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Gene Dmel\ndl

General Information
Symbol	Dmel\ndl	Species	D. melanogaster
Name	nudel	Annotation symbol	CG10129
Feature type	protein_coding_gene	FlyBase ID	FBgn0002926
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	3L	Recombination map	3-17
Cytogenetic map	65B5-65B5	Sequence location	3L:6,587,038..6,596,466 [-]
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 nudel is referred to in FlyBase by the symbol ndl (CG10129, FBgn0002926). It has the cytological map location 65B5. Its sequence location is 3L:6587038..6596466. Its molecular function is described as: serine-type peptidase activity; trypsin activity; serine-type endopeptidase activity; peptidase activity. It is involved in the biological processes: dorsal/ventral axis specification; Toll signaling pathway; maternal determination of dorsal/ventral axis, oocyte, soma encoded; protein processing; eggshell chorion formation; proteolysis; oocyte dorsal/ventral axis determination; egg activation. 29 alleles are reported. The phenotypes of these alleles are annotated with: vitelline membrane; embryonic/first instar larval cuticle; embryonic epidermis; egg; chorion; blastoderm embryo; embryo. It has one annotated transcript and one annotated polypeptide.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	ndl: nudel Maternal effect mutation producing totally dorsalized embryos. Spacing of transverse stripes of ftz protein altered in mutant embryos (Carroll, Winslow, Twombly, and Scott, 1987, Development 99: 327-32).
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 65B5-65B5   Limits computationally determined from genome sequence between P{PZ}l(3)0209402094 and P{lacW}l(3)L4060L4060
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location	3-17 (Tearle and Nusslein-Volhard, 1987)
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology) References In direction of increasing cytology: anon-65Ba? ndl- anon-65Bb? (Hong and Hashimoto, 1995) In direction of increasing cytology: ndl- CG8368+ zpg- CG8368+ (Tazuke et al., 2002) Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\ndl for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) ndl-RA FBtr0076984  NM_079223   8230   2616
Additional Transcript Data & Comments
Reported size (kB)	8.4 (northern blot) (Hong and Hashimoto, 1995)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein ndl-PA   FBpp0076693   292.5   2616   5.77     NP_523947   AAF50656
Additional Polypeptide Data & Comments
Reported size (kD)	2616 (aa); 292 (kD predicted) (Hong and Hashimoto, 1995)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0002926
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Peptidase S1 and S6, chymotrypsin/Hap (IPR001254) Peptidase S1A, chymotrypsin (IPR001314) Low density lipoprotein-receptor, class A, cysteine-rich (IPR002172) Peptidase, trypsin-like serine and cysteine (IPR009003) Region of unknown function DUF1986 (IPR015420) MEROPS - An information resource for peptidases and the proteins that inhibit them • S01.950
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE003562 AAF50656   EC053957   EC053958   EC055467   EC055470   EC055895   EC056350   U29153 AAA83086
UniProtKB/Swiss-Prot	P98159
UniProtKB/TrEMBL
Maps to
Does NOT map to
Identified with
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 deletion ndl[18] 3L:6,587,149..6,596,198 evidence=experimental comment=569bp deletion causes a frameshift during translation that truncates the follicle cell-specific transcript. (Hong and Hashimoto, 1995) point mutation ndl[14] 3L:6,592,467..6,592,467 evidence=experimental na_change=G6573314A pr_change=W1044@|ndl-PA reported_na_change=G3400A reported_pr_change=W1044@ (LeMosy et al., 2000) point mutation ndl[9] 3L:6,592,259..6,592,259 evidence=experimental na_change=T6573106A pr_change=C1114S|ndl-PA reported_na_change=T3608A reported_pr_change=C1114S comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. (LeMosy et al., 2000) point mutation ndl[1] 3L:6,591,712..6,591,712 na_change=G6572559A pr_change=V1278M|ndl-PA reported_na_change=G?A reported_pr_change=V1278M comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. evidence=experimental (Hong and Hashimoto, 1996, LeMosy et al., 2000) point mutation ndl[LP-1] 3L:6,591,706..6,591,706 evidence=experimental na_change=G6572553A pr_change=G1280S|ndl-PA reported_na_change=G4106A reported_pr_change=G1280S (LeMosy et al., 2000) point mutation ndl[6] 3L:6,591,700..6,591,700 reported_na_change=G?A na_change=G6572547A pr_change=G1282R|ndl-PA comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. Residue G1282 is a highly conserved glycine in the core structure of the serine protease. evidence=experimental reported_pr_change=G1282R (LeMosy et al., 2000) point mutation ndl[3] 3L:6,591,483..6,591,483 comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. evidence=experimental na_change=G6572330A pr_change=G1334R|ndl-PA reported_na_change=G?A reported_pr_change=G1334R (Hong and Hashimoto, 1996, LeMosy et al., 2000) point mutation ndl[2] 3L:6,591,419..6,591,419 pr_change=H1355L|ndl-PA comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. evidence=experimental na_change=A6572266T reported_na_change=A4332T reported_pr_change=H1355L (LeMosy et al., 2000) point mutation ndl[rm5] 3L:6,591,405..6,591,405 comment=Position of mutation on reference sequence inferred by FlyBase curator based on author statement. evidence=experimental na_change=G6572252A pr_change=A1360T|ndl-PA reported_na_change=G4346A reported_pr_change=A1360T (LeMosy et al., 2000)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 5021
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  oogenesis stage,adult stage | stage S7-S10  oocyte | anterior (Hong and Hashimoto, 1995)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference
Marker for
Subcellular Localization
CV Term
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002926 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0002926 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0002926
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | maternal effect | recessive ndl10 ndl11 ndl12 ndl13 ndl14 ndl15 ndl16 ndl17 ndl18 ndl1 ndl3 ndl4 ndl5 ndl6 ndl9 lethal | maternal effect | partially | recessive ndlLP-2 lethal | embryonic stage | recessive ndl1 Phenotype manifest in Allele vitelline membrane ndl1 ndl3 ndl6 ndl9 embryonic/first instar larval cuticle ndl1 embryonic epidermis | maternal effect ndl1 ndl3 ndl6 ndl9 egg | maternal effect ndl10 ndl11 ndl12 ndl13 ndl14 ndl15 ndl16 ndl17 ndl18 ndl4 ndl5 ndl6 chorion | maternal effect ndl10 ndl11 ndl12 ndl13 ndl14 ndl15 ndl16 ndl17 ndl18 ndl4 ndl5 blastoderm embryo | maternal effect ndl10 ndl11 ndl12 ndl13 ndl14 ndl15 ndl16 ndl17 ndl18 ndl4 ndl5 embryonic epidermis | ventral ndl3 embryo ndl9 egg ndl9 ndlunspecified embryo | ventral ndlunspecified
Classical Alleles ( 21 )
For All Classical Alleles Show
Allele of ndl Class Mutagen Stocks Known lesion ndl10 0 -- ndl11 0 -- ndl12 0 -- ndl13 0 -- ndl14 0 Yes ndl15 0 -- ndl16 0 -- ndl17 0 -- ndl18 ethyl methanesulfonate 0 Yes ndl1 hypomorph ethyl methanesulfonate 0 Yes ndl2 loss of function ethyl methanesulfonate 0 -- ndl3 loss of function ethyl methanesulfonate 0 Yes ndl4 ethyl methanesulfonate 0 -- ndl5 ethyl methanesulfonate 0 -- ndl6 loss of function ethyl methanesulfonate 0 Yes ndl7 ethyl methanesulfonate 1 -- ndl9 hypomorph 0 -- ndlLP-1 0 -- ndlLP-2 hypomorph 0 -- ndlrm5 loss of function 1 -- ndlunspecified 0 --
Alleles Carried on Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Allele of ndl Class Mutagen Stocks Known lesion ndlGAG.S-A in vitro construct | site directed mutagenesis 0 Yes ndlGD2337 in vitro construct | RNAi in vitro construct | regulatory fusion 2 Yes ndlPD.T:ea in vitro construct | coding region fusion 0 Yes ndlR1144L loss of function in vitro construct | amino acid replacement in vitro construct | site directed mutagenesis 0 Yes ndlRAA in vitro construct | site directed mutagenesis in vitro construct | amino acid replacement 0 Yes ndlS1332A loss of function in vitro construct | amino acid replacement in vitro construct | site directed mutagenesis 0 Yes ndlcLa in vitro construct | other 0 Yes ndltLa in vitro construct | genomic fragment 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(3L)03844
