Ambiguous splice sites distinguish circRNA and linear splicing in the human genome.

ABSTRACT:

Motivation

Identification of splice sites is critical to gene annotation and to determine which sequences control circRNA biogenesis. Full-length RNA transcripts could in principle complete annotations of introns and exons in genomes without external ontologies, i.e., ab initio. However, whether it is possible to reconstruct genomic positions where splicing occurs from full-length transcripts, even if sampled in the absence of noise, depends on the genome sequence composition. If it is not, there exist provable limits on the use of RNA-Seq to define splice locations (linear or circular) in the genome.

Results

We provide a formal definition of splice site ambiguity due to the genomic sequence by introducing equivalent junction, which is the set of local genomic positions resu

SUBMITTER: Dehghannasiri R 

PROVIDER: S-EPMC6477988 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature