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Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions

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Abstract

A comprehensive representation of the gene content of the long arm of human chromosome 21 (Hsa21q) remains of interest for the study of Down syndrome, its associated phenotypic features, and mouse models. Here we compare transcript catalogs for Hsa21q, chimpanzee chromosome 21 (Ptr21q), and orthologous regions of mouse chromosomes 16, 17, and 10 for open reading frame (ORF) characteristics and conservation. The Hsa21q and mouse catalogs contain 552 and 444 gene models, respectively, of which only 162 are highly conserved. Hsa21q transcripts were used to identify orthologous exons in Ptr21q and assemble 533 putative transcripts. Transcript catalogs for all three organisms are searchable for nucleotide and amino acid sequence features of ORF length, repeat content, experimental support, gene structure, and conservation. For human and mouse comparisons, three additional summaries are provided: (1) the chromosomal distribution of novel ORF transcripts versus potential functional RNAs, (2) the distribution of species-specific transcripts within Hsa21q and mouse models of Down syndrome, and (3) the organization of sense–antisense and putative sense–antisense structures defining potential regulatory mechanisms. Catalogs, summaries, and nucleotide and amino acid sequences of all composite transcripts are available and searchable at http://gfuncpathdb.ucdenver.edu/iddrc/chr21/home.php. These data sets provide comprehensive information useful for evaluation of candidate genes and mouse models of Down syndrome and for identification of potential functional RNA genes and novel regulatory mechanisms involving Hsa21q genes. These catalogs and search tools complement and extend information available from other gene annotation projects.

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Acknowledgments

This work was supported by the Fondation Jerome Lejeune, the Anna and John J. Sie Foundation, the Coleman Institute for Cognitive Disabilities, and the National Institutes of Health (HD056235).

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Authors and Affiliations

  1. Department of Pediatrics, Computational Biosciences Program, University of Colorado Denver, Aurora, CO, 80045, USA

    Xiaolu Sturgeon & Katheleen J. Gardiner

  2. Intellectual and Developmental Disabilities Research Center, Neuroscience and Human Medical Genetics Programs, University of Colorado Denver, Mail Stop 8313, 12800 E. 19th Avenue, PO Box 6511, Aurora, CO, 80045, USA

    Katheleen J. Gardiner

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Correspondence to Katheleen J. Gardiner.

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Sturgeon, X., Gardiner, K.J. Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions. Mamm Genome 22, 261–271 (2011). https://doi.org/10.1007/s00335-011-9321-y

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