Preferentially retained introns and differentially used exons in the affected genes contain weak 5′ splice sites, but are ... of spliceosome components reveals that PRPF8 depletion decreases RNP complex formation at most splice sites in exon-intron ... otherwise indistinguishable from adjacent spliced introns. Experimental enhancement of splice-site strength in mini-gene ... transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns ...

The NetGene2 server uses a neural network combined with a rule-based system to predict intron splice sites in Arabidopsis ... The NetGene2 server uses a neural network combined with a rule-based system to predict intron splice sites in Arabidopsis ... The NetGene2 server uses a neural network combined with a rule-based system to predict intron splice sites in Arabidopsis ... Richmond, T. Prediction of intron splice sites. Genome Biol 1, reports223 (2000). https://doi.org/10.1186/gb-2000-1-1- ...

... and plncRNA introns (dplncRNA-intron = 0.165, turquoise), and ARs (white). Two-tailed Mann-Whitney test, ***P , 0.001; **P , ... We found that plncRNA exons (two-tailed Mann-Whitney test, P , 0.01; Figure 4C) but not introns (two-tailed Mann-Whitney test, ... Neither elncRNA exons nor their introns exhibited non-neutral evolution (two-tailed Mann-Whitney test, P , 0.1; Additional file ... Next we investigated the evolutionary signatures, in the two rodents, across the full length (exons and introns) of elncRNA or ...

The second class of methods focuses on specific types of alternative splicing (e.g., retained introns or alternative exons) and ... This was not surprising since the counting bins were similar between these methods (exons and introns). The transcript-level ... representing exons or introns) (SplicingGraph). Since the reads spanning exon junctions are expected to be the most informative ...

In non-coding regions, slightly more de novo events were found in introns than expected by chance (Additional file 1: Table S2 ... Using the UCSC Genome Browser, we identified all exons, introns, 3′-UTRs, and 5′-UTRs in the genome (hg19). We then intersected ... After identifying de novo mutations in STRs, we intersected the location of these mutations with exons, introns, 5′-UTRs, and 3 ...

4c, pFLI1, P1-P2). There was no binding of the circular RNA to remote intron regions (I1-I3) and the 5′-upstream control region ... The FECR1 expression cassette is composed of FLI1 exons 4-2-3 and the intron fragments containing the back-splicing elements. ... The expression cassette was synthesized by including part of the intron 1 sequence carrying the splicing acceptor sequence, ... exon 2, exon 3, exon 4, and part of intron 4 containing the splicing donor sequence. The synthetic expression cassette was ...

... cyanobacterial introns and shared ancestry of red and green algae. Plant Cell. 1999, 11: 1675-1694. 10.1105/tpc.11.9.1675. ...

... c HP1β distribution within an average intron. Introns are overall enriched for HP1β but depleted when compared with exons. d ... 6b), yet showed a clear enrichment gradient that increased from introns to exons: indeed, HP1β is more strongly enriched on ... Schwartz S, Meshorer E, Ast G. Chromatin organization marks exon-intron structure. Nat Struct Mol Biol. 2009;16:990-5. ... exons than on introns (Fig. 6c-e). This preferential association of HP1β with exons is consistent with a unique role in ...

This striking inefficiency deepens the mystery of the proliferation and persistence of introns. ... 0.74 introns per ribosomal gene). Pleiss et al. showed that introns in ribosomal protein genes, but not introns in other genes ... Many eukaryotes have reduced genomes with few introns. The few introns in Saccharomyces cerevisiae (only 0.05 per gene on ... This is that a large fraction of the introns in reduced genomes may serve important functions, whereas the numerous introns and ...

Intron comparisons. Related to the question of novel genes is the question of how many exons and introns are shared among CHESS ... Among the 533,563 introns contained in the union of the databases, 248,368 (47%) are shared among all three. 67,542 introns are ... Intron and transcript comparisons. We used a custom program to generate and compare lists of introns in RefSeq (release 108), ... introns and (b) transcripts that were shared among all combinations of the three databases. For the CHESS introns and ...

sgRNA directed Cas9 endonuclease cleavage in intron 2-3 and downstream of 3′UTR, and created double-strand break. By homologous ...

... in intron 9 [17]. A higher C4A copy number is associated with a greater risk for schizophrenia, proportional to its effects on ...

