti0071006 FBti0055696 FBti0070402 FBti0037169 FBti0023317 FBti0056344
Comments on Gene Model
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
FBtr0078212
  3786
  647
Additional Transcript Data & Comments
Reported size (kB)
3.8 (northern blot)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
FBpp0077870  
68.3  
647  
5.72  
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
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
    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 | cellular blastoderm
     embryonic stage
     embryonic stage | embryonic cycle 12
     larval stage | third instar
     wing vein L2 | precursor
     embryonic stage | <embryonic cycle 8
     embryonic stage | cellular blastoderm
     adult stage
     embryonic stage | cellular blastoderm
     larval stage
    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 FBtr0078212
        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
        Other Phenotypes
        Allele
        Phenotype manifest in
        Allele
        adult thorax & macrochaeta, with Scer\GAL4Bx-MS1096
        hide Classical Alleles ( 1 )
        For All Classical Alleles Show

        Allele of knrlClassMutagenStocksKnown lesion
        knrlMB05076
          1 --
          hide Alleles Carried on Transgenic Constructs ( 5 )
          For All Alleles Carried on Transgenic Constructs Show

          Allele of knrlClassMutagenStocksKnown lesion
          knrlGD169012 Yes
          knrlScer\UAS.cFa0 Yes
          knrlScer\UAS.cLa0 Yes
          knrlhs.PR0 Yes
          knrlkni.PR0 Yes
          hide Aneuploid Aberrations
          Useful deficiency
          Useful duplication
          Disrupted in
          hide Transgenic Constructs & Insertions
          Transgenic Constructs
          Type of construct
          Name
          Expression data
          characterization construct
          heat-shock construct
          reporter construct
          UAS construct
          Insertions
          Type of insertions
          Name
          Expression data
          insertion of enhancer trap binary system
          hide Related Comments
          Please look at the allele reports for the complete phenotype data
          knrl is closely related to kni. knrl is one of the most diverged steroid receptor-like molecules.
          Rescue of the kni- embryonic abdominal segmentation phenotype by Res requires another gene, it is likely this is knrl.
          hide Gene Ontology: Function, Process & Cellular Component ( 11 )
          hide Molecular Function
          CV term
          References
          inferred from sequence or structural similarity with UniProt:Q60674
          non-traceable author statement
          non-traceable author statement
          inferred from electronic annotation with InterPro:IPR001628
          inferred from sequence or structural similarity with UniProt:Q60674
          inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR013088
          hide Biological Process
          CV term
          References
          traceable author statement
          traceable author statement
          traceable author statement
          traceable author statement
          inferred from mutant phenotype
          inferred from electronic annotation with InterPro:IPR000324, InterPro:IPR001628, InterPro:IPR013088
          traceable author statement
          hide Cellular Component
          CV term
          References
          inferred from sequence or structural similarity with UniProt:Q60674
          non-traceable author statement
          hide Sequence Ontology: Class of Gene
          hide Interactions & Pathways
          hide Summary of Genetic Interactions
          Interacts with
          Please look at the allele data for full details of the genetic interactions
          knrl 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
          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
          Bloomington
          hide Genomic Clones ( 1 )
          hide cDNA Clones ( 6 )
          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
          Additional comments
          No loss-of-function alleles have been isolated.
          hide Comments About Role
          kni and knrl appear to be important in spatially restricting endoreduplication domains.
          The biochemically equivalent gene products of kni and knrl are both functional in the head anlage and lack of one gene can be overcome by the activity of the other. kni is also required for abdominal segmentation and knrl is nonfunctional in its posterior expression domain. Therefore the kni/knrl pair of genes provides a region-specific buffering system, rather than global functional redundancy.
          knrl and kni possess multiple and redundant functions during tracheal development. knrl/ kni activity is necessary to mediate dpp signalling (which is required for tracheal cell migration and formation of dorsal and ventral branches). knrl/ kni activity in dorsal tracheal cells is essential for secondary and terminal branch formation, via repression of salm.
          hide Comments About Molecular Function
          knrl differs from kni with respect to transcrition unit size, kni contains 1kb and knrl contains 19kb intron sequences. The consequence of the intron difference is that knrl cannot substitute for kni segmentation function. The length of the mitotic cycle provides a physiological barrier to transcript size and could be a significant factor in controlling developmental gene activity during short phenocritical periods.
          Regulation of kni and knrl in their common anterior expression domain requires the same trans-acting factors. Both genes fail to be activated by bcd or dl.
          Both Dpp and FGF pathways control knrl expression.
          hide Other Comments
          Identification: Isolated from a genomic library using a human retinoic acid receptor cDNA probe.
          Identification: Isolated from a genomic library using a Drosophila kni zinc-finger probe.
          hide External Crossreferences & Linkouts
          Sequence Crossreferences
          RefSeq (Transcripts)
          RefSeq (Proteins)
          Other Crossreferences
          InterPro domains - A database of protein families, domains, and functional sites
          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
          PANTHER - Protein classification by function, families, and pathways
          REDfly - Regulatory element database for Drosophila
          hide Synonyms & Secondary IDs ( 8 )
          Reported As
          Symbol Synonym
          CG4761
           
          Name Synonym
          knirps-like
           
          knirps related
          Secondary FlyBase IDs
            hide References ( 63 )
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            hide Recent research papers ( 3 )
            Segal et al., 2008, Nature 451(7178): 535--540
            Predicting expression patterns from regulatory sequence in Drosophila segmentation. [FBrf0202696]
            Maines et al., 2007, Development 134(8): 1471--1479
            Stonewalling Drosophila stem cell differentiation by epigenetic controls. [FBrf0200664]
            Jiang and Crews, 2006, Molec. Cell. Biol. 26(17): 6547--6556
            Dysfusion transcriptional control of Drosophila tracheal migration, adhesion, and fusion. [FBrf0193980]
            hide Recent reviews (0)
            All reviews listed in FlyBase were published before 2006