Mammalian Genome

, Volume 22, Issue 5, pp 261–271

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


DOI: 10.1007/s00335-011-9321-y

Cite this article as:
Sturgeon, X. & Gardiner, K.J. Mamm Genome (2011) 22: 261. doi:10.1007/s00335-011-9321-y


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 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.

Supplementary material

335_2011_9321_MOESM1_ESM.xls (106 kb)
Supplementary material 1 (XLS 105 kb)
335_2011_9321_MOESM2_ESM.xls (758 kb)
Supplementary material 2 (XLS 758 kb)
335_2011_9321_MOESM3_ESM.xls (384 kb)
Supplementary material 3 (XLS 384 kb)
335_2011_9321_MOESM4_ESM.xls (537 kb)
Supplementary material 4 (XLS 537 kb)
335_2011_9321_MOESM5_ESM.xls (298 kb)
Supplementary material 5 (XLS 297 kb)

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Pediatrics, Computational Biosciences ProgramUniversity of Colorado DenverAuroraUSA
  2. 2.Intellectual and Developmental Disabilities Research Center, Neuroscience and Human Medical Genetics ProgramsUniversity of Colorado DenverAuroraUSA