Gene Dmel\knrl

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General Information

Symbol

Dmel\knrl

Species

D. melanogaster

Name

knirps-like

Annotation symbol

CG4761

Feature type

protein_coding_gene

FlyBase ID

FBgn0001323

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

77D4-77E1

Sequence location

3L:20,590,241..20,613,636 [-]

Map ( GBrowse )

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.

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).

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

77D4-77E1

Limits computationally determined from genome sequence between P{EP}trbl^EP3519 and P{EP}fng^EP3082&P{lacW}skd^L7062

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

77E1-77E2

(determined by in situ hybridisation)

(Oro et al., 1988)

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

Gene Model & Products

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

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

knrl-RA

FBtr0078212

NM_176374

3786

647

Additional Transcript Data & Comments

Reported size (kB)

3.8 (northern blot)

(Oro et al., 1988)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kD)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

knrl-PA

FBpp0077870

68.3

647

5.72

NP_788552

AAF51627

Additional Polypeptide Data & Comments

Reported size (kD)

647 (aa)

(Oro et al., 1988)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0001323

Crossreferences

InterPro domains - A database of protein families, domains, and functional sites

•

Vitamin D receptor (IPR000324)

Zinc finger, nuclear hormone receptor-type (IPR001628)

Zinc finger, NHR/GATA-type (IPR013088)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

P13054

UniProtKB/TrEMBL

Maps to

Does NOT map to

Identified with

LD23140

(BDGP Project Members, 2000-)

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

External Data

Linkouts

DEDB - Drosophila exon database: splicing graphs

•

5918

Crossreferences

Expression Data

FlyBase-Curated Data

Transcript and
Protein data

Please see the FlyBase Gene Expression Report for details of gene expression from the literature.

Summary of Transcript Expression

Stage

Tissue/Position

Reference

embryonic stage | cellular blastoderm

(Oro et al., 1988)

embryonic stage

(Oro et al., 1988)

embryonic stage | embryonic cycle 12

(Oro et al., 1988)

larval stage | third instar

wing vein L2 | precursor

(Lunde et al., 1998)

embryonic stage | <embryonic cycle 8

(Oro et al., 1988)

embryonic stage | cellular blastoderm

(Oro et al., 1988)

adult stage

(Oro et al., 1988)

embryonic stage | cellular blastoderm

(Oro et al., 1988)

larval stage

(Oro et al., 1988)

Marker for

Subcellular Localization

CV Term

Summary of Polypeptide Expression

Stage

Tissue/Position

Reference

Marker for

Subcellular Localization

CV Term

Microarray Data

Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)

Untitled Document detailed view

AA940859

External Data & Images

Linkouts

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

•

FBgn0001323

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0001323

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0001323

BDGP expression data

•

Show all BDGP original images, annotations and embryonic microarray data for knrl

FlyExpress - Embryonic expression images (BDGP data)

•

Show all FlyExpress processed images for knrl

Alleles & Phenotypes

Summary of Allele Phenotypes

Other Phenotypes

Allele

visible, with Scer\GAL4^Bx-MS1096

knrl^Scer\UAS.cLa

mitotic, with Scer\GAL4^fkh.14-3

knrl^Scer\UAS.cFa

Phenotype manifest in

Allele

dorsal closure embryo, with Scer\GAL4^pnr-MD237

knrl^Scer\UAS.cLa

embryonic dorsal epidermis, with Scer\GAL4^pnr-MD237

knrl^Scer\UAS.cLa

metathoracic femur, with Scer\GAL4^Bx-MS1096

knrl^Scer\UAS.cLa

adult thorax & macrochaeta, with Scer\GAL4^Bx-MS1096

knrl^Scer\UAS.cLa

Classical Alleles ( 1 )

For All Classical Alleles Show

Allele of knrl	Class	Mutagen	Stocks	Known lesion
knrl^MB05076			1	--

Alleles Carried on Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Allele of knrl	Mutagen	Stocks	Known lesion
knrl^GD16901	in vitro construct \| RNAi in vitro construct \| regulatory fusion	2	Yes
knrl^Scer\UAS.cFa	in vitro construct \| regulatory fusion	0	Yes
knrl^Scer\UAS.cLa	in vitro construct \| regulatory fusion	0	Yes
knrl^hs.PR	in vitro construct \| regulatory fusion	0	Yes
knrl^kni.PR	in vitro construct \| regulatory fusion	0	Yes

Aneuploid Aberrations

Useful deficiency

Df(3L)ri-XT1

Useful duplication

Dp(3;3)M72

Disrupted in

Df(3L)kni-FC82

(Lunde et al., 1998)

Df(3L)ri-XT1

(Chen et al., 1998, Boube et al., 2001, Oro et al., 1989, Rothe et al., 1992, Gonzalez-Gaitan et al., 1994, Ruden and Jaeckle, 1995)

Df(3L)ri^XT106

(Oro et al., 1989)

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

Mi{ET1}knrl^MB05076

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.

(Oro et al., 1989)

Rescue of the kni^- embryonic abdominal segmentation phenotype by Res requires another gene, it is likely this is knrl.

