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Gene Dmel\tra2

General Information
Symbol	Dmel\tra2	Species	D. melanogaster
Name	transformer 2	Annotation symbol	CG10128
Feature type	protein_coding_gene	FlyBase ID	FBgn0003742
Created / Updated	2005-03-17/2005-03-17
Genomic Location
Chromosome (arm)	2R	Recombination map	2-70
Cytogenetic map	51B6-51B6	Sequence location	2R:10,489,509..10,491,857 [-]
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 transformer 2 is referred to in FlyBase by the symbol tra2 (CG10128, FBgn0003742). It has the cytological map location 51B6. Its sequence location is 2R:10489509..10491857. Its molecular function is described as: mRNA binding; nucleic acid binding; nucleotide binding. It is involved in the biological processes: sex determination; mRNA processing; female sex determination; reproduction; regulation of nuclear mRNA splicing, via spliceosome; RNA splicing; female somatic sex determination; male somatic sex determination; spermatogenesis; spliceosome assembly. 65 alleles are reported. The phenotypes of these alleles are annotated with 20 unique terms, many of which group under: adult segment; adult; organ system; anatomical structure; larval abdominal segment; larval abdominal segment 8; imaginal precursor; germ cell; female analia; tergite. It has 7 annotated transcripts and 7 annotated polypeptides.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	tra2: transformer 2 One role of tra2+ (like tra+) is to regulate sex determination by directing dsx+ in such a way that female primodia are expressed and male primodia repressed in chromosomal females. In addition, tra2+ serves as a regulator of spermiogenesis and copulation; as a result, functional sperm are produced by chromosomal males and transmitted to the females. Null or amorphic tra2 mutations, however, transform chromosomal females into flies that are phenotypically male in regard to external cuticular morphology, pigment pattern, internal genital ducts, and mating behavior. Their gonads are much reduced and lack sperm and they are not affected by mle (Fujihara et al., 1978). tra2 mutations in chromosomal males produce normal looking adult males showing normal sexual behavior, but the sperm are amotile (Watanabe, 1975; Belote and Baker, 1981). Some tra2 mutants are temperature-sensitive; homozygotes become phenotypic males when reared at 29, but phenotypic females when reared at 16 (Belote and Baker, 1983). When X/X;tra2ts2 homozygotes are shifted to the female-specifying temperature during or before the third instar, no development of the male accessory glands occurs (Chapman and Wolfner, 1988, Dev. Biol. 126: 195-202). In X/X;tra2ts2 homozygotes reared throughout development at the permissive temperature of 16, yolk polypeptide synthesis occurs as in X/X;tra2ts2/+ controls; in X/X;tra2ts2 homozygotes raised and kept at 29, however, no synthesis of yolk polypeptides can be detected (Belote et al., 1985). Temperature shift experiments with this temperature-sensitive allele show that tra2+ function must be present in the adult for the initiation and maintenance of yolk polypeptide synthesis. This control over YP on the part of tra2+ was shown to be at the level of transcription (Kraus, Lee, Lis, and Wolfner, 1988, Mol. Cell Biol. 8: 4756-64). tra2ts homozygous females do not always maintain male courtship behavior at 29, but transformed females hemizygous for tra2 [tra2ts1/Df(2R)trix] court in a reliably male fashion (Belote and Baker, 1987). Temperature-shift experiments indicate that the TSP for induction of male courtship starts in the last half of the pupal period and ends before the end of pupation.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 51B6-51B6   Limits computationally determined from genome sequence between P{lacW}ttvk03617&P{EP}ttvEP765 and P{lacW}Rpn6k00103
