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Gene Dmel\exex

General Information
Symbol	Dmel\exex	Species	D. melanogaster
Name	extra-extra	Annotation symbol	CG8254
Feature type	protein_coding_gene	FlyBase ID	FBgn0041156
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	66A21-66A21	Sequence location	3L:7,941,291..7,944,667 [+]
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 extra-extra is referred to in FlyBase by the symbol exex (CG8254, FBgn0041156). It has the cytological map location 66A21. Its sequence location is 3L:7941291..7944667. Its molecular function is described as: transcription factor activity; sequence-specific DNA binding. It is involved in the biological processes: central nervous system development; nervous system development; axon target recognition; regulation of transcription; regulation of transcription, DNA-dependent. 11 alleles are reported. The phenotypes of these alleles are annotated with: anterior fascicle; embryonic central nervous system; RP1 neuron; RP3 neuron; RP4 neuron; RP5 neuron; EW1 neuron; EW2 neuron; EW3 neuron. It has one annotated transcript and one annotated polypeptide.
External Summaries
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 66A21-66A21   Limits computationally determined from genome sequence between P{PZ}l(3)0721708223&P{EP}Rac2EP3118 and P{lacW}Nmtj1C7
Experimentally Determined Cytological Location
Cytogenetic map Notes References 66B1-66B2 Determined by deficiency mapping (details unspecified).   (Broihier and Skeath, 2000)
Experimentally Determined Recombination Data
Location
Left of (cM)	h (Broihier and Skeath, 2002)
Right of (cM)	ru (Broihier and Skeath, 2002)
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\exex for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) exex-RA FBtr0076751  NM_139907   2377   525
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein exex-PA   FBpp0076468   56.8   525   10.10     NP_648164   AAF50503
Additional Polypeptide Data & Comments
Reported size (kD)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0041156
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE003557 AAF50503   AY084165 AAL89903   BI241888   BI243312   CO267440   EC199157
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9VSC2
Maps to
Does NOT map to
Identified with	RE39081 (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 point mutation exex[KK30] 3L:7,942,111..7,942,111 evidence=experimental pr_change=Q216@|exex-PA reported_na_change=C646T reported_pr_change=Q?@ na_change=C7942111T point mutation exex[TT219] 3L:7,943,792..7,943,792 evidence=experimental pr_change=R443@|exex-PA reported_na_change=C1435T reported_pr_change=R?@ na_change=C7943792T (Broihier and Skeath, 2002) point mutation exex[JJ154] 3L:7,943,947..7,943,947 evidence=experimental pr_change=W494@|exex-PA reported_na_change=G1589A reported_pr_change=W?@ na_change=G7943947A
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 4868
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
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 • FBgn0041156 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0041156 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0041156 BDGP expression data • Show all BDGP original images, annotations and embryonic microarray data for exex FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for exex 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
Other Phenotypes Allele neuroanatomy defective exexKK30 neuroanatomy defective | embryonic stage exexdsRNA.cOa neuroanatomy defective | embryonic stage, with Scer\GAL4sca-109-68 exexScer\UAS.cOa neuroanatomy defective, with Scer\GAL4elav-C155 exexScer\UAS.cBa Phenotype manifest in Allele embryonic ventral nervous system & neuron exexKK30 anterior fascicle exexKK30 anterior fascicle, with Scer\GAL4elav-C155 exexScer\UAS.cBa embryonic central nervous system, with Scer\GAL4elav.PLu exexScer\UAS.cBa abdominal posterior fascicle & embryo, with Scer\GAL4sca-109-68 exexScer\UAS.cOa anterior fascicle & embryo, with Scer\GAL4sca-109-68 exexScer\UAS.cOa embryonic central nervous system, with Scer\GAL4sca-109-68 exexScer\UAS.cOa longitudinal connective & embryo, with Scer\GAL4sca-109-68 exexScer\UAS.cOa neuromuscular junction & embryo exexdsRNA.cOa RP1 neuron exexdsRNA.cOa RP3 neuron exexdsRNA.cOa RP4 neuron exexdsRNA.cOa RP5 neuron exexdsRNA.cOa axon & embryo exexdsRNA.cOa growth cone & embryo exexdsRNA.cOa anterior fascicle & embryo exexdsRNA.cOa EW1 neuron exexdsRNA.cOa EW2 neuron exexdsRNA.cOa EW3 neuron exexdsRNA.cOa
