Preferentially retained introns and differentially used exons in the affected genes contain weak 5′ splice sites, but are ... iCLIP of spliceosome components reveals that PRPF8 depletion decreases RNP complex formation at most splice sites in exon- ... Primers spanning exon 4: intron 4 of CDC23, exon 10: intron 10 of CDC20, exon 19: intron 19 and exon 2: intron 2 of ASPM, and ... Primers spanning exon 3: intron 4 of CDC23, exon 9: intron 10 of CDC20, exon 18: intron 19 and exon 1: intron 2 of ASPM, and ...

... consisting of FLI1 exons 4-2-3, referred to as FECR1.Overexpression of FECR1 enhances invasiveness of MDA-MB231 breast cancer ... Region 1, the PCR product covers exon 4 to exon 6; region 2, the PCR product covers exon 3 to exon 4. **p , 0.01 as compared ... FECR1 is formed by back splicing of FLI1 exon 4 to exon 2 and is composed of exons 4-2-3. b Detection of FECR1 circular RNA ... exon 2, exon 3, exon 4, and part of intron 4 containing the splicing donor sequence. The synthetic expression cassette was ...

1C. De novo STR events are significantly underrepresented in the coding regions of exons (p , 1e − 6) but not in the 5′- and 3 ... Only two mutations were found in exons: a trinucleotide (CCG) repeat mutation in USP24 and a second trinucleotide (CGG) repeat ... 1C), similar to previous findings of variability at these loci[26]. Only two of these mutations occur in exons, and ... Using the UCSC Genome Browser, we identified all exons, introns, 3′-UTRs, and 5′-UTRs in the genome (hg19). We then intersected ...

... number of exons or transcriptional orientation relative to their closest neighboring gene. Nevertheless, elncRNAs are more ... we compared the substitution rates of plncRNA introns and exons. We found that plncRNA exons (two-tailed Mann-Whitney test, P ... Mouse-rat nucleotide substitution rate for transcribed and spliced plncRNA exons (dplncRNA-exon = 0.156, violet) and plncRNA ... Neither elncRNA exons nor their introns exhibited non-neutral evolution (two-tailed Mann-Whitney test, P , 0.1; Additional file ...

... such as annotation-based exon-level counting, differential analysis of the percentage spliced in, or quantitative analysis of ... In addition, using exon-level bins allows the detection of events (such as exon skipping) that are not annotated as part of an ... For methods based on the original (non-disjoint) exons (such as featureCounts-exon), we expect a lower power to detect switches ... representing exons or introns) (SplicingGraph). Since the reads spanning exon junctions are expected to be the most informative ...

The maize transposable Ds1 element is alternatively spliced from exon sequences. Mol Cell Biol. 1991;11:6192-6. ...

... first exon, or last exon) without spanning beyond the first or last exon of the gene and were classified as whole-gene copy ... Recurring exon deletions in the HP (haptoglobin) gene contribute to lower blood cholesterol levels. Nat Genet. 2016;48:359-66. ... Duplications were classified as LoF if they duplicated one or more bases from any annotated internal exon (i.e. neither the 5 ... ACVR2A (exons 5-6, forward): 5′ GTT ACA CCT AAG CCA CCC TAT TAC 3′ ...

b) Enrichment analysis for the HCR CNVs that overlap with exons of UCSC gene track. For calculating the significance ...

The minor fraction of HP1β that is chromatin-bound in ESCs is enriched within exons, unlike the situation in differentiated ... d HP1β distribution within an average exon. e HP1β is localized in gene bodies and exons. Examples of HP1β ChIP-Seq signal in ... HP1β is more strongly enriched on exons than on introns (Fig. 6c-e). This preferential association of HP1β with exons is ... Microarray analysis was performed with Affymetrix Exon Arrays MoEx-1_0-st-v1, with RNA purified from ESCs and EBs using the ...

Briefly, to generate mice carrying loxP-flanked alleles of Pcdh20 (Pcdh20fl/fl), the exon 3 of Pcdh20-001 gene was targeted, ... By homologous recombination, LoxP sites was inserted to flank exon 3 of Pcdh20. Pcdh20fl/fl mice were crossed with Villin-Cre ...

We estimate that the genome contains 65,000-75,000 transcriptional units, with exon sequences comprising 4%. The creation of a ... starting position of exon on BAC contig, end position of exon on BAC contig, exon orientation, transcript orientation ( ... starting position on exon (or feature), end position on exon (or feature), score (BlastN, BlastX). The index was first ordered ... Multiple exons not residing in intact ORFs were consolidated until the occurrence of exons in a partial or complete ORF. ...

... initial exon, initial intron, internal exons, internal introns, terminal exon, 1 bp-1 kbp 3 flanking, and 1-10 kbp 3′ flanking ... 3a). The first exon of some genes is annotated as Promoter rather than Transcribed (Fig. 3a); this is likely due either to ... The input data sets do not distinguish exons from introns, so Transcribed labels include both types. For this reason, even ... Box-and-arrow pictograms indicate genes, where boxes indicate exons and arrows indicate the direction of transcription. Genome ...