(Ruden and Jaeckle, 1995)

Gene Ontology: Function, Process & Cellular Component ( 11 )

Molecular Function

CV term

Evidence

References

ligand-dependent nuclear receptor activity

inferred from sequence or structural similarity with UniProt:Q60674

(FlyBase, 1992-)

non-traceable author statement

(Swiss-Prot Project Members, 1990.1.1)

non-traceable author statement

(Maglich et al., 2001)

sequence-specific DNA binding

inferred from electronic annotation with InterPro:IPR001628

(FlyBase Curators et al., 2004-)

transcription factor activity

inferred from sequence or structural similarity with UniProt:Q60674

(FlyBase, 1992-)

zinc ion binding

inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR013088

(FlyBase Curators et al., 2004-)

Biological Process

CV term

Evidence

References

branched duct epithelial cell fate determination, open tracheal system

traceable author statement

(Affolter and Shilo, 2000)

traceable author statement

(Uv et al., 2003)

epithelial cell migration, open tracheal system

traceable author statement

(Affolter, 2000)

open tracheal system development

traceable author statement

(Ghabrial et al., 2003)

regulation of mitosis

inferred from mutant phenotype

(Fuss et al., 2001)

regulation of transcription, DNA-dependent

inferred from electronic annotation with InterPro:IPR000324, InterPro:IPR001628, InterPro:IPR013088

(FlyBase Curators et al., 2004-)

regulation of tube size, open tracheal system

traceable author statement

(Affolter and Shilo, 2000)

Cellular Component

CV term

Evidence

References

nucleus

inferred from sequence or structural similarity with UniProt:Q60674

(FlyBase, 1992-)

non-traceable author statement

(Swiss-Prot Project Members, 1990.1.1)

Sequence Ontology: Class of Gene

protein_coding_gene

nuclear_gene

Interactions & Pathways

Summary of Genetic Interactions

Interacts with

Please look at the allele data for full details of the genetic interactions

knrl allele

Gene

References

(Gritzan et al., 2002)

puc

(Gritzan et al., 2002)

unspecified

btl

(Myat et al., 2005)

Res

(Ruden and Jaeckle, 1995)

External Data

Linkouts

BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions

•

65542

Orthologs

Genome-wide drosophilid orthologs

Dana\GF24122

Dere\GG13294

Dgri\GH16982

Dmoj\GI11900

Dper\GL12764

Dpse\GA18413

Dsec\GM22199

Dsim\GD12173

Dvir\GJ13774

Dwil\GK10566

Curated drosophilid orthologs

Dpse\GA18413

Linkouts

Functional Complementation between Species

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 3 )

VDRC

v47216

w¹¹¹⁸; P{GD16901}v47216/CyO

v47217

w¹¹¹⁸; P{GD16901}v47217/CyO

Bloomington

24320

w¹¹¹⁸; Mi{ET1}knrl^MB05076

Genomic Clones ( 1 )

BACR21J02

cDNA Clones ( 6 )

cDNA Clones, Fully Sequenced

BDGP DGC clones

LD23140

Other clones

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi & Array Information

Affy Oligo

Linkouts

DRSC - RNAi screening (Harvard): high-throughput cell culture data and design

•

FBgn0001323

GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data

•

FBgn0001323

Antibody Information

Other Information

Discoverer

Etymology

Identification

Position Effect Variegation Data

Relationship to Other Genes

Source for database identity of

Source for database merge of

Additional comments

No loss-of-function alleles have been isolated.

(Lindsley and Zimm, 1992)

Comments About Role

kni and knrl appear to be important in spatially restricting endoreduplication domains.

(Fuss et al., 2001)

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.

(Gonzalez-Gaitan et al., 1994)

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.

(Chen et al., 1998)

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.

(Rothe et al., 1992)

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.

(Rothe et al., 1994)

Both Dpp and FGF pathways control knrl expression.

(Myat et al., 2005)

Other Comments

Identification: Isolated from a genomic library using a human retinoic acid receptor cDNA probe.

(Oro et al., 1988)

Identification: Isolated from a genomic library using a Drosophila kni zinc-finger probe.

(Rothe et al., 1989)

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)

•

NM_176374

RefSeq (Proteins)

•

NP_788552

DDBJ / EMBL / GenBank

•

UniProtKB/Swiss-Prot

•

P13054

Other Crossreferences

InterPro domains - A database of protein families, domains, and functional sites

•

Vitamin D receptor (IPR000324)

Zinc finger, nuclear hormone receptor-type (IPR001628)

Zinc finger, NHR/GATA-type (IPR013088)

Linkouts

BDGP expression data

•

Show all BDGP original images, annotations and embryonic microarray data for knrl

BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions

•

65542

DEDB - Drosophila exon database: splicing graphs

•

5918

DRSC - RNAi screening (Harvard): high-throughput cell culture data and design

•

FBgn0001323

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

•

FBgn0001323

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0001323

FlyExpress - Embryonic expression images (BDGP data)

•

FBgn0001323

FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans

•

FBgn0001323

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0001323

GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data

•

FBgn0001323

PANTHER - Protein classification by function, families, and pathways

•

FBgn0001323

REDfly - Regulatory element database for Drosophila

•

FBgn0001323

University of Chicago Dev. Expression

•

FBgn0001323

Synonyms & Secondary IDs ( 8 )

Reported As

Symbol Synonym

CG4761

Knrl

(Petit et al., 2002)

knrl

(Chen et al., 1998, Jiang and Crews, 2006, Maines et al., 2007, Segal et al., 2008)

NR0A2

(Nuclear Receptors Nomenclature Committee, 1999)

Name Synonym

knirps-like

knirps related

(Affolter, 2000)

Secondary FlyBase IDs

References ( 63 )

Generate a list of

All references relating to this gene ( 63 )

List References by type

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]

Show all research papers ...

Recent reviews (0)

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