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SL Acceptor Site Confirmation in C. elegans

experiment: SL Acceptor Site Confirmation in C. elegans project: The C. elegans Transcriptome PI: Robert Waterston Labs: Phil Green
This experiment identifies splice leader acceptor sites 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-splice leader alignments are used to identify splice leader acceptor sites.

All features generated by this experiment:
Feature Export
Primer 2 TAB CSV GFF3 SEQ
SL7AcceptorSite 1 TAB CSV GFF3 (for UCSC) SEQ
SL1AcceptorSite ? 987
This represents 984 unique SL1AcceptorSites
TAB CSV GFF3 (for UCSC) SEQ
TranscriptRegion ? 1533
This represents 1351 unique TranscriptRegions
TAB CSV GFF3 (for UCSC) SEQ
EST ? 1483 TAB CSV GFF3 SEQ
SL2AcceptorSite ? 46 TAB CSV GFF3 (for UCSC) SEQ
SL4AcceptorSite 1 TAB CSV GFF3 (for UCSC) SEQ
SplicedLeaderRNA 13 TAB CSV GFF3 SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All 7 tracks I II III IV V X
All entries in public repositories generated by this experiment
There are 2 RACE submissions for this experiment:
DCC id Name developmental stage strain Embargoed until Features, GBrowse and Data Files
modENCODE_2968

SL Acceptor Site Confirmation 2010-06-04 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
Primer: 1   export: TAB   CSV GFF3 SEQ    create LIST
SL7AcceptorSite: 1   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL1AcceptorSite: 54   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptRegion: 80   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 3   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 78   export: TAB   CSV GFF3 SEQ    create LIST
SL4AcceptorSite: 1   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
SplicedLeaderRNA: 4   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: SL_Acceptor_Site
Waterston_match_part_10850_2968
Waterston_match_part_7691_3312
SL_Acceptor_site_W2968
Trace Archive: 2262244679
Trace Archive: 2262244688
Trace Archive: 2262244695
Trace Archive: 2262244696
Trace Archive: 2262244717
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_2720

SL Acceptor Site Confirmation 2010-01-28 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
Primer: 1   export: TAB   CSV GFF3 SEQ    create LIST
? SL1AcceptorSite: 933   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptRegion: 1453   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 1405   export: TAB   CSV GFF3 SEQ    create LIST
? SL2AcceptorSite: 43   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
SplicedLeaderRNA: 9   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: SL_Acceptor_Site
Waterston_match_part_5277_2720
SL_Acceptor_site_W2720
Trace Archive: 1971697210
Trace Archive: 1971697211
Trace Archive: 1971697214
Trace Archive: 1971697217
Trace Archive: 1971697249
...All entries in public repositories generated by this submission



1 files Download data files