[Universität Potsdam]

Universität Potsdam
Mathematisch-Naturwissenschaftliche Fakultät
Institut für Biochemie und Biologie


Arabidopsis thaliana Orphan Transcript Database


The Arabidopsis thaliana Orphan Transcript Database (AtoRNA DB) is a computational effort to look for overlooked genes in the plant model Arabidopsis thaliana.

Very briefly, this work is based on the mapping of ESTs onto the genome sequence of A. thaliana, and the subsequent removal of all already annotated transcripts. The remaining transcripts are called Orphans.

This database collects a set of 591 orphan transcripts, originated from the A. thaliana's EST collection as collected in February 2003.

There are different ways to use this site:

  1. The oRNA info page is a web form that provides query capabilities to retrieve basic information (sequence, associated EST, alignments to the corresponding gene locations, multiple aligments etc) about the orphan transcripts in a tabular format. It is possible to retrieve the information for only one orphan transcript or for a batch of them.
  2. The oRNA features page is another web form to query the database, filtering for the type of features found in the reported orphan transcripts, with this page it is only possible to retrieve information on a chromosome basis.
  3. The Gbrowser page allows to browse along the chromosomes with a graphical display. It is possible to query the database with identifiers of orphan transcripts or annotated genes or with a pair of coordinates in the chromosome. Clicking in an orphan transcript led to a graphical display of its features
  4. The download page allows to download of some of the database content in the form of plain-text files.

A publication related to this database has appeared in The Plant Journal:
Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mueller-Roeber, Bernd. 2005. Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognised genes. The Plant Journal. 43(2): 205-212. doi: 10.1111/j.1365-313X.2005.02438.x
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