The Transcript-inferred Pathogenicity (TraP) score, presented here, is constructed to evaluate a single nucleotide variant's ability to cause disease by damaging a gene's transcripts and subsequently also its p
Noncoding transcript exon variant 3 4 3 Intron variant 46 83 97 Upstream gene variant 258 351 424 Downstream gene variant 28 36 51 TABLE S2. 10.1128/mSystems.00346-20.3 Functional prediction and annotation of mutated genes. Download Download: Download file (25KB). Dynamics of TEs in experiment...
The risk allele of rs356168 residing in a distal enhancer in intron 4 [96] is correlated with higher expression of an SNCA transcript with a 2.5-kb-long 3′UTR (third red arrow; 2520-nt 3′UTR length), suggesting implication of this variant in alternative polyadenylation [98]. (C) ...
(darker shade for peptides) are in the same reading frame.dAlternative protein N terminus for geneC1orf122was identified with two novel peptides.eTwo novel peptides serving as evidence for the existence of “retained intron” translation for theEGFRgene.fExtended exon protein variant of gene...
Intriguingly, lncRNAs produce more splice variants per exon, referred to as Transcript Complexity, than mRNAs. Most lncRNA splice variants are the product of the alternative last exon and exon skipping. LncRNAs and mRNAs with higher transcript complexity have shorter intron lengths. Longer exon ...
The Transcript-inferred Pathogenicity (TraP) score, presented here, is constructed to evaluate a single nucleotide variant's ability to cause disease by damaging a gene's transcripts and subsequently also its protein products. To ensure that TraP captures signals unrelated to amino-acid substitutions...
(Pol III) transcripts (such as tRNAs, 5S rRNA,7SK,7SL, and Alu, vault and Y RNAs37),Pol V transcriptsin plants and small Pol II transcripts such as (most) snRNAs and intron-derived snoRNAs38,39(~50–500 nt); and (3) lncRNAs (more than 500 nt), which are mostly generated by ...
An increase in sequence depth significantly improves both the accuracy and sensitivity of variant detection [4]. The accuracy of variant detection and detection rate is also dependent on the different variant detection algorithms [4]. Over the last few years, a number of bovine whole-genome ...
Furthermore, we found that 2,378 of the 5,127 lncRNA genes encoded more than one transcript variant, suggesting alternative splicing of a substantial portion of the lncRNAs inB.hordei(Fig.4F). Two lncRNAs gave rise to eleven separate isoforms, another three lncRNAs contained up to nine isofor...
back-spliced exons of precursor linear RNAs, including mRNAs and lncRNAs, and they account for a major portion of the circRNA family. In addition, the intron lariats escaping from degradation can also form intronic circRNAs. Although there are some other variant forms of circRNAs, such as ...