Human Chromosome 21 Gene Annotation II: Refining Gene Structures and Expression Analysis

Dobromir Slavov
Eleanor Roosevelt Institute
1899 Gaylord Street
Denver, CO 80206 USA
telephone: 1-303-336-5684
fax: 1-303-333-8423
prestype: Poster
presenter: Dobromir Slavov

Dobromir Slavov, Alla Rynditch and Katheleen Gardiner
Eleanor Roosevelt Institute

The 225 genes and gene models recently reported within human chromosome 21 provide an approximately complete set of candidates for relevance to Down syndrome and other chromosome 21 associated diseases. However, annotation of the genomic sequence and the genes/models is not complete and remains an ongoing process. We are focusing on the generation of complete cDNAs, the analysis of gene-specific genomic structures , and the development of expression patterns for a number of chromosome 21 genes. These aims are being pursued by: i) sequencing of ESTs, and RACE and RT-PCR products; ii) analysis of genomic sequence annotation; iii) qualitative and quantitative RT-PCR in >30 human tissues and cell lines; and iv) creation of an expression database containing dbEST- derived information on tissues of expression. Results of these investigations include: discovery of previously unannotated genes, correction of previous gene models, completion or increased length of cDNA sequences, and expression analysis of >40 genes that complements data from dbEST and identifies genes with very restricted expression. Gene- specific features of particular interest include: i) organization and expression patterns of a glutamate receptor gene and its apparent antisense RNA; ii) a gene spanning >500 kb with ubiquitous expression, comprising >8 exons and at least 4 splice variants, but as yet showing no significant open reading frame; iii) an apparently complete cDNA with multiple, short, sequential open reading frames; and iv) 5' and 3' overlapping gene structures. These data also show that thorough and complete annotation of human genomic sequence remains a time consuming and gene-specific process.

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