Classical Alleles ( 7 )
For All Classical Alleles Show
Allele of exex Class Mutagen Stocks Known lesion exexAD121 ethyl methanesulfonate 0 Yes exexGal4 Δ2-3 gene conversion 0 -- exexJJ154 antimorph ethyl methanesulfonate 1 Yes exexKK30 amorph ethyl methanesulfonate 1 Yes exexLacZ P-element activity 0 -- exexTT219 ethyl methanesulfonate 0 Yes exexunspecified 0 --
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of exex Class Mutagen Stocks Known lesion exexGD4341 in vitro construct | RNAi in vitro construct | regulatory fusion 1 Yes exexScer\UAS.cBa in vitro construct | regulatory fusion 1 Yes exexScer\UAS.cOa in vitro construct | regulatory fusion 0 Yes exexdsRNA.cOa in vitro construct | RNAi 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(3L)pbl-X1
Useful duplication	Dp(3;3)M67C+2
Disrupted in	Df(3L)Exel6279 (Ryder, 2004.4.26) Df(3L)pbl-NR (Broihier and Skeath, 2002)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD4341} NA P{UAS-exex.B} NA P{UAS-exex.O} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions P{GT1}BG02871 NA insertion of enhancer trap binary system P{GAL4}exexGal4 No insertion of enhancer trap P{lacW}exexLacZ No
Related Comments
	Please look at the allele reports for the complete phenotype data Mutant embryos have extra eve-expressing neurons in the developing central nervous system. (Broihier and Skeath, 2000) Mis-expression of exex causes a thickening of ventral motor projections (but not dorsal motor projections), defects in longitudinal connectives and collapse of commissures. (Odden and Doe, 2001)
Gene Ontology: Function, Process & Cellular Component ( 8 )
Molecular Function
CV term Evidence References
sequence-specific DNA binding inferred from electronic annotation with InterPro:IPR001356 (FlyBase Curators et al., 2004-)
transcription factor activity inferred from sequence or structural similarity with EMBL:AF066860 (FlyBase, 1992-)
Biological Process
CV term Evidence References
axon target recognition inferred from mutant phenotype (Odden et al., 2002)
central nervous system development inferred from mutant phenotype (Odden and Doe, 2001) inferred from mutant phenotype (Broihier and Skeath, 2002)
nervous system development traceable author statement (Skeath and Thor, 2003)
regulation of transcription inferred from sequence or structural similarity with EMBL:AF066860 (FlyBase, 1992-)
regulation of transcription, DNA-dependent inferred from electronic annotation with InterPro:IPR001356 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with EMBL:AF066860 (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 exex allele Gene References exexKK30 HGTX (Broihier et al., 2004) exexunspecified tup (Broihier and Skeath, 2002)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 64310
Orthologs
Genome-wide drosophilid orthologs	Dana\GF23802 Dere\GG14457 Dgri\GH14983 Dmoj\GI13145 Dper\GL18045 Dpse\GA20934 Dsec\GM25007 Dsim\GD14043 Dvir\GJ13893 Dwil\GK20585 Dyak\GE21647
Curated drosophilid orthologs	Dpse\GA20934
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSCAFP00000024813 Canis familiaris (Ensembl) ENSCINP00000011818 Ciona intestinalis (Ensembl) NEWSINFRUP00000139897 Takifugu rubripes (Ensembl) ENSGALP00000010375 Gallus gallus (Ensembl) ENSP00000252971 Homo sapiens (Ensembl) ENSMMUP00000008418 Macaca mulatta (Ensembl) ENSMODP00000006391 Monodelphis domestica (Ensembl) ENSRNOP00000003080 Rattus norvegicus (Ensembl) GSTENP00031609001 Tetraodon nigroviridis (Ensembl) ENSXETP00000030365 Xenopus tropicalis (Ensembl) ENSXETP00000046719 Xenopus tropicalis (Ensembl) WBGene00041461 Caenorhabditis briggsae (Wormbase) WBGene00000446 Caenorhabditis elegans (Wormbase) ZDB-GENE-040415-2 Danio rerio (Zfin) MGI:95843 Mus musculus (Informatics)
Functional Complementation between Species
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
VDRC	v13716 w1118; P{GD4341}v13716
Bloomington	9929 w*; P{UAS-exex.B}H1/CyO 9930 w*; exexKK30 es/TM3, P{ftz-lacZ.ry+}TM3, Sb1 ry* 9931 w*; exexJJ154 h1 es/TM3, P{ftz-lacZ.ry+}TM3, Sb1 ry*
Genomic Clones ( 1 )
	BACR27G13
cDNA Clones ( 3 )
	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	RE39081
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE40904
Other clones	EK150131
