which is much lower than the 100% conservation over 200 bp used to define mammalian ultraconserved elements4. Nonetheless, the set of 2,012 most highly conserved noncoding sequences (with, at most, 0.5 substitutions per site over at least 50 bp;Supplementary...
Therefore, accurate sequence-based prediction of chromatin features requires a flexible quantitative model capable of modeling such complex dependencies—and those predictions may then be used to estimate functional effects of noncoding variants.基于序列的,可以考虑到更多复杂的情况,这比单纯的依赖现有的motif...
Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection
Alterations in the nucleotide sequence of key TFBS or deviations in transcription of noncoding RNA genes likely have adverse effects on normal vascular cell phenotype and function. Here, the subject of noncoding sequences that influence smooth muscle cell or endothelial cell phenotype will be ...
The years following publication of the draft human genome sequence brought about a dramatic change in our understanding of the organization and expression of genetic information. Discoveries of new classes of RNA without protein coding potential and larg
Please cite:Musacchia F, Basu S, Petrosino G, Salvemini M, Sanges R. Annocript: a flexible pipeline for the annotation of transcriptomes which can also identify putative long non-coding RNA To start using it you must follow instructions in theGUIDEfolder. Below is a simple introduction of wh...
Concerted evolution events amongBEX1andBEX2protein-coding sequences.A maximum likelihood phylogenetic tree for theBEXfamily members' protein-coding regions was constructed using the program BASEML [54] and a DNA sequence alignment. The alignment was bootstrapped a 1000 times using the neighbour-joinin...
are short and contribute to regulating the translation of the longer coding sequences (CDSs) located downstream.94,95,96,97,98 With this mindboggling complexity in mind, in this review we aim to provide an overview of cases in which the categorization of “coding gene” vs “non-coding gene...
1a, b). We then used RiboTaper13 to identify all expressed ORFs from our dataset that belong to known consensus coding sequence (CCDS) regions of the genome. These were filtered to include only ORFs encoding peptides less than 100 amino acids and exclude those overlapping with larger proteins...
Innovations in high-throughout sequencing approaches are being marshaled to both reveal the composition of the abundant and heterogeneous noncoding RNAs th