Useful duplication	Dp(3;3)M67C+1
Disrupted in	Df(3L)03844 (Hong and Hashimoto, 1995, Hong and Hashimoto, 1996) Df(3L)CH12 (Turcotte and Hashimoto, 2002, Hong and Hashimoto, 1995, Hong and Hashimoto, 1996)
Not disrupted in	Df(3L)CH39 (Hong and Hashimoto, 1995)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD2337} NA characterization construct P{ndl.GAG.SA} NA P{ndlR1144L} NA P{ndlRAA} NA P{ndlS1332A} NA P{ndlcLa} NA P{ndltLa} NA
Insertions
	Type of insertions Name Expression data
Related Comments
	Please look at the allele reports for the complete phenotype data Strong dorsalizing mutants of ndl, snk, gd or pip have wild type axial ratios in pupae. (Letsou et al., 1991)
Gene Ontology: Function, Process & Cellular Component ( 13 )
Molecular Function
CV term Evidence References
peptidase activity traceable author statement (Lall and Patel, 2001)
serine-type endopeptidase activity non-traceable author statement (Coates et al., 2000) inferred from electronic annotation with InterPro:IPR001254, InterPro:IPR001314 (FlyBase Curators et al., 2004-)
serine-type peptidase activity traceable author statement (Hong and Hashimoto, 1996) non-traceable author statement (van Eeden and St. Johnston, 1999)
trypsin activity non-traceable author statement (Ross et al., 2003)
Biological Process
CV term Evidence References
Toll signaling pathway traceable author statement (Chasan et al., 1992) traceable author statement (Hong and Hashimoto, 1996)
dorsal/ventral axis specification inferred from mutant phenotype (Stein et al., 1991) inferred from mutant phenotype (Hong and Hashimoto, 1996)
egg activation inferred from mutant phenotype (Tadros et al., 2003)
eggshell chorion formation inferred from mutant phenotype (Hong and Hashimoto, 1996)
maternal determination of dorsal/ventral axis, oocyte, soma encoded traceable author statement (Chasan et al., 1992)
oocyte dorsal/ventral axis determination non-traceable author statement (van Eeden and St. Johnston, 1999)
protein processing inferred from genetic interaction with FLYBASE:ea; FB:FBgn0000533 (Chasan et al., 1992)
proteolysis non-traceable author statement (Ross et al., 2003) traceable author statement (Lall and Patel, 2001) inferred from electronic annotation with InterPro:IPR001254, InterPro:IPR001314 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
extracellular region non-traceable author statement (Swiss-Prot Project Members, 2000.5.30)
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 ndl allele Gene References ndl3 gd (Han et al., 2000)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 64189
Orthologs
Genome-wide drosophilid orthologs	Dana\GF10896 Dere\GG14054 Dgri\GH16271 Dmoj\GI13207 Dpse\GA10095 Dsec\GM13834 Dsim\GD13121 Dwil\GK12588 Dyak\GE20478
Curated drosophilid orthologs	Dmir\CG10129 (Thornton, 2005.12.20) Dpse\GA10095
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000015896 Anopheles gambiae (Ensembl) ENSCAFP00000015316 Canis familiaris (Ensembl) ENSGALP00000024779 Gallus gallus (Ensembl) GSTENP00003546001 Tetraodon nigroviridis (Ensembl) ENSXETP00000013811 Xenopus tropicalis (Ensembl) ZDB-CDNA-040425-1762 Danio rerio (Zfin) ZDB-GENE-040426-834 Danio rerio (Zfin)
Functional Complementation between Species
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
VDRC	v44384 w1118; P{GD2337}v44384 v44385 w1118; P{GD2337}v44385
Bloomington	9036 mwh1 ndl7 red1 e1/TM1 9038 mwh1 ndlrm5 red1 e1/TM1
Genomic Clones ( 2 )
	BACR26E20 BACR26E12
cDNA Clones ( 6 )
	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	EC055895 EC056350 EC053957 EC053958 EC055467 EC055470
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0002926 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0002926
Antibody Information
Other Information
Discoverer
Etymology
Identification
Position Effect Variegation Data
Relationship to Other Genes
Source for database identity of	Source for identity of: ndl CG10129 (Gabrielian, 1999.11)
Source for database merge of
Additional comments
Comments About Role
