Splicing definition

Zhang XH, Chasin LA (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 18 1241-1250... 

The possibility to identify and quantify protein-splicing variants by mass spectrometry has certainly attracted great interest from researchers in recent years, due to their variety of biological functions and their importance in many health- and disease-related processes. However, database searches are not yet optimized, and the ability to find a balance between the inclusion of all putative proteoform sequences (163) and the reduction of database size to control sequence redundancy and false-positives will definitely determine the success of this approach. 

Traditionally, a splicing construct contains an intron flanked by two exons. However, interactions across the exons play an important role in spliceosome assembly, a phenomenon termed exon definition.6 The presence of an upstream 3 -splice site generally stimulates the function of a weak downstream 5 -splice site. Similarly, a downstream 5 -splice site induces the usage of a weak upstream 3 -splice site. In this transactivation model, the 5 -cap structure of the first exon and the polyadenylation site in the terminal exons act as 3 - and 5 -splice sites, respectively, in promoting the spliceosome assembly. This view is reinforced by the observation that less efficiently spliced introns may be stimulated by moving the 5 -cap closer to the 5 -splice site or by inserting a functional 5 -splice- or polyadenylation site in the 3 -exon. However, exon definition seems only to play a minor role for efficiently spliced introns in vitro. 

Splice site prediction tools will generally predict the functional impact of a polymorphism within close vicinity of a splice donor or acceptor site, although they will not predict the functional effect of polymorphisms in other elements, such as lariat branch sites. Definition of consensus motifs for these elements (fig. 4.5) makes it possible to assess the potential functional impact of polymorphisms in these gene regions by simply inspecting the location of a polymorphism in relation to the consensus motif. As with all functional predictions, laboratory investigation is required to confirm the hypothesis. 

Definitive evidence for the role of Ul snRNA in splicing came from experiments which indicated that base pairing between the 5 splice site of a pre-mRNA and the 5 region of Ul snRNA is required for RNA splicing (Figure... 

Several kinds of studies suggest that transcription and RNA processing occur largely within discrete foci within the nucleus of eukaryotic cells. For instance, digital Imaging microscopy of human fibroblasts reveals that most of the nuclear polyadenylated RNA (i.e., unspllced and partially spliced pre-mRNA and nuclear mRNA) Is localized In about 100 foci (Figure 12-13). An SR protein Involved In exon definition (SC-35) is localized to the center of these same loci. 

Up until this point, the word loop has heen used in a very general way, referring to any audio file on your computer that is used in ACID. Loop originally meant a physical loop of audiotape that had the two ends spliced together to create an infinitely repeating audio clip. In much the same way, the archetypical loop file on a computer is a short file that will play hack seamlessly end to end— and perhaps most commercial loop files are designed to work that way. But the definition has definitely expanded to include material that will not endlessly and seamlessly loop, and there are a large number of loops that don t actually loop. 

FIGURE 8 The exon definition model. Exons in a precursor-RNA are recognized as units by U2 snRNP (U2) binding to the 3 splice site and U1 snRNP (U1) binding to the downstream 5 splice site. Subsequently adjacent exons are defined across the intron. In both recognition steps SR proteins function as bridging proteins. 

Definition 4. Let a triplet Rop = S, op) be a splicing scheme that an operation op R performs only in the contexts defined by the set of splicing relations in Rop. We say that Rop is an operation class of the splicing scheme for the operation op G R. 

The substring flanked by fi-s satisfies as the smallest working place for cpy, but cpy, still can not apply to it because, on the one hand, by the definition of cpy, it applies to a substring Si flanked by fi-s and on the other hand, the substring s has to contain only one JT part as the relations in i cpy constrain it. But it is not the case with the above smallest working place. There are two Sr parts between the repeats of /j. There are splicing relations for the repeats of fi in i dei but we will check later that which are not satisfied on the current string. 

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