We prove a formula for the geometric genus of splice-quotient singularities (in the sense of Neumann and Wahl). This formula enables us to compute the invariant from the resolution graph; in fact, it reduces the computation to that for splice-quotient singularities with smaller resolution graphs. We also discuss the dimension of the first cohomology groups of certain invertible sheaves on a res...

HIV-1 RNAs are generated through a complex splicing mechanism, resulting in a great diversity of transcripts, which are classified in three major categories: unspliced, singly spliced (SS), and doubly spliced (DS). Knowledge on HIV-1 RNA splicing in vivo and by non-subtype B viruses is scarce. Here we analyze HIV-1 RNA splice site usage in CD4+CD25+ lymphocytes from HIV-1-infected individuals t...

3 Building database from a single sample 4 3.1 Filtering based on transcript expression . . . . . . . . . . . . . . . . . . . . . . . . . 4 3.2 Variation annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3.2.1 SNVs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 3.2.2 INDELs . . . . . . . . . . . . . . . . . . . . . . . . . . ...

Splicing is an essential cellular process to generate mature transcripts from pre-mRNA. It requires the splice factor U1 small nuclear ribonucleoprotein (U1), which promotes exon recognition by base-pairing interaction with the splice donor site (SD). After U1 dissociation, exon recognition is maintained by U6 small nuclear ribonucleoproteins (U6). It has been shown that SD mutations lower the ...

This study evaluated the use of splice grafting as a propagation strategy for watermelon. In experiment 1, treatments consisted sucrose, antitranspirant A, B, auxin (indole-3-butyric acid (IBA)) at two concentrations (10 and 20 mg·L−1), plus water control. The survival (%) splice-grafted watermelon plants differed due to number days after treatment (p < 0.0001, both). At 21 grafting, treated...

To date the Simian Virus 40 (SV40) is the only proven example of a virus that recruits the mechanism of RNA trans-splicing to diversify its sequences and gene products. Thereby, two identical viral transcripts are efficiently joined by homologous trans-splicing triggering the formation of a highly transforming 100 kDa super T antigen. Sequences of other viruses including HIV-1 and the human ade...

Splicing of small introns in lower eucaryotes can be distinguished from vertebrate splicing by the inability of such introns to be expanded and by the inability of splice site mutations to cause exon skipping-properties suggesting that the intron rather than the exon is the unit of recognition. Vertebrates do contain small introns. To see if they possess properties similar to small introns in l...

Splice sites are locations in DNA which separate protein-coding regions (exons) from noncoding regions (introns). Recently, several works have approached the splice-junction problem by applying methods from the field of machine learning techniques. In this work, we propose a hierarchical multiclassifier (HM) architecture, whose results show a drastically error reduction with respect to the perf...

We obtain a new important basic result on splice-quotient singularities in an elegant combinatorial-geometric way: every level of the divisorial filtration of the ring of functions is generated by monomials of the defining coordinate functions. The elegant way is the language of of line bundles based on Okuma’s description of the function ring of the universal abelian cover. As an easy applicat...