AtRTD specifications


Unique identifier OMICS_18776
Name AtRTD
Alternative name Arabidopsis Thaliana Reference Transcript Dataset
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 2
Maintained Yes


  • Plants and Fungi
    • Arabidopsis thaliana


  • person_outline John Brown
  • person_outline Maria Kalyna

Publications for Arabidopsis Thaliana Reference Transcript Dataset

AtRTD citation


Adaptation of iCLIP to plants determines the binding landscape of the clock regulated RNA binding protein AtGRP7

Genome Biol
PMCID: 5663106
PMID: 29084609
DOI: 10.1186/s13059-017-1332-x

[…] remaining reads using barcodeRemoval from PIPE-CLIP []. The resulting reads were mapped to the A. thaliana TAIR10 reference genome with STAR v2.5.2a [] using the additional transcript annotation file atRTD.gff from atRTD, a novel reference transcriptome containing more than 32,500 additional transcript isoforms []. Up to three mismatches were allowed, and only reads mapping uniquely were kept.Puta […]

AtRTD institution(s)
Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, UK; Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, UK; Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria; The Donnelly Centre, University of Toronto, Toronto, ON, Canada; Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK; Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK; Institute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay, France; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Vienna, Austria
AtRTD funding source(s)
Biotechnology and Biological Sciences Research Council (BBSRC) [BB/K013661/1 and BB/K006568/1; BB/K006835/1]; Scottish Government Rural and Environment Science and Analytical Services division (RESAS); Austrian Science Fund (FWF) [P26333, DK W1207]; LABEX Saclay Plant Sciences; BBSRC EASTBIO PhD studentships; European Alternative Splicing Network of Excellence (EURASNET) [LSHG-CT-2005- 518238] for catalyzing important collaborations.

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