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Gene Dmel\Traf4

General Information
Symbol	Dmel\Traf4	Species	D. melanogaster
Name	TNF-receptor-associated factor 4	Annotation symbol	CG3048
Feature type	protein_coding_gene	FlyBase ID	FBgn0026319
Created / Updated	2003-12-01/2008-03-13
Genomic Location
Chromosome (arm)	2L	Recombination map
Cytogenetic map	24E1-24E4	Sequence location	2L:4,362,549..4,380,725 [+]
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 TNF-receptor-associated factor 4 is referred to in FlyBase by the symbol Traf4 (CG3048, FBgn0026319). It has the cytological map location 24E1-24E4. Its sequence location is 2L:4362549..4380725. Its molecular function is described as: protein binding; zinc ion binding. It is involved in the biological processes described with 14 unique terms, many of which group under: anatomical structure development; programmed cell death; organ development; embryonic development; larval development; cell death; transport; defense response; Toll signaling pathway; positive regulation of MAPKKK cascade; regulation of apoptosis; instar larval development; cell fate commitment. 9 alleles are reported. The phenotypes of these alleles are annotated with: eye; ommatidium; eye photoreceptor cell; eye disc; imaginal disc. It has 3 annotated transcripts and 3 annotated polypeptides.
External Summaries
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 24E1-24E4   Limits computationally determined from genome sequence between P{EP}Traf1EP578 and P{lacW}Tps1k08903&P{EP}morgueEP1184
Experimentally Determined Cytological Location
Cytogenetic map Notes References
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\Traf4 for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Traf4-RA FBtr0077429  NM_058068   2370   486 Traf4-RC FBtr0112925  NM_001103610   2306   559 Traf4-RD FBtr0290244     2186   387
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 Traf4-PA   FBpp0077119   53.7   486   8.74     NP_477416   AAF51024 Traf4-PC   FBpp0111838   61.5   559   8.83     NP_001097080   ABV53619 Traf4-PD   FBpp0288683   43.2   387   8.45
Additional Polypeptide Data & Comments
Reported size (kD)	486 (aa) (Liu et al., 1999)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0026319
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Zinc finger, TRAF-type (IPR001293) MATH (IPR002083) Ankyrin (IPR002110) TRAF-like (IPR008974) TNF receptor-associated factor TRAF (IPR012227) TRAF-type (IPR013322)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA541159   AC092232   AE003576 AAF51024   AE003576 AAN10343   AF079837 AAD47894   AF111422 AAG21891   AF119794 AAD34346   AW942585   AY094792 AAM11145   BI169933   BI212663   BI240664   BI241629   BI243625   BI368766   BI370128   BI373011   BI373576   BI375262   CK658908   CO152940   CO187871   CO265781   CO267314   CO273633   CO280859   CO284211   CO291662   CO296542   CO298011   CO307506   CO317873   CO326616   CO333514   CZ466297   CZ468428   EC059759   EC061935   EC066711   EC073946   EC085121   EC088760   EC201015   EC206546   EC221766   EC224769   EC228331   EC244799   EC249447   EC256542   EC260620   EC260818
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9UAC5 Q9XYR0
Maps to	FBcl0297466 (FlyBase, 1992-)
Does NOT map to
Identified with	LD20987 (BDGP Project Members, 2000-) RE63023 (Geuking et al., 2005)
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
