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Splice junction

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Discerning novel splice junctions derived from RNA-seq alignment: A deep learning approach

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In the first mode (Splice Junction Mode), the input splice junction se- quences were with the length of 120 nucleotides, reflect- ing 30 nucleotides of upstream and downstream nucleotides for both donor and acceptor splice site. Splice Junction Mode achieved an auPRC score of for Donor+Acceptor Site Mode.. 2 The ROC curves of DeepSplice Splice Junction Mode and Donor+Acceptor Site Mode for splice junction classification on the GENCODE data set.

Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene

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S4), expressions of P4HB -02 and P4HB-027 (but not of P4HB or P4HB-021 ) decreased vs. 6 PCR amplification of the splice junction of splice variants P4HB -02, P4HB -021 and P4HB -027. The specific splice junction of P4HB -02 (89 bp) and 027 (211 bp) were amplified in HCT-116 cells and SK-N-SH cells. For the amplification of P4HB -021, the expected fragment was 148 bp.

Illuminating the dark side of the human transcriptome with long read transcript sequencing

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The TAMA High pipeline with stringent LDE filtra- tion had the lowest average wobble values per splice junction while the TAMA Low pipeline produced the highest average wobble (Fig.

Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias

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The significances of the median differences in splice junction and UTR read ratios between B73 cis-eQTL genes and Mo17 cis-eQTL genes were calculated using the Wilcoxon rank sum test.. cis-eQTL: Cis-acting expression quantitative trait loci. org/10.1186/s .

Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus

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Table 4 Splice junction sites of the VZV transcriptome. Five of the longer TSS vari- ants contain uORFs, while their shorter isoform does not. 9 panel c), making 22.07% of all As of the transcript edited.. Using the MEME software suite [70] we could de- tect a slight enrichment of the GU dinucleotide preceding.

Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data

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An average of 90% of predicted splice junctions across the nine tissues were supported by Illumina-seq reads that spanned the splice junction (Additional file 1: Figure S2), support- ing the accuracy of the transcript definition from Iso-seq reads.. We evaluated the set of Iso-seq-defined transcripts for potential tissue-specific transcripts.

Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

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For in- stance, if a read contains a single splice junction, a first seed is mapped to a donor splice site and the unmapped portion of the read is mapped again (in this case to an acceptor splice site). alignments of the entire read sequence by stitching to- gether all the seeds that were aligned to the genome in the first step [17].

Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development

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Computational identification of circRNAs and lncRNAs To detect most back-splice junction sites of circRNAs in Arabidopsis leaves, we used three tools, find_circ [14], circRNA_finder [23] and CIRI2 [24] since the combin- ation of their results could achieve more unbiased circRNA detection [25]. To predict novel lncRNAs in Arabidopsis leaves, the sequencing reads were first aligned to Arabidopsis genome using Tophat2 [26].

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

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We further required good conservation of the splice junction in the orthologous loci in other mammals, or in the closest paralogues if an orthologue could not be found. The size of the libraries was checked on high-sensitivity DNA chips (Agilent). When clear mapping artefacts were detected, the counts of the corresponding OR gene were set to 0.

he thong quan ly diem sinh vien

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(f) Trace and sequence of Dyt1 mRNA transcript in KD mice at the splice junction between exons 4 and 5 showed that KD mice have mRNA transcripts that are unaltered. NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript Neurosci Res. Page 9 NIH-PA Author Manuscript Fig. Motor performance of Dyt1 KD mice on rotarod, beam-walking and open-field tests. (a) Dyt1 KD mice performed comparable to WT mice on the accelerated rotarod test.

A high-throughput SNP discovery strategy for RNA-seq data

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The impact of read length on quantification of differentially expressed genes and splice junction detection. The impacts of read length and transcriptome complexity for de novo assembly: a simulation study.. Read length versus depth of coverage for viral quasispecies reconstruction. De novo fragment assembly with short mate-paired reads: does the read length matter? Genome Res.

A new mechanism for a familiar mutation – bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement

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Having demonstrated splice enhancement and expres- sion effects for the K232A mutation in vitro, we revisited the potential role of the variant on expression in our mammary RNA-seq dataset. The association of the two lead variants was greatly reduced (Fig. a represents the splicing ratio (spliced transcripts:unspliced transcripts) measured by qPCR in each of the individual replicates for the intron 7 junction.

Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

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back-splice and canonical junction count frequencies between time points.

Splice Enclosure Solutions

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This kit is used to protect fiber ribbons between the cable clamp and splice tray.. 1 The number of protective tubes per central tube is calculated as follows:. Divide the number of fibers per central tube (typically between 144 and 864) by the number of fibers to be spliced in each splice tray.. Example: If the central tube has 864 fibers with 36 fibers per splice tray, then the breakout base would require 24 protective tubes.. To order protective tubing cutting tool, see page 118..

Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

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Prediction and quantification of splice events from RNA-Seq data

OMGene: Mutual improvement of gene models through optimisation of evolutionary conservation

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The changes made by OMGene were assessed relative to splice-mapped RNA-seq data to assess the level to which it had improved the gene models. The low resolution of junction data for fungal genes reflects the rarity of complex gene models in these species, and thus the low likelihood that deviations from simple, single-exon gene models are correct.

FiberGuide® Snap-Fit Junction

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Snap-Fit Junction. ADC’s FiberGuide Snap-Fit Junction is a completely tool-less junction. Quick, and easy to use, the FiberGuide Snap-Fit Junction saves installers valuable time and money.. 4x4 Snap-Fit Junction Kit Assembly 4x6 Snap-Fit Junction Kit Assembly 4x12 Snap-Fit Junction Kit Assembly. 4x12 Snap-Fit Junction 4x4 Snap-Fit Junction 4x6 Snap-Fit Junction

FL1000 High-Density Termination and Splice Panels

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AE FL1000 144- and 288-Position 13 RU Panels. 144- and 288-Position 13 RU Panels Specifications (H x W x D). 144- and 288-position panel (13 RU): 578 mm x 483/584 mm x 305mm. 288-Position Termination/Splice Chassis. 288-position termination/splice panels. 288-Position Termination/Splice Panel. 6 144-position. termination/splice (13 RU). 2 Heat shrink (single fiber fusion) 3 Mechanical (mass fusion)*. 144-Position Empty Termination/Splice Chassis.

Junction Field Effect Transistors

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Application of a reverse bias voltage on the drain/gate terminals results in the formation of depletion regions at the PN junction. Continuing to increase the voltage will result in the depletion regions touching in the middle of the channel. H-2 01/99. Databook.fxp PM Page H-2. Connecting the gate to the source and applying a voltage between the drain and source also produces the formation of a depletion region at the PN junction..

Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

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Splice sites with one difference to a canonical splice site are more frequent than more diverged splice sites. A similar trend can be observed around the major non-canonical splice sites AT-AC (Fig. vinifera (Additional files 10, 11 and 12), there were slightly less genes with non-canonical splice sites close to the centro- meres. RNA-Seq reads supported 224 of these CA-GG splice sites. Non-canonical splice sites in single copy genes.