Experimentally Determined Cytological Location
Cytogenetic map Notes References 51B4-51B6 (determined by in situ hybridisation)   (Mattox et al., 1990) 51B4-51B6 (determined by in situ hybridisation)   (Goralski et al., 1989) 51B-51B (determined by in situ hybridisation)   (Amrein et al., 1988)
Experimentally Determined Recombination Data
Location	2-70 (Watanabe, 1975)
Left of (cM)	L (Watanabe, 1975)
Right of (cM)	Bl (Watanabe, 1975)
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\tra2 for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) tra2-RA FBtr0089617  NM_057416   1391   264 tra2-RB FBtr0089618  NM_057415   1420   136 tra2-RC FBtr0089619  NM_057417   1583   226 tra2-RD FBtr0089615  NM_134280   1228   226 tra2-RE FBtr0089616  NM_057418   1460   179 tra2-RF FBtr0089620  NM_206113   1396   264 tra2-RG FBtr0089621  NM_206112   1406   264
Additional Transcript Data & Comments
Reported size (kB)	1.7 (northern blot); 1.427 (longest cDNA) (Mattox et al., 1990) 1.7 (northern blot) (Goralski et al., 1989)
Comments	Type E transcripts are a second type of male-specific transcript that do not contain a 232-nucleotide intron retained by Type C male-specific transcripts. Type E transcripts start at the same 3 transcription start sites as Type C transcripts. Type E transcripts have not been sequenced. (Mattox et al., 1990) Type A and type B transcripts initiate at several non-sex-specific transcription start sites. Three closely spaced splice acceptor sites (x, y, z) are used in splicing exon 1 to exon 2; although y and z are similar to eukaryotic consensus splice acceptor sequence, x is not. Nuclease protection experiments show that acceptor sites y and z are used in type A and type B transcripts. (Mattox et al., 1990) Type A and type B transcripts initiate at several non-sex-specific transcription start sites. Three closely spaced splice acceptor sites (x, y, z) are used in splicing exon 1 to exon 2; although y and z are similar to eukaryotic consensus splice acceptor sequence, x is not. Nuclease digestion experiments show that acceptor sites y and z are used in type A and type B transcripts. (Mattox et al., 1990) Type C transcripts initiate at 3 sex-specific transcription start sites. Type C transcripts retain a 232 nucleotide intron between exons 3 and 4. (Mattox et al., 1990) The type D transcript uses an alternate acceptor when splicing exon 5 to exon 6. (Mattox et al., 1990)
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein tra2-PA   FBpp0088562   31.0   264   11.85     NP_476764   AAF58232 tra2-PB   FBpp0088563   15.6   136   11.76     NP_476763   AAM68560 tra2-PC   FBpp0088564   26.9   226   11.84     NP_476765   AAM68557 tra2-PD   FBpp0088560   26.9   226   11.84     NP_599107   AAM68558 tra2-PE   FBpp0088561   21.3   179   11.63     NP_476766   AAM68559 tra2-PF   FBpp0088947   31.0   264   11.85     NP_995835   AAS64910 tra2-PG   FBpp0088946   31.0   264   11.85     NP_995834   AAS64911
Additional Polypeptide Data & Comments
Reported size (kD)	264, 226, 179, 136 (aa) (Mattox et al., 1990) 256 (aa); 30 (kD) (Goralski et al., 1989)
Comments	Transcripts encoding the type C protein are male specific. (Mattox et al., 1990) The RNA binding domain, or ribonucleoprotein consensus sequence (RNP-CS) of tra2 protein is required for known tra2 functions. Mutations in this domain (amino acids 91-169, with numbering based on the 264 amino acid tra2 protein) affect male fertility, control of alternate splicing in transgenic flies, and in vitro binding of the protein to dsx and tra2 mRNAs. The tra2 protein also contains two arginine-serine (RS) rich domains, RS1 and RS2. Although RS1 is dispensable, RS2 is essential. In vitro, a region of RS2 is required for RNA binding. RS2 is also required for specific protein-protein interactions. tra2 protein interacts with itself, with tra protein, and the general splicing factor SF2 in vitro and in a yeast 2-hybrid system. (Amrein et al., 1994) tra and tra2 proteins as well as a set of SR proteins isolated from HeLa cells were shown to be necessary for the formation of a complex which commits the dsx pre-mRNA to the female-specific splicing pathway. The factors bind to a regulatory element located downstream of the 3\\' female-specific splice site. (Amrein et al., 1994)
