SplicePort--An interactive splice-site analysis tool

Doğan, Rezarta Islamaj; Getoor, Lise; Wilbur, W. John; Mount, Stephen M.

doi:10.1093/nar/gkm407

Cited by 193 publications

(150 citation statements)

References 15 publications

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“…Among the 36 Arabidopsis lincRNAs annotated in TAIR9, 18 lincRNAs have introns (see Supplemental Data Set 14A online). Using SplicePort with Arabidopsis-specific parameters to scan for possible intron-exon splicing sites on lincRNAs (Dogan et al, 2007), we predicted full intron features with both conserved splicing donor and acceptor motifs on 595 lincRNAs and partial intron features on 1295 lincRNAs (see Supplemental Data Set 14B online).…”

Section: Design Of An Identifier System Of Arabidopsis Lincrnasmentioning

confidence: 99%

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

et al. 2012

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Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of introncontaining lincRNAs.

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Section: Design Of An Identifier System Of Arabidopsis Lincrnasmentioning

confidence: 99%

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

et al. 2012

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“…19 The effect on splicing of LDLR putative splice site variants was assessed using Splice-Site Predictor (Splice Port), 20 Neural Network Splice Site Prediction Tool (NNSSP), 21 and Neural Network Predictions of Splice Sites in Humans (NetGen2). 22 Functional assays of LDLR variants: c.-13a>G, c.818-3c>G, and c.1706-10G>a…”

Section: In Silico Analysismentioning

confidence: 99%

The importance of an integrated analysis of clinical, molecular, and functional data for the genetic diagnosis of familial hypercholesterolemia

Benito‐Vicente

Alves

Etxebarria

et al. 2015

Genetics in Medicine

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“…The potential interference of exon-intron boundary mutations with normal splicing efficiency was predicted by two web server programs: Splice Site Prediction by Neural Network (BDGP, http:==www.fruitfly.org=seq_tools=splice.html) [38] and SplicePort (http:==spliceport.cs.umd.edu=) [39].…”

Section: Splicing Predictionmentioning

confidence: 99%

Molecular basis of protein S deficiency in China

et al. 2013

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Protein S (ProS) is a physiological inhibitor of coagulation with an important function in the downregulation of thrombin generation. ProS deficiency is a major risk factor for venous thrombosis. This study enrolled 40 ProS-deficient probands to investigate the molecular basis of hereditary ProS deficiency in Chinese patients. A mutation analysis was performed by resequencing the PROS1 gene. Large deletions were identified by multiplex ligation-dependent probe amplification (MLPA) analysis. A total of 20 different mutations, including 15 novel mutations, were identified in 21 of the 40 index probands. Small mutations were detected in 18 (45.0%) probands, and large deletions were found in 3 (7.5%) probands, leaving 19 (47.5%) patients without causative variants. To evaluate the functional consequences of 2 novel missense variants, ex vivo thrombin-generation assays, bioinformatics tools, and in vitro expression studies were employed. The p.Asn365Lys ProS variant was found to have moderately impaired secretion and reduced activated protein C cofactor activity. In contrast, the p.Pro410His mutant appeared to have severely impaired secretion but full anticoagulant activity. This study is the largest investigation of ProS deficiency in China and the first investigation of the influence of Type I ProS missense mutations on the global level of coagulation function. The p.K196E mutation, which is common in the neighboring Japanese population, was not found in our Chinese population, and null mutations were common in our Chinese population but not common in Japan. Further genetic analysis is warranted to understand the causes of ProS deficiency in patients without a genetic explanation. Am. J.

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SplicePort--An interactive splice-site analysis tool

Cited by 193 publications

References 15 publications

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

The importance of an integrated analysis of clinical, molecular, and functional data for the genetic diagnosis of familial hypercholesterolemia

Molecular basis of protein S deficiency in China

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