The input data sets do not distinguish exons from introns, so Transcribed labels include both types. For this reason, even ... initial intron, internal exons, internal introns, terminal exon, 1 bp-1 kbp 3 flanking, and 1-10 kbp 3′ flanking (https://www. ... transcribed regions have only an intermediate conservation-associated activity score because these regions include introns as ...

... particularly prokaryotes since transcript structural variation is quite different and intron/exon differences cannot be used to ...

One (HNF4 γ-related) contained no introns and expressed no detectable mRNA, whereas the other (FXR-related) produced mRNA at ... The positions of the intron gaps within FXR-r and FXR are boxed. Positions of termination codons within FXR-r are indicated by ...

There are also many more introns (4,730 in 43% of genes) than in S. cerevisiae (5% of genes); this suggests greater opportunity ...

... as a result of longer introns. Alternative splice forms are predicted to occur, but the extent to which each splice form is ... A third issue is the striking differences in gene size and intron length between the two types of protein prenyltransferases. ... as a result of longer introns. Alternative splice forms are predicted to occur, but the extent to which each splice form is ... the differences in gene size therefore result from differing intron lengths. ...

Seventy percent of motifs had a mean PhyloP above the intron baseline mean, exemplified again by an L1MC4a motif found for PTB ... A) Across the entire transcriptome (including introns), we counted overlapping aligned reads in the CLIP-Seq and null model ... In order to account for introns, we augmented the GENCODE v18 annotation with unspliced pre-RNA isoforms [65]. Using these ... As described above, we augmented the reference transcriptome with unspliced pre-RNA isoforms in order to capture intron binding ...

Two LoxP sites were inserted, flanking the upstream of 5′ UTR and intron 1 regions, resulting in loss and changes in size of ... and converted from genome-based coordinates to isoform-based coordinates to eliminate interference from introns in peak calling ...

One of these introns was also present in Ce-mif-3, but Ce-mif-3 and the other two C. elegans mif genes shared a set of introns ... There was an average of 9.3 introns per gene, with an average intron length of 316 bp (range 48-2,767 bp). The C. elegans ... 29 of 56 introns), and 25% of B. malayi introns (29 of 107) were conserved in C. elegans (Table 1). Of the 12 predicted B. ... As described above, however, Ce-mif-1 and Bm-mif-1 share two intron positions and are more similar to each other than either is ...

The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of ...

Additionally, mouse introns can exceed 100 kb and are on average 36 times longer than in Arabidopsis. Many isoforms per gene ... A reads Membership includes each frag it overlaps and excludes each incompatible frag (e.g., a spanned intron, a region ... S5C). Of all combinations tested, both sensitivity and precision were highest at the intron chain and full transcript level in ... or spurious intron retention. Long-read sequencing methods are designed to read RNA from TSS to PAS, but they remain ...

Jacquier A, Dujon B: An intron-encoded protein is active in a gene conversion process that spreads an intron into a ...

SNVs in untranslated regions and introns were not considered, as their somatic status and functional implications are unclear. ...

Two CpG sites in the first intron of the non-coding RNA gene LOC146880 (ENSG00000215769/hsa-mir-6080) in patients harboring t(9 ...

The deletion/insertion is situated 16 bp 5 to a splice site of the first intron, as can be ascertained from the sequence ... is situated in the first intron and 5 to the start codon. The allele is viable over a deficiency uncovering the CG17367 locus. ...

NeatCanvasFeatures is a specialized track which extends CanvasFeatures with "hat" cartoons for introns. It is described in the ... An experimental third type of feature track, NeatCanvasFeatures, which extends CanvasFeatures with specialized intron cartoons ... introns, UTRs), transcript alignments, single-nucleotide polymorphisms (SNPs), transposons, repeats, and so on. ... illustrates implementations of a custom intron rendering using both types of track. ...

Michel F, Westhof E. Modelling of the three-dimensional architecture of group i catalytic introns based on comparative sequence ...

... the exon-intron boundaries in the last exons of Cav-1, Cav-2, and Cav-3 are in analogous positions; and secondly, exon 2 of Cav ... is divided into two parts (2a and 2b) by an intron, whereas the two homologous portions in the Cav-1 and Cav-3 sequences are ...

... predictions are not expected to be very accurate and cannot show a name for the gene but give a rough idea of a possible intron ...