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0041156 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0041156
Antibody Information
Other Information
Discoverer
Etymology
Identification
Position Effect Variegation Data
Relationship to Other Genes
Source for database identity of	Source for identity of: exex CG8254 (Broihier and Skeath, 2002)
Source for database merge of	Source for merge of: exex HB9 CG8254 (Odden, 2002.3.5)
Additional comments
Comments About Role
	exex plays a role in the development or differentiation of ventrally projecting motoneurons. (Odden and Doe, 2001) exex is central to motorneuron development. exex regulates neuronal fate by restricting expression of Lim3 and eve. (Broihier and Skeath, 2002)
Comments About Molecular Function
	Lim3 and exex are expressed in near identical patterns though neither is required for the activation of expression of the other. tup and exex also do not regulate each other's expression. exex represses Lim3 cell-non-autonomously in a subset of dorsally projecting motorneurons. exex and eve regulate each other's expression through gro-dependent crossrepression. Cross-repressive interactions between exex and eve delimit exex expression to ventral and lateral motor neurons and eve expression to dorsal motor neurons. (Broihier and Skeath, 2002)
Other Comments
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_139907 RefSeq (Proteins) • NP_648164 DDBJ / EMBL / GenBank • AE003557 AAF50503 AY084165 AAL89903 BI241888 UniProtKB/TrEMBL • Q9VSC2
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287)
Linkouts
	BDGP expression data • Show all BDGP original images, annotations and embryonic microarray data for exex BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 64310 DEDB - Drosophila exon database: splicing graphs • 4868 DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0041156 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0041156 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0041156 FlyExpress - Embryonic expression images (BDGP data) • FBgn0041156 FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0041156 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0041156 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0041156 InParanoid orthologs - Eukaryotic orthologs • ENSCAFP00000024813 Canis familiaris (Ensembl) ENSCINP00000011818 Ciona intestinalis (Ensembl) NEWSINFRUP00000139897 Takifugu rubripes (Ensembl) ENSGALP00000010375 Gallus gallus (Ensembl) ENSP00000252971 Homo sapiens (Ensembl) ENSMMUP00000008418 Macaca mulatta (Ensembl) ENSMODP00000006391 Monodelphis domestica (Ensembl) ENSRNOP00000003080 Rattus norvegicus (Ensembl) GSTENP00031609001 Tetraodon nigroviridis (Ensembl) ENSXETP00000030365 Xenopus tropicalis (Ensembl) ENSXETP00000046719 Xenopus tropicalis (Ensembl) WBGene00041461 Caenorhabditis briggsae (Wormbase) WBGene00000446 Caenorhabditis elegans (Wormbase) ZDB-GENE-040415-2 Danio rerio (Zfin) MGI:95843 Mus musculus (Informatics) Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /hjmuller/exex1.htm PANTHER - Protein classification by function, families, and pathways • FBgn0041156
Synonyms & Secondary IDs ( 9 )
Reported As
Symbol Synonym	CG8254 (Odden et al., 2002, Brody et al., 2002, Popovici et al., 2001, ) dHb9 (Broihier and Skeath, 2002, Rogulja-Ortmann et al., 2007, Fernandes et al., 2007) DHB9 (Odden and Doe, 2001) exex (Skeath, 2007.3.20) hb9 (Certel and Thor, 2004, Broihier et al., 2004, Yeh et al., 2006) HB9 (Odden et al., 2002, Skeath and Thor, 2003, Thor and Thomas, 2002, Cheesman et al., 2004) Hb9 (Layden et al., 2004, Layden et al., 2006)
Name Synonym	extra-extra (Broihier and Skeath, 2000) Extra-extra (Cho et al., 2005)
Secondary FlyBase IDs
	FBgn0035828
References ( 30 )
Generate a list of	All references relating to this gene ( 30 )
List References by type	Research paper  ( 11 ) Review  ( 2 ) Personal communication to FlyBase  ( 5 ) Abstract  ( 7 ) FlyBase analysis  ( 1 ) Computer file  ( 2 ) Automatic genome annotation  ( 1 ) Curated genome annotation  ( 1 )
Recent research papers ( 2 )
	Rogulja-Ortmann et al., 2007, Development 134(1): 105--116 Programmed cell death in the embryonic central nervous system of Drosophila melanogaster. [FBrf0194301] Layden et al., 2006, Dev. Biol. 291(2): 253--263 Zfh1, a somatic motor neuron transcription factor, regulates axon exit from the CNS. [FBrf0190136] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2006 Show reviews ...