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0003742
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • RNA recognition motif, RNP-1 (IPR000504) Nucleotide-binding, alpha-beta plait (IPR012677)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AC008306   AE003814 AAF58232   AE003814 AAM68557   AE003814 AAM68558   AE003814 AAM68559   AE003814 AAM68560   AE003814 AAS64910   AE003814 AAS64911   AI532731   AW944357   AX093890   AY058768 AAL13997   BH901023   BI373206   BI373244   BI568071   BP553916   BP553917   CO291090   CO312551   CO317269   CO319015   CO321334   CO327100   CO329358   CO336180   CZ477063   EC070597   EC089516   EC204825   EC211853   EC213799   EC233095   EC239001   EC244939   EC251908   EC265972   EL872816   J03155 AAA62771   M23633 AAA28953   M30939 AAA28954   M30939 AAA28955   M30939 AAA28956   M30939 AAA28957   M76381 AAA69686   X57484 CAA40722
UniProtKB/Swiss-Prot	P19018
UniProtKB/TrEMBL
Maps to	FBcl0297699 (FlyBase, 1992-)
Does NOT map to
Identified with	SD04329 (BDGP Project Members, 2000-) D1412 (BDGP Project Members, 1994-1999)
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 point mutation tra2[A15] 2R:10,490,263..10,490,263 na_change=C6595T reported_pr_change=S173F|FBrf0068398 evidence=experimental (Amrein et al., 1994) point mutation tra2[B] 2R:10,490,737..10,490,737 evidence=experimental na_change=C6121T comment=altered sequence presented in Figure 4 of FBrf0054067; introduces stop codon in the polypeptides encoded by each of the major tra2 transcripts, 155 amino acids upstream from their shared carboxyl terminus (Mattox and Baker, 1991) point mutation tra2[ts1] 2R:10,490,329..10,490,329 comment=amino acid numbering with respect to the 264 amino acid tra2-P1 evidence=experimental na_change=C6529T pr_change=A151V reported_na_change=C1667T|FBrf0051656 reported_pr_change=A151V|FBrf0051656 (Amrein et al., 1990) point mutation tra2[ts2] 2R:10,490,240..10,490,240 comment=amino acid numbering with respect to tra2-P1 evidence=experimental na_change=C6618T pr_change=P181S reported_na_change=C1756T|FBrf0051656 reported_pr_change=P181S|FBrf0051656 (Amrein et al., 1990) rescue fragment tra2[+t3.6] 2R:10,488,986..10,492,577 comment=position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental (McGuffin et al., 1998) rescue fragment tra2[+t3.9] 2R:10,488,570..10,492,509 comment=position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=EcoRI-EcoRI_rfrag linked_to=EcoRI-EcoRI_rfrag (Goralski et al., 1989) sequence variant tra2[A36] 2R:10,490,696..10,490,728 comment=11 amino acid deletion between aa 113-123; coordinates with respect to tra2-P1. evidence=experimental (Amrein et al., 1994)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 12526
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  adult stage | female   (Mattox et al., 1990)  adult stage | male  testis (Mattox et al., 1990)  adult stage | male   (Mattox et al., 1990)  adult stage | male   (Mattox et al., 1990)  adult stage | female   (Mattox et al., 1990)  adult stage | female  germline (Mattox et al., 1990)  adult stage | male   (Mattox et al., 1990)  adult stage | male   (Mattox et al., 1990)
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) AI532731
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003742 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0003742 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0003742
