Arabidopsis SAGE Tags

The data provided here are described in "Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis thaliana" [manuscript submitted for publication]. Correspondence should be addressed to Steve Robinson.

Conceptual Transcripts

FASTA files representing transcripts of genes and pseudogenes from the A. thaliana nuclear and organellar genomes are provided here. Sequence for the nuclear transcripts was extracted from TIGR's Arabidopsis thaliana Annotation Database, release 4. These sequences include both exonic and UTR regions. Sequences for the mitochondrial transcripts were extracted from Y08501 and Y08502, and sequences for the chloroplastic transcripts were extracted from NC_000932.

The nuclear transcripts have been partitioned into two sets based on the source of their UTR sequence. Transcripts for which TIGR has annotated the length of the UTRs are included in the defined-UTR set. All other transcripts have UTRs of a default length added to them and are included in the virtual-UTR set. The default length is 350 bp for the 5' UTRs and 500 bp for the 3' UTRs, except in cases where truncation was necessary to prevent overlap between adjacent transcripts.

Defined-UTR sequences
Virtual-UTR sequences
Pseudo-gene sequences
Mitochondria sequences
Chloroplast sequences

Tag Mapping

Tag mapping data is provided as tab-delimited files with the following format:

Tag Sequence      Tag frequency      Hit #1    ...    Hit #n

Sense canonical matches
Sense non-canonical matches
Sense intron matches
Sense intergenic matches
Antisense genic matches
Antisense intron matches
Antisense intergenic matches
Gene descriptions

SaskSAGE @ Sourceforge

This work was supported by