antiCODE: Sense/Antisense Database
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Revised: Jun 24, 2006.
antiCODE::Web News
What does antiCODE do?

antiCODE is a comprehensive database that contains almost all currently detected and irredundant natural sense-antisense transcription (NAT) pairs, i.e. endogenous RNA molecules that exhibit partial or complete complementarity to each other. antiCODE intends to provide an integrated platform for effective browsing and searching information on NATs through the options of species, pair ID, overlapping pattern, coding potentials, category etc. In addition to integrated information, antiCODE has also introduced a classification system in order to facilitate the study of natural sense/antisense transcription pairs.

Getting started

Browse the database: In the browse webpage, you can browse NATs by pair NO., three classifition systems (coding/noncoding, 3/5/c/o, cis/trans) and species.

Search your interesting information: In search webpage, you can find out useful information via entering gene name, pair NO., accession number etc.(in quick search) or any your interestin keywords(in text search). More detail search help please see the search tip.

Blast your interesting sequence: If you want to see whether one interesting sequence is homology to known NATs, you could use blast service. In the blast page, you can paste your sequence in the box or load it directly. Select the BLAST database which you want your sequence to compare to, otherwise the Homo sapiens database will be used. Then press the search button.

Data processing track descriptions

All the data in the database have been collected from recent literature and related databases. These are human NATs in which 2667 are from Yelin et al., 372 from Lehner et al., 5880 from Chen et al., mouse NATs in which 3380 are from Kiyosawa et al. and 9713 from the RIKEN group, 1340 Arabidopsis thaliana NATs from Wang et al., 3168 rice NATs from Osato et al. and more than 10,000 NATs of 10 species (including human and mouse) from Zhang et al.

We get accession numbers or gene names from the supplementary material of respective articles and fetch the annotation information and sequences from NCBI RIKEN website and relative databases. From the supplementary material or annotation information we could find out whether the gene is coding or noncoding. Then we have calculated the overlap position of each NATs pair using Blat through which we could know the overlapped position of the pairs. Because some data of human and mouse are not from only one dataset, we have compared the difference of diverse datasets and eliminated the redundancy.

classification system in antiCODE

In antiCODE, based on previous classification system of sense-antisense transcription pairs we have classified the NATs according to three compact and practical schemes or "dimensions", the "coding/noncoding", the "3/5/c/o (overlapping position)", and the "cis/trans" scheme, which we hope may facilitate integration of data from future natural sense/antisense transcription research.

The coding/noncoding scheme indicates whether the RNAs of the overlapping pairs are (protein) coding RNAs and noncoding RNA. The cis/trans scheme tells whether the two sequences of the NAT pair are located in the same chromosomal position, i.e. if the two sequences of the pair are located in the same position on the chromosome, they are named a cis-overlapping pair, otherwise a trans-overlapping pair. The 3/5/c/o scheme indicates which parts of the two sequences are overlapped, that is to say, the 5' ends (5' overlapping) or the 3' ends (3' overlapping), or whether one sequence is covered completely by the other (complete). If the pairs are not overlapped on their ends or covered completely, they will be marked "o" (others) which maybe overlapped partially. In this classification system we do not adopt previous customs, which fractionize NATs according to their exon-intron structure. We hope antiCODE could give users the most compact and practical information and help them filter useful signals out of abundant information. For more detailed things about users' interesting gene, the clients could visit professional databases through given links.

Downloading NAT data

Homo sapiens NATs sequences in fasta format: Homo_sapiens.fa.tar
Mus musculus NATs sequences in fasta format: Mus_musculus.fa.tar
Oryza sativa NATs sequences in fasta format: Oryza_sativa.fa.tar
Arabidopsis thaliana NATs sequences in fasta format Arabidopsis_thaliana.fa.tar

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