General Information
Symbol
Dmel\knrl
Species
D. melanogaster
Name
knirps-like
Annotation Symbol
CG4761
Feature Type
FlyBase ID
FBgn0001323
Gene Model Status
Stock Availability
Gene Snapshot
Knirps-like an orphan nuclear hormone receptor with a C4 zinc finger motif, without ligand-binding domain. It is a target gene of the Hedgehog, Wingless and Notch signaling pathways. It controls endoreduplication domains and epithelial morphogenesis in the fore- and hindgut. [Date last reviewed: 2016-08-25]
Genomic Location
Cytogenetic map
Sequence location
3L:20,597,141..20,620,659 [-]
Recombination map
3-47
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Protein Family (UniProt, Sequence Similarities)
Belongs to the nuclear hormone receptor family. NR0 subfamily. (P13054)
Molecular Function (see GO section for details)
Summaries
Gene Group Membership
NUCLEAR RECEPTOR SUBFAMILY 0 (LIGAND-INDEPENDENT) TRANSCRIPTION FACTORS -
The nuclear receptor subfamily 0 (NR0) are C4 zinc finger sequence-specific DNA-binding proteins that regulate transcription. The NR0 subfamily are atypical, highly divergent members of the nuclear receptor superfamily that have only retained the DNA-binding domain. The absence of a ligand-binding domain suggests that NR0 transcription factors function in a ligand-independent manner. (Adapted from FBrf0086042 and FBrf0184203).
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
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).
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\knrl or the JBrowse view of Dmel\knrl for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

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
Gene model reviewed during 5.45
Gene model reviewed during 6.02
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0078212
3909
647
FBtr0346815
2925
647
Additional Transcript Data and Comments
Reported size (kB)
3.8 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0077870
68.3
647
5.72
FBpp0312390
68.3
647
5.72
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

647 aa isoforms: knrl-PA, knrl-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

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

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (8 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001628
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000637642
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001628
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR013088
(assigned by InterPro )
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001628
(assigned by InterPro )
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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
anterior endoderm anlage

Comment: anlage in statu nascendi

dorsal ectoderm anlage

Comment: anlage in statu nascendi

ventral ectoderm anlage

Comment: anlage in statu nascendi

antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

antennal anlage

Comment: reported as procephalic ectoderm anlage

central brain anlage

Comment: reported as procephalic ectoderm anlage

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

visual anlage

Comment: reported as procephalic ectoderm anlage

antennal primordium

Comment: reported as procephalic ectoderm primordium

central brain primordium

Comment: reported as procephalic ectoderm primordium

visual primordium

Comment: reported as procephalic ectoderm primordium

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

embryonic large intestine | restricted

Comment: two lateral cells rows on either side of embryonic large intestine

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
knrl is expressed in the third instar wing disc in a narrow stripe corresponding to the position of the L2 primordium.
The knrl transcript is expressed at low levels from 0-3 hours of embryogenesis. Expression levels increase in late embryogenesis and in larvae and adults. In situ hybridization experiments show that, from egg deposition until embryonic cycle 8, the knrl transcript is ubiquitous in the embryo. At embryonic cycle 12, expression is detected at 80-100% egg length in a ventral and anterior region. This expression intensifies at the cellular blastoderm stage, and additional intense expression appears at about 70% and 25% egg length. The e pression at 70% egg length is more intense ventrally than dorsally.
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\knrl 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
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Allele of knrl
Class
Mutagen
Associated Insertion
Stocks
Known lesion
Other relevant insertions
Transgenic Constructs ( 8 )
Deletions and Duplications ( 3 )
Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
1 of 15
Yes
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (0)
No orthologs reported.
Rattus norvegicus (Norway rat) (0)
No orthologs reported.
Xenopus tropicalis (Western clawed frog) (0)
No orthologs reported.
Danio rerio (Zebrafish) (0)
No orthologs reported.
Caenorhabditis elegans (Nematode, roundworm) (5)
2 of 15
Yes
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No orthologs reported.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No orthologs reported.
Schizosaccharomyces pombe (Fission yeast) (0)
No orthologs reported.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091908DW )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091509IE )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Musca domestica
House fly
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Lucilia cuprina
Australian sheep blowfly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0AD0 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0AGS )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0960 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    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
    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
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please look at the Interaction Group reports for full details of the physical interactions
    protein-protein
    Interacting group
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    Pathways
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-47
    Cytogenetic map
    Sequence location
    3L:20,597,141..20,620,659 [-]
    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
    Stocks and Reagents
    Stocks (6)
    Genomic Clones (27)
    cDNA Clones (7)
     

    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 sequences
    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
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      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
      No loss-of-function alleles have been isolated.
      Other Comments
      Both Dpp and FGF pathways control knrl expression.
      kni and knrl appear to be important in spatially restricting endoreduplication domains.
      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.
      Rescue of the kni- embryonic abdominal segmentation phenotype by Res requires another gene, it is likely this is knrl.
      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.
      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.
      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.
      knrl is closely related to kni. knrl is one of the most diverged steroid receptor-like molecules.
      Identification: Isolated from a genomic library using a Drosophila kni zinc-finger probe.
      Identification: Isolated from a genomic library using a human retinoic acid receptor cDNA probe.
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 42 )
      Sequence Crossreferences
      NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
      GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
      GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
      RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
      UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      InterPro - A database of protein families, domains and functional sites
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
      DPiM - Drosophila Protein interaction map
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      FlyMine - An integrated database for Drosophila genomics
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      modMine - A data warehouse for the modENCODE project
      Synonyms and Secondary IDs (9)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (106)