When the cost of the assay is high and there are many candidate guide sequences, e.g., for a long exon in rats, the priority ... Potential off-targets can be filtered to retain only those in exons, those that may be of concern when isolating cell clones, ... and split them by exon and cell type. For the newer dataset from Doench et al. [34], we used their Supplemental Table 16 and ... NGG guide sequences in human coding exons, the ones with a GC content ,75 % constitute only 13 %, so they can usually be ...

The first mutation detected was a 41-bp deletion in the first exon of CG15000, which during the course of this study turned out ... Exons are depicted and coding region is symbolized by filled rectangles. Small half arrows indicate primer-binding sites of the ... We designed PCR primers for each gene to be scored such that they encompass the first coding exon and the PCR products are ... HMPA-induced deletions are very likely to induce null mutations when hitting an exon. EMS, on the other hand, primarily induces ...

The Alu exon and TE exon coefficients have large error bars because there were few examples to learn from. ... Enrichments and depletions of RBP-TE associations were broadly similar in mRNA exons, lncRNA exons, and introns (Figure S1 in ... The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science. 2003, 300: 1288-1291. 10.1126/ ... The top track draws an example gene with blue boxes representing exons. The track below draws a set of example TEs, colored by ...

The chromosomal locations and number of exons from protein prenyltransferase genes in the major eukaryotic model organisms are ... The number of exons in the two types of genes are similar; the differences in gene size therefore result from differing intron ...

Conditional Ythdf2 gene-targeted mouse contains LoxP sites flanking the 5′ UTR and exon 1 of the endogenous Ythdf2 locus. WT_F ... UTR and exon 1 of the endogenous Ythdf2 locus using CRISPR-Cas9 technology (Fig. 1a). The Ythdf2+/loxp mice were crossed with ... wild-type forward primer, WT_R wild-type reverse primer, KO_F Ythdf2−/− forward primer, WT_R Ythdf2−/− reverse primer, Ex exon ...

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

Exon shuffling has led to transcription factors unique to plants that contain both homeodomains and leucine zippers. In ...

The assay was targeted at the exons and proximal splice sites. Forward and reverse primers were tailed with Illumina Adapter ...

Reads mapped to exons were used for scRNA-seq samples, whereas both intronic and exonic reads were counted for snRNA-seq. ...

Rogozin I, Sverdlov A, Babenko V, Koonin E: Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform ... Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Mol Biol Evol. 2008, 25: 375-382. ... but the inclusion or exclusion of exons, the evolution of which may proceed differently [10]. ...

... was present in both the transcription start site and the first exon, both annotations were used. ...

We used HT-Seq with the following arguments: -t exon -i gene_name -m intersection-strict -r pos to count reads overlapping gene ...

Intron/exon boundaries that are conserved between the nematodes are indicated by asterisks. White boxes represent the ... Genes are indicated by exon (box) and intron (bracket) structures. For each species, the direction of transcription of the ... revealed that Bm-mif-1 and Ce-mif-1 shared two intron/exon boundaries also found in vertebrate MIFs. One of these introns was ...

Martin F, Bovet L, Cordier A, Stanke M, Gunduz I, Peitsch MC, Ivanov NV: Design of a Tobacco Exon Array with application to ... The results show that the design of the Affymetrix exon probes is suitable for the analyses of gene expression in both tobacco ... Probes from the Tobacco Exon Array [49] were selected by mapping them to the identified genome regions using LAST [87] and ... Similar to the Cd genes described above, this type of comparison confirms that the design of the Affymetrix exon probes is ...

Exome sequencing projects use exon capture kits that target most "known" exons. Any exons that are not listed in standard human ... This 4-exon gene occurs on the forward strand of chromosome 10 at the coordinates shown. The exon lengths are 134, 30, 136, and ... Novel transcripts may in some cases represent novel combinations of exons-e.g., exon-skipping events-but in many cases, they ... We considered a gene to be supported if any GTEx transcript matched any of the genes exons; we did not require support for the ...

Assemblies with a matching exon chain to a RefSeq transcript (left) or no match to a RefSeq transcript (right). B F-measure of ... All matching exon chains were considered matches, and precision was measured as the percent of all assemblies that match RefSeq ... F Performance of three transcript assemblers, measured by total number of reference-matching exon chains (x-axis) vs. percent ... Although 79% of FLNC alignments fully matched the exon chain of a TAIR10 or Araport11 transcript, most were copies of a few ...

Exon Atlas layout displays a plugin showing data for a previously unpublished reference expression data set using a mouse exon ...

... then it may be difficult to identify the actual gene that is trapped because splicing may occur with exons that reside hundreds ... a functional splice donor site and the resulting fusion must result in the reporter gene being in frame with the upstream exons ...