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 • FBgn0026319 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0026319 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0026319 BDGP expression data • Show all BDGP original images, annotations and embryonic microarray data for Traf1 FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Traf4 Stage(s) 1-3 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 | larval stage Traf4ex1 lethal | pupal stage Traf4L2 Other Phenotypes Allele visible, with Scer\GAL4ey.PH Traf4EP578 size defective | larval stage Traf4ex1 cell death increase, with Scer\GAL4GMR.PF Traf4EP578 Traf4Scer\UAS.T:Ivir\HA1 cell death increase, with Scer\GAL4Act5C.PHb Traf4Scer\UAS.T:Ivir\HA1 Phenotype manifest in Allele eye, with Scer\GAL4ey.PH Traf4EP578 ommatidium, with Scer\GAL4GMR.PF Traf4EP578 Traf4Scer\UAS.T:Ivir\HA1 eye, with Scer\GAL4GMR.PF Traf4EP578 Traf4Scer\UAS.T:Ivir\HA1 eye photoreceptor cell, with Scer\GAL4GMR.PF Traf4EP578 eye disc, with Scer\GAL4GMR.PF Traf4EP578 Traf4Scer\UAS.T:Ivir\HA1 imaginal disc Traf4ex1 eye disc Traf4ex1 eye photoreceptor cell & axon Traf4ex1
Classical Alleles ( 5 )
For All Classical Alleles Show
Allele of Traf4 Class Mutagen Stocks Known lesion Traf4EP578 P-element activity 2 Yes Traf4L2 P-element activity 0 Yes Traf4c00231 piggyBac transposase 0 -- Traf4c03104 piggyBac transposase 1 -- Traf4ex1 amorph Δ2-3 0 Yes
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Traf4 Class Mutagen Stocks Known lesion Traf4GD10100 in vitro construct | RNAi in vitro construct | regulatory fusion 2 Yes Traf4Scer\UAS.T:Ivir\HA1 in vitro construct | coding region fusion in vitro construct | regulatory fusion 0 Yes Traf4Scer\UAS.cGa.T:Ivir\HA1 in vitro construct | regulatory fusion in vitro construct | coding region fusion 0 Yes Traf4dsRNA.cSa in vitro construct | RNAi 0 Yes
Aneuploid Aberrations
Useful deficiency	Df(2L)M24F-B
Disrupted in	Df(2L)Exel8011 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data miscellaneous insertions PBac{PB}Traf4c00231 NA PBac{PB}Traf4c03104 NA insertion of mobile activating element P{EP}Traf4EP578 NA
Related Comments
	Please look at the allele reports for the complete phenotype data S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells. (Stroschein-Stevenson et al., 2006)
Gene Ontology: Function, Process & Cellular Component ( 18 )
Molecular Function
CV term Evidence References
protein binding inferred from physical interaction with FLYBASE:baz; FB:FBgn0000163 (Wang et al., 2006)
zinc ion binding inferred from electronic annotation with InterPro:IPR001293, InterPro:IPR012227 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
Toll signaling pathway non-traceable author statement (Preiss et al., 2001)
asymmetric protein localization during cell fate commitment inferred from mutant phenotype (Wang et al., 2006)
autophagic cell death inferred from expression pattern (Gorski et al., 2003)
defense response non-traceable author statement (Lemaitre, 2000.12.20)
dorsal closure traceable author statement (Noselli and Agnes, 1999)
embryonic development inferred from expression pattern (Preiss et al., 2001)
eye development inferred from mutant phenotype (Cha et al., 2003)
imaginal disc fusion, thorax closure inferred from genetic interaction with FLYBASE:bsk; FB:FBgn0000229 (Cha et al., 2003)
instar larval development inferred from expression pattern (Preiss et al., 2001)
phagocytosis, engulfment inferred from mutant phenotype (Stroschein-Stevenson et al., 2006)
positive regulation of JNK cascade inferred from genetic interaction with FLYBASE:bsk; FB:FBgn0000229 inferred from genetic interaction with FLYBASE:hep; FB:FBgn0010303 inferred from genetic interaction with FLYBASE:Tak1; FB:FBgn0026323 (Cha et al., 2003)
