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Published online before print December 30, 2002, 10.1101/gr.695703
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Vol 13, Issue 1, 27-36, January 2003

Reevaluating Human Gene Annotation: A Second-Generation Analysis of Chromosome 22

John E. Collins, Melanie E. Goward, Charlotte G. Cole, Luc J. Smink1, Elizabeth J. Huckle, Sarah Knowles, Jacqueline M. Bye, David M. Beare and Ian Dunham2

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

We report a second-generation gene annotation of human chromosome 22. Using expressed sequence databases, comparative sequence analysis, and experimental verification, we have extended genes, fused previously fragmented structures, and identified new genes. The total length in exons of annotation was increased by 74% over our previously published annotation and includes 546 protein-coding genes and 234 pseudogenes. Thirty-two potential protein-coding annotations are partial copies of other genes, and may represent duplications on an evolutionary path to change or loss of function. We also identified 31 non-protein-coding transcripts, including 16 possible antisense RNAs. By extrapolation, we estimate the human genome contains 29,000–36,000 protein-coding genes, 21,300 pseudogenes, and 1500 antisense RNAs. We suggest that our revised annotation criteria provide a paradigm for future annotation of the human genome.

[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. AL009266, AL021682-3, AL021708, AL022729, AL035081-2, AL035364, AL035366, AL035545, AL049654, AL050253-8, AL050345-6, AL079310, AL096779-81, AL096879-81, AL096883, AL096886, AL138578, AL157851, AL159142-3, AL160111-2, AL160131-2, AL160311, AL355092, AL355192, AL355841, AL359401, AL359403, AL365511-5, AL442116, AL449243, AL449244, AL450314, AL589866-7, AL590120, AL590887-8, BU583989–BU585359. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Seilhamer, L. Stuve, H. Roest-Crollius, A. Levine, G. Slater, and J. Kent.]

1 Present address: JDRF/WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrookes Hospital, Cambridge CB2 2XY, UK.

2 Corresponding author.

E-MAIL id1{at}sanger.ac.uk; FAX +44 (0) 1223 494919

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.695703. Article published online before print in December 2002.


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