9 research outputs found

    De novo genes in chimpanzee - Origins of de novo genes in human and chimpanzee

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    <p>GTF with the exonic coordinates of de novo genes in chimpanzee</p

    Additional File 1

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    Excel file with properties of the defined lncRNA regions and genes, a list of functionally characterized lncRNAs, and peptide sequences in mouse and human for the 10 functional micropeptides

    Long non-coding RNAs as a source of new peptides

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    <p>Supplementary data for the article: Ruiz-Orera, J., Messeguer, X., Subirana, J. A., & Alba, M. M. (2014). Long non-coding RNAs as a source of new peptides. eLife, 3, 1–24. doi:10.7554/eLife.03523</p> <p>Datasets contain genomic coordinates of the expressed transcripts (GTF) and putative translated peptides from lncRNA ORFs displaying significantly higher coding scores than expected for non-coding sequences (p-value < 0.05) (FASTA).</p

    De novo genes in human - Origins of de novo genes in human and chimpanzee

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    <p>GTF with the exonic coordinates of de novo genes in human</p

    Additional File 2

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    BED file with the coordinates of the lncRNA regions (exon), the 492 translated sequences (ORF) and the defined ribonucleoproteins (RNP)

    Functional and non-functional classes of peptides produced by long non-coding RNAs

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    Supplementary data for the article by Ruiz-Orera et al. (Functional and non-functional classes of peptides produced by long non-coding RNAs). It contains transcript assemblies for  human (hsa) and mouse (mmu) - hsa_transcripts.gtf, mmu_transcripts.gtf - as well as mouse ORF sequences and genomic coordinates - total_orfs.fa, total_orfs.gtf<br><br

    Villanueva-Cañas_etal_transcript_asemblies.tar.gz

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    Compressed file (.tar.gz) that contains the sequences of transcripts assembled from RNA-Seq data for different mammalian species. There are two types of files, novel.fa refers to transcripts that did not map to the gene annotations and annotated.fa to transcripts of already annotated genes. The data has been used in the publication Villanueva-Cañas et al. The uncompressed files occupy about 15 Gb.<br><br

    Villanueva-Cañas_etal_RNA-Seq_samples

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    File with information on the RNA-Seq datasets used to perform de novo transcript assembly for 30 different mammalian species from the publication Villanueva-Cañas et al. <br

    Villanueva-Cañas_etal_families_sequences

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    Compressed file (.tar.gz) that contains the protein sequences for all gene families generated in the publication Villanueva-Cañas et al. Uncompressing the file will generates a folder with subfolders for the families in each node. It occupies ~7.1 Mb.<br
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