Computational protocol: Characterization of TTN Novex Splicing Variants across Species and the Role of RBM20 in Novex-Specific Exon Splicing

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Protocol publication

[…] The TTN gene sequences of eight species were obtained through gene database from either University of California Santa Cruz (UCSC, Santa Cruz, CA, USA) [] or Ensembl [] genome browsers or National Center for Biotechnology Information (NCBI, Bethesda, MD, USA) nucleotide database []. The investigated species were human (Homo sapiens, GRCh38), pig (Sus scrofa, Sscrofa11), mouse (Mus musculus, GRCm38), rat (Rattus norvegicus, Rnor_6), chicken (Gallus gallus, Gallus_gallus-5), anole lizard (Anolis carolinensis, AnoCar2), frog (Xenopus laevis, Xenopus_laevis_v2), and zebrafish (Danio rerio, GRCz11). The sequences around Novex-1-, -2-, and -3-specific regions were retrieved by basic local alignment search tool (BLAST) []. All assembled Novex 1, 2, and 3 sequences were manually edited and checked for consistency. Multiple sequence alignments were processed with ClustalX [] and manually edited to be optimized. Genomic comparisons of cross-species were carried out by an online tool mVISTA []. […]

Pipeline specifications

Software tools BLASTN, Clustal W, mVISTA
Application Nucleotide sequence alignment
Organisms Homo sapiens, Sus scrofa, Mus musculus, Rattus norvegicus, Gallus gallus
Diseases Cardiomyopathy, Dilated, Heart Diseases, Cardiomyopathies