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Gene Dmel\bnl

General Information
Symbol	Dmel\bnl	Species	D. melanogaster
Name	branchless	Annotation symbol	CG4608
Feature type	protein_coding_gene	FlyBase ID	FBgn0014135
Created / Updated	2005-01-10/2005-01-10
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	92B2-92B3	Sequence location	3R:15,619,795..15,662,539 [-]
Map ( GBrowse )	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene branchless is referred to in FlyBase by the symbol bnl (CG4608, FBgn0014135). It has the cytological map location 92B2-92B3. Its sequence location is 3R:15619795..15662539. Its molecular function is described as: fibroblast growth factor receptor binding; growth factor activity. It is involved in the biological processes described with 14 unique terms, many of which group under: anatomical structure development; open tracheal system development; morphogenesis of a branching structure; system development; taxis; locomotory behavior; cell projection organization and biogenesis; tube morphogenesis; response to chemical stimulus; transmembrane receptor protein tyrosine kinase signaling pathway; cell morphogenesis. 18 alleles are reported. The phenotypes of these alleles are annotated with 14 unique terms, many of which group under: organ system; embryonic/larval tracheal system; tracheal system; trachea; anatomical structure; embryonic/larval dorsal branch; adult tracheal system; dorsal thoracic disc; embryonic ganglionic branch; adult trachea; thoracic segment. It has 2 annotated transcripts and 2 annotated polypeptides.
External Summaries
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 92B2-92B3   Limits computationally determined from genome sequence between P{EP}EP650 and P{PZ}l(3)1058510585
Experimentally Determined Cytological Location
Cytogenetic map Notes References 92B2-92B3 (determined by in situ hybridisation)   (Spradling et al., 1999) 92B-92B (determined by in situ hybridisation)   (Sutherland et al., 1996) 92B-92B (determined by in situ hybridisation)   (Sutherland et al., 1995) 92B-92B (determined by in situ hybridisation) 92B2--3 (determined by in situ hybridisation)   (BDGP Project Members, 1994-1999) 92B-92B (determined by in situ hybridisation)   (Cooley 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\bnl for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) bnl-RA FBtr0083795  NM_169874   3632   770 bnl-RC FBtr0300123     4295   760
Additional Transcript Data & Comments
Reported size (kB)	4 (northern blot) (Sutherland et al., 1996)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein bnl-PA   FBpp0083206   84.1   770   9.97     NP_732452   AAF55701 bnl-PC   FBpp0289400   82.9   760   9.97
Additional Polypeptide Data & Comments
Reported size (kD)	770 (aa); 84 (kD predicted) (Sutherland et al., 1996)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0014135
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Heparin-binding growth factor/Fibroblast growth factor (IPR002209) Interleukin 1/heparin-binding growth factor (IPR002348) Cytokine, IL-1-like (IPR008996)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE003727 AAF55701   AE003727 AAN13809   AI109644   AI294514   AI945472   BH610002   BH610003   BP544142   BP544143   BT003790   CO266289   CO266347   CO300084   CO323276   CO344788   CZ467569   CZ477941   CZ480880   CZ480881   CZ484361   CZ484362   EC064208   EC200193   EC235401   EC244872   EC246587   G00595   U82273 AAC47427
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	P91672 Q9VDT9
Maps to
Does NOT map to
Identified with	bs13c07 (Oliver, 2001.8.16) GH08887 (Spradling et al., 1999, BDGP Project Members, 2000-) Dm0323 (BDGP Project Members, 1994-1999, Spradling et al., 1999)
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 • 10014
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  cephalic furrow (Sutherland et al., 1996)  embryonic stage  posterior transverse furrow (Sutherland et al., 1996)  embryonic stage | stage >=11  tracheal air sac | surrounding (Sutherland et al., 1996)  embryonic stage   (Sutherland et al., 1996)  larval stage | third instar  dorsal mesothoracic disc | anterior/posterior compartment boundary & vicinity of & dorsal & restricted (Sato and Kornberg, 2002)
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) AI109644
