We are analyzing https://link.springer.com/article/10.1186/1471-2164-10-162.

Title:
Evolution of alternative and constitutive regions of mammalian 5'UTRs | BMC Genomics
Description:
Background Alternative splicing (AS) in protein-coding sequences has emerged as an important mechanism of regulation and diversification of animal gene function. By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5
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Keywords {🔍}

alternative, regions, uorfs, pubmed, utrs, article, genes, human, alt, google, scholar, utr, cas, constit, mouse, gene, analysis, control, set, uaugs, expression, constitutive, sequences, elements, table, translation, mammalian, data, central, regulation, nucleotides, upstream, translational, isoforms, nonalt, selection, cds, splicing, conserved, uorf, res, start, sequence, codon, altutr, sets, levels, regulatory, transcripts, length,

Topics {✒️}

open access article neuronal nitric-oxide synthase mu-opioid receptor gene article download pdf wnt/b-catenin signaling pamilo-bianchi-li method [64 transcription factor-encoding genes exert species-specific regulation intermolecular mrna-rrna hybridization alternative pre-mrna splicing genome-wide studies aimed potential regulatory elements post-transcriptional levels tissue-specific gene regulation large-scale studies based open reading frames similar tissue-specific preferences related subjects closely related species full size image gene-specific est sequences post-transcriptional regulation alternative splice forms translational control element de serres fj transcription-initiation sites putative regulatory motifs conserved species-specific uaugs conserved regulatory elements potential control elements privacy choices/manage cookies human protein-encoding transcriptomes hereinafter alt_5'utr sets important regulatory factor alternative transcription initiation original alt_5'utr set putative control elements genome-wide comparative analysis transcription start sites background levels genome-wide comparative study post-genome biology inhibitory peptide encoded species-specific fashion [38] full access european economic area transcription factors translational regulatory properties biomed central species-specific level

Questions {❓}

Are 5'UTR lengths distributed differently between genes that exhibit 5'UTR transcript diversity versus those that do not?
We further addressed the question whether uORFs are more prevalent in 5'UTRs of genes that contain alternative regions?

Schema {🗺️}

WebPage:
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         headline:Evolution of alternative and constitutive regions of mammalian 5'UTRs
         description:Alternative splicing (AS) in protein-coding sequences has emerged as an important mechanism of regulation and diversification of animal gene function. By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized. We evaluated the abundance, conservation and evolution of putative regulatory control elements, namely, upstream start codons (uAUGs) and open reading frames (uORFs), in the 5'UTRs of human and mouse genes impacted by alternative events. For genes with alternative 5'UTRs, the fraction of alternative sequences (those present in a subset of the transcripts) is much greater than that in the corresponding coding sequence, conceivably, because 5'UTRs are not bound by constraints on protein structure that limit AS in coding regions. Alternative regions of mammalian 5'UTRs evolve faster and are subject to a weaker purifying selection than constitutive portions. This relatively weak selection results in over-abundance of uAUGs and uORFs in the alternative regions of 5'UTRs compared to constitutive regions. Nevertheless, even in alternative regions, uORFs evolve under a stronger selection than the rest of the sequences, indicating that some of the uORFs are conserved regulatory elements; some of the non-conserved uORFs could be involved in species-specific regulation. The findings on the evolution and selection in alternative and constitutive regions presented here are consistent with the hypothesis that alternative events, namely, AS and ATI, in 5'UTRs of mammalian genes are likely to contribute to the regulation of translation.
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            Alternative Event
            Alternative Region
            Potential Regulatory Element
            Alternative Transcription Initiation
            Life Sciences
            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
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      headline:Evolution of alternative and constitutive regions of mammalian 5'UTRs
      description:Alternative splicing (AS) in protein-coding sequences has emerged as an important mechanism of regulation and diversification of animal gene function. By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized. We evaluated the abundance, conservation and evolution of putative regulatory control elements, namely, upstream start codons (uAUGs) and open reading frames (uORFs), in the 5'UTRs of human and mouse genes impacted by alternative events. For genes with alternative 5'UTRs, the fraction of alternative sequences (those present in a subset of the transcripts) is much greater than that in the corresponding coding sequence, conceivably, because 5'UTRs are not bound by constraints on protein structure that limit AS in coding regions. Alternative regions of mammalian 5'UTRs evolve faster and are subject to a weaker purifying selection than constitutive portions. This relatively weak selection results in over-abundance of uAUGs and uORFs in the alternative regions of 5'UTRs compared to constitutive regions. Nevertheless, even in alternative regions, uORFs evolve under a stronger selection than the rest of the sequences, indicating that some of the uORFs are conserved regulatory elements; some of the non-conserved uORFs could be involved in species-specific regulation. The findings on the evolution and selection in alternative and constitutive regions presented here are consistent with the hypothesis that alternative events, namely, AS and ATI, in 5'UTRs of mammalian genes are likely to contribute to the regulation of translation.
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      dateModified:2009-04-16T00:00:00Z
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      pageEnd:14
      license:https://creativecommons.org/licenses/by/2.0
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         Alternative Splice
         Alternative Event
         Alternative Region
         Potential Regulatory Element
         Alternative Transcription Initiation
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2164-10-162/MediaObjects/12864_2009_Article_2046_Fig1_HTML.jpg
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            address:
               name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
               type:PostalAddress
            type:Organization
      name:Aleksey Y Ogurtsov
      affiliation:
            name:National Institutes of Health
            address:
               name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
               type:PostalAddress
            type:Organization
      name:Igor B Rogozin
      affiliation:
            name:National Institutes of Health
            address:
               name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
               type:PostalAddress
            type:Organization
      name:Svetlana A Shabalina
      affiliation:
            name:National Institutes of Health
            address:
               name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
               type:PostalAddress
            type:Organization
      name:Eugene V Koonin
      affiliation:
            name:National Institutes of Health
            address:
               name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
               type:PostalAddress
            type:Organization
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      name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
      name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
      name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
      name:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA

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