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. 2007 Aug 30:8:319.
doi: 10.1186/1471-2105-8-319.

antiCODE: a natural sense-antisense transcripts database

Yifei Yin  1 , Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen, Haitao Zhao
Affiliations

antiCODE: a natural sense-antisense transcripts database

Yifei Yin et al. BMC Bioinformatics. .

Abstract

Background: Natural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs, and that may contribute to the regulation of molecular functions at various levels. In recent years, large-scale NAT screens in several model organisms have produced much data, but there is no database to assemble all these data. AntiCODE intends to function as an integrated NAT database for this purpose.

Results: This release of antiCODE contains more than 30,000 non-redundant natural sense-antisense transcript pairs from 12 eukaryotic model organisms. In order to provide an integrated NAT research platform, efficient browser, search and Blast functions have been included to enable users to easily access information through parameters such as species, accession number, overlapping patterns, coding potential etc. In addition to the collected information, antiCODE also introduces a simple classification system to facilitate the study of natural antisense transcripts.

Conclusion: Though a few similar databases also dealing with NATs have appeared lately, antiCODE is the most comprehensive among these, comprising almost all currently detected NAT pairs.

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Figures

Figure 1
Figure 1
The "5/3/c/o" classification system. The arrows indicate the transcriptional orientation of the NAT pair. A solid line indicates an exon and a broken line an intron.
Figure 2
Figure 2
The Blast options. In the database frame, 12 genomes could be selected as Blast databases. More detailed options could be found below which allow users to personalize the Blast results according to complexity, expect value and graphical overview options.
See this image and copyright information in PMC

References

    1. Billy E, Brondani V, Zhang H, Muller U, Filipowicz W. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci U S A. 2001;98:14428–14433. doi: 10.1073/pnas.261562698. - DOI - PMC - PubMed
    1. Faghihi MA, Wahlestedt C. RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals. Genome Biol. 2006;7:R38. doi: 10.1186/gb-2006-7-5-r38. - DOI - PMC - PubMed
    1. Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L. Complex Loci in human and mouse genomes. PLoS Genet. 2006;2:e47. doi: 10.1371/journal.pgen.0020047. - DOI - PMC - PubMed
    1. Lehner B, Williams G, Campbell RD, Sanderson CM. Antisense transcripts in the human genome. Trends Genet. 2002;18:63–65. doi: 10.1016/S0168-9525(02)02598-2. - DOI - PubMed
    1. Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, Nemzer S, Pinner E, Walach S, Bernstein J, Savitsky K, Rotman G. Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol. 2003;21:379–386. doi: 10.1038/nbt808. - DOI - PubMed

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