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0014135 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0014135 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0014135 BDGP expression data • Show all BDGP original images, annotations and embryonic microarray data for bnl FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for bnl Stage(s) 4-6 Stage(s) 7-8 Stage(s) 9-10 Stage(s) 11-12 Stage(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | recessive bnl00857 bnl06916 bnlneo52 Phenotype manifest in Allele air sac tracheoblast of dorsal mesothoracic disc & filopodium | somatic clone | cell non-autonomous bnlαTub84B.PS air sac tracheoblast of dorsal mesothoracic disc | cell non-autonomous | somatic clone bnl00857 embryonic/larval trachea bnl00857 lateral H branch bnl00857 lateral G branch bnl00857 embryonic/larval ganglionic branch bnl00857 embryonic tracheal system bnl00857 embryonic/larval tracheal system bnl00857 bnl06916 bnlPL00790 tracheal metamere 1 & embryo bnl00857 tracheal metamere 2 & embryo bnl00857 tracheal metamere 3 & embryo bnl00857 tracheal metamere 4 & embryo bnl00857 tracheal metamere 5 & embryo bnl00857 tracheal metamere 6 & embryo bnl00857 tracheal metamere 7 & embryo bnl00857 tracheal metamere 8 & embryo bnl00857 tracheal metamere 9 & embryo bnl00857 tracheal metamere 10 & embryo bnl00857 embryonic ganglionic branch bnl00857 bnlunspecified tracheal system bnl708 embryonic/larval tracheal system, with Scer\GAL4ptc-559.1 bnlScer\UAS.P\T.cRa trachea, with Scer\GAL4sim.PS bnlScer\UAS.cSa embryonic tracheal system & filopodium | ectopic, with Scer\GAL4btl.PS bnlScer\UAS.cSa embryonic/larval trachea, with Scer\GAL4btl.PS bnlScer\UAS.cSa embryonic/larval dorsal branch, with Scer\GAL4btl.PS bnlScer\UAS.cSa embryonic/larval lateral trunk, with Scer\GAL4btl.PS bnlScer\UAS.cSa embryonic/larval dorsal trunk, with Scer\GAL4btl.PS bnlScer\UAS.cSa visceral branch, with Scer\GAL4bap.3 bnlScer\UAS.cSa embryonic/larval tracheal system, with Scer\GAL4C49 bnlScer\UAS.cSa embryonic/larval tracheal system, with Scer\GAL469B bnlScer\UAS.cSa embryonic/larval tracheal system, with Scer\GAL4hs.PB bnlScer\UAS.cSa embryonic/larval trachea, with Scer\GAL4hs.PB bnlScer\UAS.cSa lateral G branch, with Scer\GAL4hs.PB bnlScer\UAS.cSa tracheal tip cell & embryo, with Scer\GAL4hs.PB bnlScer\UAS.cSa embryonic/larval trachea, with Scer\GAL4A9 bnlScer\UAS.cSa embryonic/larval ganglionic branch, with Scer\GAL4A9 bnlScer\UAS.cSa embryonic/larval trachea, with Scer\GAL471B bnlScer\UAS.cSa embryonic/larval trachea, with Scer\GAL45053A bnlScer\UAS.cSa lateral G branch, with Scer\GAL45053A bnlScer\UAS.cSa embryonic/larval trachea | somatic clone, with Scer\GAL4Act5C.PP bnlScer\UAS.cSa air sac tracheoblast of dorsal mesothoracic disc, with Scer\GAL4Act5C.PI bnlScer\UAS.cSa air sac tracheoblast of dorsal mesothoracic disc & filopodium bnlhs.PS
Classical Alleles ( 12 )
For All Classical Alleles Show
Allele of bnl Class Mutagen Stocks Known lesion bnl00857 amorph, loss of function P-element activity 1 Yes bnl06916 hypomorph P-element activity 1 Yes bnl708 ethyl methanesulfonate 0 -- bnlKG00157 P-element activity 1 -- bnlPL00790 piggyBac transposase 0 Yes bnlS044026 P-element activity 1 -- bnlc01939 piggyBac transposase 0 -- bnle00029 piggyBac transposase 0 -- bnle03115 piggyBac transposase 1 -- bnlf01868 piggyBac transposase 1 -- bnlneo52 P-element activity 1 -- bnlunspecified 0 --
Alleles Carried on Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Allele of bnl Class Mutagen Stocks Known lesion bnlGD3070 in vitro construct | RNAi in vitro construct | regulatory fusion 2 Yes bnlScer\FRT.Disc\RFP-DsRed2.y.αTub84B in vitro construct | regulatory fusion in vitro construct | other 0 Yes bnlScer\UAS.P\T.cRa in vitro construct | regulatory fusion 0 Yes bnlScer\UAS.cSa in vitro construct | regulatory fusion 0 -- bnlhs.PS in vitro construct | regulatory fusion 0 Yes bnlαTub84B.PS FLPase 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(3R)Dl-BX12
Useful duplication	Dp(3;3)C123.3
Disrupted in	Df(3R)Dl-BX12 (Spradling et al., 1999, Jarecki et al., 1999, BDGP Project Members, 1994-1999, Sutherland et al., 1996) Df(3R)ED6025 (Ryder and Roote, 2004.11.10)