	ndl has an integral role in the biogenesis of the vitelline membrane and may function in embryonic dorsal ventral patterning through creation of a matrix structure necessary for activity of the dorsal ventral protease cascade. (LeMosy and Hashimoto, 2000) Analysis of mosaic females indicates that the expression of ndl, pip and wbl is required in the somatic tissue, in the follicle cells that surround the oocyte, for the production of embryos with the correct dorsoventral axis. (Stein et al., 1991) Double mutant combinations of ndl with ea alleles demonstrate that spatial regulation of ea activity by localized zymogen activation is a key initial event in defining the polarity of the dorsal-ventral embryonic pattern. (Chasan et al., 1992) ndl is a somatic-dependent gene required to activate and localise the serine protease cascade that produces Tls ligand. (Hong and Hashimoto, 1995) Local activation of the protease cascade within the extra embryonic perivitelline compartment that defines embryonic dorsoventral polarity depends on a positional cue that is laid down during oogenesis outside the oocyte, ndl encodes an essential component of this cue. ndl function is required during oogenesis and also during the early stages of embryogenesis. (Hong and Hashimoto, 1995) Phenotypic and genetic analysis reveals that ndl has two distinct roles important for embryogenesis: one in establishing dorsoventral polarity, the other in ensuring structural integrity of the egg. (Hong and Hashimoto, 1996) A follicular cell marker system that yields a visible phenotype within the mature egg shell allows direct comparison of a clone and its effect on the dorsal ventral pattern of the embryos. Follicular epithelium has a lack of a localised requirement for ndl protease activity. (Nilson and Schupbach, 1998) The serine protease activity of ndl protein is essential for embryonic dorsoventral polarity. Active ndl protease is generated by autoproteolytic cleavage of a zymogen form. This activation is independent of the other known proteases involved in establishment of dorsoventral polarity and appears to occur symmetrically on the surface of the embryo. (LeMosy et al., 1998)
Comments About Molecular Function
	Catalytic activity of the protease domain of the modular ndl protein is required for dorsoventral patterning of the embryo. (LeMosy et al., 2000)
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_079223 RefSeq (Proteins) • NP_523947 DDBJ / EMBL / GenBank • AE003562 AAF50656 U29153 AAA83086 UniProtKB/Swiss-Prot • P98159
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Peptidase S1 and S6, chymotrypsin/Hap (IPR001254) Peptidase S1A, chymotrypsin (IPR001314) Low density lipoprotein-receptor, class A, cysteine-rich (IPR002172) Peptidase, trypsin-like serine and cysteine (IPR009003) Region of unknown function DUF1986 (IPR015420) MEROPS - An information resource for peptidases and the proteins that inhibit them • S01.950
Linkouts
	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 64189 DEDB - Drosophila exon database: splicing graphs • 5021 DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0002926 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0002926 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0002926 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0002926 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0002926 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0002926 InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000015896 Anopheles gambiae (Ensembl) ENSCAFP00000015316 Canis familiaris (Ensembl) ENSGALP00000024779 Gallus gallus (Ensembl) GSTENP00003546001 Tetraodon nigroviridis (Ensembl) ENSXETP00000013811 Xenopus tropicalis (Ensembl) ZDB-CDNA-040425-1762 Danio rerio (Zfin) ZDB-GENE-040426-834 Danio rerio (Zfin) Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /torstoll/nudel1.htm PANTHER - Protein classification by function, families, and pathways • FBgn0002926
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	CG10129 (Fakhouri et al., 2006) mat(3)2   mel(3)5   Ndl (Kim et al., 2002) ndl   nud (Ray and Schupbach, 1996) SP89 (Ross et al., 2003)
Name Synonym	nudel   Nudel (Fakhouri et al., 2006, D'Alterio et al., 2005, Tian and LeMosy, 2008)