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Intron Confirmation in C. elegans

experiment: Intron Confirmation in C. elegans project: The C. elegans Transcriptome PI: Robert Waterston Labs: Phil Green
This experiment identifies intron boundary coordinates 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 unconfirmed by these alignments are tested for confirmation using RT-PCR, DNA sequencing, and sequence alignment. These PCR experiments use gene-specific/gene-specific, 5' RACE/gene-specific, and gene-specific/3' RACE primer pairs.

All features generated by this experiment:
Feature Export
Intron ? 10284
This represents 9979 unique Introns
TAB CSV GFF3 (for UCSC) SEQ
EST ? 6855 TAB CSV GFF3 SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All 24 tracks I II III IV V X
All entries in public repositories generated by this experiment
There are 6 RTPCR submissions for this experiment:
DCC id Name developmental stage strain Embargoed until Features, GBrowse and Data Files
modENCODE_447


Related to: modENCODE_2934

C. elegans Intron Identification set.20090106.2 3 2 2 5 3 3 2 2 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
? Intron: 187   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 108   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: IntronsS2
IntronsS2
Waterston_match_part_3641_447
Waterston_intron_3641_447
Trace Archive: 2022157854
Trace Archive: 2022157855
Trace Archive: 2022157879
Trace Archive: 2022157900
Trace Archive: 2022157913
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_2718

Intron Confirmation Chromosome I 2010-01-28 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
? Intron: 572   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 447   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: IntronsChrI
IntronsChrI
Waterston_match_part_5252_2718
Waterston_intron_5252_2718
Trace Archive: 2262244677
Trace Archive: 2262244678
Trace Archive: 2262244679
Trace Archive: 2262244680
Trace Archive: 2262244681
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_2304


Related to: modENCODE_2934

Intron Confirmation Chromosome II 2009-09-21 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
? Intron: 709   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 473   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: IntronsChrII
IntronsChrII
Waterston_match_part_3637_2304
Waterston_intron_3637_2304
Trace Archive: 2245122449
Trace Archive: 2245122450
Trace Archive: 2245122451
Trace Archive: 2245122452
Trace Archive: 2245122453
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_448


Related to: modENCODE_2934

C. elegans Intron Identification set.20090106.2 3 2 2 4 3 3 2 2 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
? Intron: 7374   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 4781   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: IntronsS3
IntronsS3
Waterston_match_part_3655_448
Waterston_intron_3655_448
Trace Archive: 1971697196
Trace Archive: 1971697197
Trace Archive: 1971697199
Trace Archive: 1971697200
Trace Archive: 1971697202
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_445


Related to: modENCODE_2934

C. elegans Intron Identification.set.20090106.2 3 2 2 3 2 2 2 2 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
? Intron: 1411   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 1020   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: IntronsS4
IntronsS4
Waterston_match_part_3553_445
Waterston_intron_3553_445
Trace Archive: 1902857087
Trace Archive: 1902857088
Trace Archive: 1902857089
Trace Archive: 1902857090
Trace Archive: 1902857091
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_446


Related to: modENCODE_2934

C. elegans Intron Identification set.20090106.2 3 2 2 4 4 3 2 2 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
? Intron: 31   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 26   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: IntronsS1
IntronsS1
Waterston_match_part_3633_446
Waterston_intron_3633_446
Trace Archive: 1971697209
Trace Archive: 1971697428
Trace Archive: 2131354407
Trace Archive: 2131354408
Trace Archive: 2131354409
...All entries in public repositories generated by this submission



1 files Download data files