Not disrupted in	Df(3R)H-B79 (Spradling et al., 1999) Df(3R)p712 (BDGP Project Members, 1994-1999)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD3070} NA P{UAS-bnl.S} NA P{UASp-bnl.R} NA characterization construct P{αTub84B(-FRT)bnl} NA P{αTub84B(FRT.Disc\RFPDsRed2.y+)bnl} NA heat-shock construct P{hs-bnl.S} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{PB}bnlc01939 NA PBac{RB}bnle00029 NA PBac{RB}bnle03115 NA PBac{WH}bnlf01868 NA P{PTT-GB}CB02854 NA P{SUPor-P}bnlKG00157 NA P{UAST-YFP.Rab6.T26N}03 NA P{UASp-YFP.Rab39.Q69L}14 NA P{UASp-YFP.RabX1.Q66L}02 NA P{hsneo}bnlneo52 NA insertion of enhancer trap binary system PBac{GAL4D,EYFP}bnlPL00790 No insertion of enhancer trap P{PZ}bnl00857 No P{PZ}bnl06916 Yes P{lacW}bnlS044026 No insertion of mobile activating element P{GSV1}C904.1C904.1 NA
Related Comments
	Please look at the allele reports for the complete phenotype data RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells. (Boutros et al., 2004)
Gene Ontology: Function, Process & Cellular Component ( 17 )
Molecular Function
CV term Evidence References
fibroblast growth factor receptor binding non-traceable author statement (Sutherland, 1996.12.15) inferred from sequence or structural similarity with MGD:Fgf10; MGI:MGI:1099809 (FlyBase, 1992-) traceable author statement (Affolter, 2000) traceable author statement (Wilson and Leptin, 2000) traceable author statement (Ghabrial et al., 2003) traceable author statement (Itoh and Ornitz, 2004)
growth factor activity inferred from electronic annotation with InterPro:IPR002209, InterPro:IPR002348 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
chemotaxis traceable author statement (Wilson and Leptin, 2000)
cytoneme biogenesis inferred from direct assay (Ramirez-Weber and Kornberg, 1999)
epithelial cell migration, open tracheal system traceable author statement (Zelzer and Shilo, 2000) traceable author statement (Affolter, 2000) traceable author statement (Rosin and Shilo, 2002) traceable author statement (Uv et al., 2003) traceable author statement (Nelson, 2003)
fibroblast growth factor receptor signaling pathway traceable author statement (Affolter, 2000) non-traceable author statement (Rosin and Shilo, 2002) traceable author statement (Ghabrial et al., 2003) traceable author statement (Itoh and Ornitz, 2004)
filopodium formation inferred from mutant phenotype (Ribeiro et al., 2002)
genital disc development inferred from expression pattern (Ahmad and Baker, 2002)
morphogenesis of a branching structure traceable author statement (Affolter and Shilo, 2000)
open tracheal system development non-traceable author statement (Wilson and Leptin, 2000) traceable author statement (Ribeiro et al., 2003) inferred from mutant phenotype (Jarvis et al., 2006)
positive chemotaxis inferred from direct assay (Sato and Kornberg, 2002) traceable author statement (Affolter, 2000) traceable author statement (Ribeiro et al., 2003) traceable author statement (Ghabrial et al., 2003)
primary branching, open tracheal system traceable author statement (Uv et al., 2003) traceable author statement (Ghabrial et al., 2003)
regulation of tube architecture, open tracheal system traceable author statement (Uv et al., 2003)
secondary branching, open tracheal system traceable author statement (Ghabrial et al., 2003)
terminal branching, open tracheal system traceable author statement (Ghabrial et al., 2003)
tracheal outgrowth, open tracheal system traceable author statement (Ghabrial et al., 2003)
Cellular Component
CV term Evidence References
extracellular region inferred from sequence or structural similarity (Sutherland et al., 1996) inferred from sequence or structural similarity (FlyBase, 1992-)
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 bnl allele Gene References bnl00857 stumps (Imam et al., 1999) btl (Sutherland et al., 1996) btl::tor (Sutherland et al., 1996) grh (Hemphala et al., 2003) bnlScer\UAS.cSa sgl (Lin et al., 1999) sfl (Lin et al., 1999) hb (Wolf and Schuh, 2000) stumps (Imam et al., 1999) sr (Dorfman et al., 2002) unspecified csw (Jarvis et al., 2006) stumps (Michelson et al., 1998) trimmed (Shim et al., 1998)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 67346
Orthologs
Genome-wide drosophilid orthologs	Dana\GF17357 Dere\GG15841 Dgri\GH23362 Dmoj\GI10332 Dper\GL11947 Dpse\GA18297 Dsec\GM26894 Dsim\GD20101 Dvir\GJ10186 Dwil\GK22814 Dyak\GE25113
Curated drosophilid orthologs	Dpse\GA18297
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSBTAP00000008839 Bos taurus (Ensembl) ENSCAFP00000025396 Canis familiaris (Ensembl) NEWSINFRUP00000152407 Takifugu rubripes (Ensembl) ENSGALP00000022184 Gallus gallus (Ensembl) ENSP00000264664 Homo sapiens (Ensembl)