positive regulation of apoptosis inferred from mutant phenotype (Cha et al., 2003)
salivary gland cell autophagic cell death inferred from expression pattern (Gorski et al., 2003)
signal transduction non-traceable author statement (Lemaitre, 2000.12.20)
Cellular Component
CV term Evidence References
apical cortex inferred from direct assay (Wang et al., 2006)
cytoplasm inferred from direct assay (Wang et al., 2006)
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 Traf4 allele Gene References Traf1EP578 CycE (Tseng and Hariharan, 2002) Traf1Scer\UAS.T:Ivir\HA1 th (Kuranaga et al., 2002) unspecified hep (Cha et al., 2003, Kuranaga et al., 2002) Tak1 (Cha et al., 2003) park (Cha et al., 2005) bsk (Cha et al., 2003)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 59832
Orthologs
Genome-wide drosophilid orthologs	Dana\GF21137 Dere\GG24997 Dgri\GH13208 Dmoj\GI22040 Dper\GL15107 Dpse\GA15869 Dsec\GM18466 Dsim\GD23279 Dvir\GJ16121 Dwil\GK24337 Dyak\Traf1
Curated drosophilid orthologs	Dpse\GA15869   Dyak\Traf1
Linkouts	InParanoid orthologs - Eukaryotic orthologs • ENSANGP00000024649 Anopheles gambiae (Ensembl) ENSBTAP00000016271 Bos taurus (Ensembl) ENSCAFP00000027741 Canis familiaris (Ensembl) ENSCINP00000008928 Ciona intestinalis (Ensembl) NEWSINFRUP00000168767 Takifugu rubripes (Ensembl) ENSGALP00000006340 Gallus gallus (Ensembl) ENSP00000262395 Homo sapiens (Ensembl) ENSMMUP00000028200 Macaca mulatta (Ensembl) ENSMODP00000024090 Monodelphis domestica (Ensembl) ENSPTRP00000015252 Pan troglodytes (Ensembl) ENSRNOP00000018468 Rattus norvegicus (Ensembl) GSTENP00030113001 Tetraodon nigroviridis (Ensembl) ENSXETP00000027864 Xenopus tropicalis (Ensembl) WBGene00040060 Caenorhabditis briggsae (Wormbase) WBGene00006612 Caenorhabditis elegans (Wormbase) ZDB-CDNA-040425-938 Danio rerio (Zfin) ZDB-GENE-040308-1 Danio rerio (Zfin) DDB0189132 Dictyostelium discoideum (Dictybase) DDB0216198 Dictyostelium discoideum (Dictybase) MGI:1202880 Mus musculus (Informatics)
Functional Complementation between Species
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 5 )
Szeged	- P{EP}Traf4EP578
Harvard	- PBac{PB}Traf4c03104
VDRC	v21214 w1118 P{GD10100}v21214 v21213 w1118; P{GD10100}v21213/TM3
Bloomington	17285 w1118; P{EP}Traf4EP578
Genomic Clones ( 2 )
	BACR09F08 BACR28K16
cDNA Clones ( 26 )
	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	LD20987
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE41320 RE60222 RE11250 RE38745 RE60905 RE56539 LP16207 RE37566 RE63023 RE17787 RE54796
Other clones	EK171117 EN00858 EK254720 EK197926 EK269563 EP04320 EK034521 EK155146 EK213938 EK165515 EK111702 EK149421 EK143625 EK307147
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0026319 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0026319
Antibody Information
Other Information
Discoverer
Etymology
Identification
Position Effect Variegation Data
Relationship to Other Genes
Source for database identity of	Source for identity of: Traf4 Traf1 (Leptin et al., 2008.2.11)
Source for database merge of
Additional comments
Comments About Role
Comments About Molecular Function
Other Comments
	Identification: Identified as a protein that interacts with msn in a yeast two-hybrid screen. (Liu et al., 1999)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_058068 NM_001103610 RefSeq (Proteins) • NP_477416 NP_001097080 DDBJ / EMBL / GenBank • AA541159 AC092232 AE003576 AAF51024 AAN10343 AF079837 AAD47894 AF111422 AAG21891 AF119794 AAD34346 AW942585 AY094792 AAM11145 CZ466297 CZ468428 UniProtKB/TrEMBL • Q9UAC5 Q9XYR0
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites •