This study underlines the importance of visual inspection of RNA-seq alignments when investigating alternatively spliced genes. We showed that heat and dehydration stresses increase overall abundance of SR45a mRNA while also increasing production of transcripts encoding the full-length SR45a protein relative to other splice variants.

Hyperhomocysteinemia known to be associated with increased thrombotic tendency has been considered as a risk factor for coronary artery disease, atherosclerosis, venous thrombosis, and stroke. There are three main genes MTHFR, cystathionine beta-synthase (CBS) and methionine synthase (MS) and it's genetic variant that are known to influence the homocysteine metabolism leading to hyperhomocysteinemia. There is scarcity of Indian data on hyperhomocysteinemia and genetics variants in patients with thrombosis. Hence the objective of present study was to determine MTHFR, CBS, and MS genetic variants in thrombosis patients from Indian population. Genetic variant analysis was performed on thrombosis patients to detect MTHFR C677T (rs1801133), MTHFR A1298C (rs1801131), MS A2756G (rs1805087) and CBS T833C (rs5742905) mutations. The mutant allele frequencies of MTHFR 677T, MTHFR 1298C, MS2756G and CBS 833C were observed to be 16.1%, 37.5%, 34.1% and 5.8% respectively. MTHFR 677TT genotype was observed to be significantly associated with elevated homocysteine (Hcy) levels (64.65 lmol/L) alleles as compared to CC alleles (32.43 lmol/L) and CT alleles (30.54 lmol/L). MTHFR A1298C, MS A2756G and CBS T833C genotypes did not showed significant association with higher Hcy levels. Thus, in Indian patients with thrombosis only MTHFR T677T genotype was observed to be significantly associated with hyperhomocysteinemia.

Summary: One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing and 3′ end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists.Availability and implementation: ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org.Contact: aloraine@uncc.edu

Summary Ultra-high throughput sequencing of cDNA (RNA-Seq) is an invaluable resource for investigating alternative splicing in an organism. Alternative splicing is a form of post-transcriptional regulation in which primary RNA transcripts from a single gene can be spliced in multiple ways leading to different RNA and protein products. In plants and other species, it has been shown that many genes involved in circadian regulation are alternatively spliced. As new RNA-Seq data sets become available, these data will lead to new insights into links between regulation RNA splicing and the circadian system. Analyzing RNA-Seq data sets requires software tools that can display RNA-Seq read alignments alongside gene models, enabling assessment of how treatments or developmental stages affect splicing patterns and production of novel variants. The Integrated Genome Browser software program (IGB) is a free and flexible desktop tool that enables discovery and quantification of alternative splicing. In this protocol, we use IGB and a cold-stress RNA-Seq data set to examine alternative splicing of Arabidopsis thaliana LHY, a circadian clock regulator. Integrated Genome Browser is freely available from http://www.bioviz.org.

Summary:One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing, and 3' end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists. Availability and Implementation: ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org.