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable tra2CC01925 lethal | recessive tra2Pd2 Other Phenotypes Allele wild-type tra2+t3.9 tra2N.T:Zzzz\FLAG tra2RS2.carb.N.T:Zzzz\FLAG tra2Δ179 tra2Δ226-179 tra2Δ226 tra2Δ264-179 tra2Δ264 visible | conditional - heat sensitive tra2ts1 tra2ts2 visible, with Scer\GAL4Act5C tra2GD768 courtship defective | female | recessive tra2933 courtship defective, with Scer\GAL4fru.P1 tra2dsRNA.Scer\UAS sex-determination defective tra2A15 tra2A36 tra2D1 tra2D3 tra2D4 tra2D5.T:Zzzz\nls1 tra2D5 tra2OTF tra2P tra2PM1 tra2PM2 tra2Pd4 sex-determination defective (with Df(2R)trix) tra2B sex-determination defective | recessive tra21 tra2B tra2Δ264-226 sex-determination defective | conditional - heat sensitive tra2PM3 tra2PM4 tra2ts1 tra2ts2 sex-determination defective | female (with Df(2R)trix) tra2B sex-determination defective | female | conditional - heat sensitive tra2ts1 Sterility Allele sterile | recessive tra2933 female sterile | recessive tra2B male sterile tra2ts1 tra2Δ226-179 tra2Δ226 tra2Δ264-226 tra2Δ264 tra2ΔM1 male sterile | recessive tra2B male sterile | conditional - heat sensitive tra2ts2 male fertile tra2+t3.6 tra2+t3.9 tra2P tra2Pd1 tra2Pd4 tra2Δ179 tra2Δ264-179 male fertile | conditional - heat sensitive tra2ts2 female fertile tra2+t3.9 tra2Δ179 tra2Δ226-179 tra2Δ226 tra2Δ264-179 tra2Δ264 Phenotype manifest in Allele sex comb tra2Δ264-226 tra2B spermatozoon tra2ΔM1 female genitalia tra2933 female reproductive system tra2B spermatocyte | ectopic tra2B spermatid | ectopic tra2B spermatozoon | ectopic tra2B gonad tra2B tra2unspecified germ cell tra2B female genitalia, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS sex comb, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS abdominal tergite 6, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS abdominal tergite 7, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS abdominal tergite 5, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS abdominal sternite 6, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS anal plate, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS male repressed primordium | somatic clone, with Scer\GAL4Act5C.PP tra2dsRNA.Scer\UAS female genitalia, with Scer\GAL4T80 tra2dsRNA.Scer\UAS sex comb, with Scer\GAL4T80 tra2dsRNA.Scer\UAS abdominal tergite 6, with Scer\GAL4T80 tra2dsRNA.Scer\UAS abdominal tergite 7, with Scer\GAL4T80 tra2dsRNA.Scer\UAS abdominal tergite 5, with Scer\GAL4T80 tra2dsRNA.Scer\UAS abdominal sternite 6, with Scer\GAL4T80 tra2dsRNA.Scer\UAS anal plate, with Scer\GAL4T80 tra2dsRNA.Scer\UAS female genital disc, with Scer\GAL4ptc-559.1 tra2dsRNA.Scer\UAS male genital disc | ectopic | female, with Scer\GAL4ptc-559.1 tra2dsRNA.Scer\UAS male repressed primordium, with Scer\GAL4ptc-559.1 tra2dsRNA.Scer\UAS male repressed primordium, with Scer\GAL4en-e16E tra2dsRNA.Scer\UAS female reproductive system | conditional - heat sensitive tra2ts1 male repressed primordium | somatic clone tra2ts1 male repressed primordium | conditional - heat sensitive tra2ts1 male genitalia | ectopic | conditional - heat sensitive tra2ts1 female genitalia | conditional - heat sensitive tra2ts1 female analia | conditional - heat sensitive tra2ts1 ovary tra2ts2 male genitalia | ectopic, with Scer\GAL4Act5C tra2GD768 female genitalia, with Scer\GAL4Act5C tra2GD768 adult abdomen, with Scer\GAL4Act5C tra2GD768
Classical Alleles ( 19 )
For All Classical Alleles Show
Allele of tra2 Class Mutagen Stocks Known lesion tra21 loss of function spontaneous 0 -- tra2933 hypomorph P-element activity 0 -- tra2A15 amorph 0 Yes tra2A36 amorph 0 Yes tra2B amorph, loss of function ethyl methanesulfonate 0 Yes tra2CC01925 P-element activity 0 Yes tra2KG08361 P-element activity 1 -- tra2OTF hypomorph spontaneous 0 Yes tra2P PM hybrid dysgenesis 0 Yes tra2PM6 0 Yes tra2PM7 P-element activity 0 Yes tra2Pd1 P-element activity 0 -- tra2Pd2 PM hybrid dysgenesis 0