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Transcription Start Site Confirmation in C. elegans

experiment: Transcription Start Site Confirmation in C. elegans project: The C. elegans Transcriptome PI: Robert Waterston Labs: Phil Green
This experiment identifies transcription start sites of non-trans-spliced transcripts in C. elegans genomic sequence. Initially, we run genefinder to predict protein-coding transcripts from the C. elegans chromosome sequences. We align existing cDNA and EST sequences to the predicted transcript sequences to confirm the transcript structure. Predicted splice junctions near the 5' transcript end that are unconfirmed by these alignments are tested for confirmation using 5' RACE, DNA sequencing, and sequence alignment. The resulting reads are aligned to the WS170 genomic sequences, the splice leader sequences, and the 5' RACE primer sequence. Combinations of the read-genomic and read-primer alignments are used to identify transcription start sites.

All features generated by this experiment:
Feature Export
TSS 1221 TAB CSV GFF3 (for UCSC) SEQ
Primer 1 TAB CSV GFF3 SEQ
TranscriptRegion 3914
This represents 3830 unique TranscriptRegions
TAB CSV GFF3 (for UCSC) SEQ
EST 1239 TAB CSV GFF3 SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All 2 tracks I II III IV V X
All entries in public repositories generated by this experiment
There is 1 RACE submission for this experiment:
DCC id Name developmental stage strain Embargoed until Features, GBrowse and Data Files
modENCODE_3312

Transcription Start Site Confirmation 2010-11-24 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
TSS: 1221   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Primer: 1   export: TAB   CSV GFF3 SEQ    create LIST
TranscriptRegion: 3914   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
EST: 1239   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: Transcription_Starting_Site
Transcription_Starting_site_W3312
Trace Archive: 1971697206
Trace Archive: 1971697207
Trace Archive: 1971697221
Trace Archive: 1971697224
Trace Archive: 1971697225
...All entries in public repositories generated by this submission



1 files Download data files