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NATsDB


NAR Molecular Biology Database Collection entry number 997
Yong Zhang1, Jiongtang Li1, Lei Kong1, Ge Gao1, Qing-Rong Liu2 and Liping Wei1
1Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China
2Molecular Neurobiology Branch, National Institute on Drug Abuse-Intramural Research Program (NIDA-IRP), NIH, Department of Health and Human Services (DHHS), Box 5180, Baltimore, MD 21224, USA

Database Description

Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense partners. They regulate sense genes at multiple levels and are implicated in various diseases. Using an improved whole-genome computational pipeline, we identified abundant cis-encoded exon-overlapping sense-antisense (SA) gene pairs in human, mouse, fly, and eight other eukaryotic species. We developed NATsDB (Natural Antisense Transcripts DataBase, http://natsdb.cbi.pku.edu.cn/) to enable efficient browsing, searching and downloading of this currently most comprehensive collection of SA genes, grouped into six classes based on their overlapping patterns. NATsDB also includes Non-exon-Overlapping Bidirectional (NOB) genes and Non-BiDirectional (NBD) genes. To facilitate the study of functions, regulations, and possible pathological implications, NATsDB includes extensive information about gene structures, polyA signals and tails, phastCons conservation, homologues in other species, repeat elements, EST expression profiles, and OMIM disease association.

NATsDB supports interactive graphical display of the alignment of all supporting EST and mRNA transcripts of the SA and NOB genes to the genomic loci. It supports advanced search by species, gene name, sequence accession number, chromosome location, coding potential, OMIM association, and sequence similarity.

Recent Developments

Alternative isoforms identified with our SVAP (Splice Variant Analysis Platform) are presented as a new track, which is hoped to assist to investigate the potential association between antisense transcription and alternative splicing.

Acknowledgements

This work was supported by China Ministry of Science and Technology High Tech 863 Programs and China Ministry of Education "Program for New Century Excellent Talents in University". We thank the two anonymous reviewers for insightful suggestions. We thank Drs. Shunong Bai and Zicai Liang for helpful discussions, Dr. Osamu Ogasawara of DDBJ for support of BodyMap-Xs, and Shuqi Zhao and Ying Sun of Center for Bioinformatics for maintenance of computing resources.

References

1. Zhang, Y., Li, J., Kong L., Gao, G., Liu QR., and Wei L. (2007) NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res. 35, in press


Go to the abstract in the NAR 2007 Database Issue.
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