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FB2026_01
,
released March 12, 2026
tra-2
RNA splice factor - functions with Transformer to bring about the sex specific splicing of Doublesex - functions in the fat body to regulate lipid storage.
Please see the JBrowse view of Dmel\tra2 for information on other features
To submit a correction to a gene model please use the Contact FlyBase form
AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.50
1.7 (northern blot); 1.427 (longest cDNA)
1.7 (northern blot)
264, 226, 179, 136 (aa)
256 (aa); 30 (kD)
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.
Extensively phosphorylated on serine residues in the RS domain.
The RS2 (Arg/Ser-rich domain 2) and RNP-CS (ribonucleoprotein consensus sequence) domains are required for both male sterility and female-specific dsx splicing but the RS1 domain is dispensable.
Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\tra2 using the Feature Mapper tool.
The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).
Comment: maternally deposited
Type A and Type B transcripts are expressed in both sexes. Type A mRNAs are predominant in somatic tissues, whereas Type B transcripts are more prominent in the female germ line.
Type C transcripts are male-specific.
tra2 transcripts are expressed throughout development and are present in both males and females in the germline and the soma.
JBrowse - Visual display of RNA-Seq signals
View Dmel\tra2 in JBrowse
Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
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 JBrowse for alignment of the cDNAs and ESTs to the gene model.
For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.
Gene expression is increased in response to the presence of two copies of Scer\GAL4hs.PB.
Area matching Drosophila Tra-2 gene. Acc. No. X57484.
Autoregulation of the tra2 226 isoform in male germ cells is necessary for normal spermatogenesis.
Hsap\tra-2α can partially replace tra2 during sexual differentiation.
Both HeLa and Kc cell nuclear extracts have been used for UV cross-linking experiments to determine which proteins bind to dsxRE as part of the native tra- and tra2-dependent dsx enhancer complex (dsxEC). Rbp1 and SRp30 have been identified that bind the 13-nucleotide repeats and purine rich element (PRE), respectively, of the dsx repeat element (dsxRE).
In somatic tissues two different tra2 isoforms function redundantly to direct female differentiation and female specific "dsx" pre-mRNA splicing. In the male germline a single isoform uniquely performs all necessary functions. This isoform regulates its own synthesis during spermatogenesis through a negative feedback mechanism involving intron retention.
Regulated alternative splicing of dsx pre-mRNA requires the dsxRE splicing enhancer, dsx repeat element. The activity of dsxRE requires tra and tra2 and one or more general splicing factors. A purine rich enhancer (PRE) sequence within the RE has been identified, this element functionally synergises with the dsxRE and is required for specific binding of tra2 to the dsxRE. Results demonstrate that positive control of dsx pre-mRNA splicing requires tra- and tra2- dependent assembly of a multiprotein complex on at least two distinct enhancer elements.
tra2 interacts with pre-mRNAs from over 60 genes and binding to pre-mRNAs is not dependent on the presence of female specific tra2 protein. tra2 is unlikely to perform a general function in constitutive RNA splicing and results suggest the existance of a distinct subset of RNAs that interact with tra2 with high affinity.
The choice of female identity in the germ line is dependent upon a somatic signalling pathway that requires the sex-non-specific tra2 gene but not the sex specific genes tra and dsx. The somatic signalling pathway appears to function continuously from embryogenesis to the larval stages to select and sustain female germ line identity.
The ribonucleoprotein consensus sequence (RNP-CS) of the tra2 product is required for male fertility and positive and negative control of alternative splicing in transgenic flies, as well as for in vitro binding of recombinant tra2 protein to dsx and tra2 pre-mRNAs. One of two arginine-serine (RS)- rich domains of tra2 is dispensable, while the other is indispensable for all in vivo functions, and is required for RNA binding and specific protein-protein interactions. Both protein-RNA and protein-protein interactions are involved in tra2-dependent activation and repression of alternative splicing.
A sequence comparison and numerical analysis of the RRM-containing (RNA recognition motif) proteins suggests that functionally related RRM-containing proteins have significant sequence similarities in their RRMs.
Female specific splicing of dsx is regulated by tra and tra2, which recruit general, serine/arginine-rich splicing factors to a regulatory element located downstream of a female-specific 3' splice site.
UV crosslinking/transfection of Kc cells showed tra2 protein binds to 13 nucleotide motif that is repeated 6 times in female-specific fourth exon that acts as cis exon for female-specific splicing of dsx pre-mRNA.
tra2 function directs the development of sexually dimorphic skeletal muscles.
Wild type functions of tra and tra2 are necessary in females for the expression of the female specific dsx function. In te absence of tra or tra2 function the alternative pattern of processing produces the dsx mRNA that encodes the male specific dsx protein.
Cotransfection analyses in which dsx, tra and tra2 cDNAs are expressed in Kc cells revealed that female specific splicing of dsx transcript is positively regulated by tra and tra2 gene products.
Cotransfection assays to examine regulatory interactions between specific cis-acting sequence elements of dsx pre-mRNA, and tra and tra2 gene products establish that tra and tra2 function to activate the use of the female specific exon.
Alternative splicing of tra2 is sex-specific in the germ line but not in the soma.
P element construct carrying a wild type copy of tra2 is capable of fully complementing both the sex determination and male sterility of the tra2 mutants. The tra2 gene product may function to control sexual differentiation by directly regulating the processing of the dsx pre-mRNA.
The mechanism of sex determination in the germ line has been analysed.
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 primordia 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, Kawabe and Oishi, 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 29oC, but phenotypic females when reared at 16oC (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). In X/X; tra2ts2 homozygotes reared throughout development at the permissive temperature of 16oC, yolk polypeptide synthesis occurs as in X/X; tra2ts2/+ controls; in X/X; tra2ts2 homozygotes raised and kept at 29oC, however, no synthesis of yolk polypeptides can be detected (Belote, Handler, Wolfner, Livak and Baker, 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 et al., 1988). tra2ts1 homozygous females do not always maintain male courtship behavior at 29oC, but transformed females hemizygous for tra2 <up>tra2ts1/Df(2R)trix</up> 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.
snoRNA:tra2-a is encoded in an intron of tra2.
