modENCODE |  Help |  blog
Hide

The table data can be sorted according to the content of a given column, just click on the column header.

Annotation of the developmental transcriptome of Drosophila melanogaster

experiment: Annotation of the developmental transcriptome of Drosophila melanogaster project: The Drosophila Transcriptome PI: Sue Celniker Labs: Brian Oliver, Sue Celniker
Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development. (from Gravely et al; Nature 2010)

All features generated by this experiment:
Feature Export
SnoRNA 39 TAB CSV GFF3 (for UCSC) SEQ
CDNAMatch 1457
This represents 1454 unique CDNAMatchs
TAB CSV GFF3 (for UCSC) SEQ
Exon 251915
This represents 95753 unique Exons
TAB CSV GFF3 (for UCSC) SEQ
Gene 16857 TAB CSV GFF3 SEQ
MRNA 39418 TAB CSV GFF3 SEQ
Transcript 4160 TAB CSV GFF3 SEQ
StopCodon 39433
This represents 16040 unique StopCodons
TAB CSV GFF3 (for UCSC) SEQ
FivePrimeUTR 60196
This represents 35007 unique FivePrimeUTRs
TAB CSV GFF3 (for UCSC) SEQ
StartCodon 39559
This represents 17548 unique StartCodons
TAB CSV GFF3 (for UCSC) SEQ
ThreePrimeUTR 37615
This represents 23321 unique ThreePrimeUTRs
TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
There are 2 Computational annotation submissions for this experiment:
DCC id Name Embargoed until Features, GBrowse and Data Files
modENCODE_4057


Related to: modENCODE_574
modENCODE_2676
modENCODE_4329
modENCODE_4330
modENCODE_4327
modENCODE_4328
modENCODE_4333
modENCODE_4334
modENCODE_4331
modENCODE_4332
modENCODE_4320
modENCODE_4322
modENCODE_4325
modENCODE_4326
modENCODE_4323
modENCODE_4324
modENCODE_4321
modENCODE_4346
modENCODE_4345
modENCODE_4344
modENCODE_4343
modENCODE_4349
modENCODE_4348
modENCODE_4347
modENCODE_4338
modENCODE_4337
modENCODE_4336
modENCODE_4335
modENCODE_4342
modENCODE_4341
modENCODE_4340
modENCODE_4339
modENCODE_2677
modENCODE_2678
modENCODE_2679
modENCODE_2680
modENCODE_2681
modENCODE_2682
modENCODE_2683
modENCODE_2684
modENCODE_2685
modENCODE_2686
modENCODE_2687

Annotation of the developmental transcriptome of Drosophila melanogaster embargo expired
SnoRNA: 39   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
CDNAMatch: 1457   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Gene: 16789   export: TAB   CSV GFF3 SEQ    create LIST
Exon: 250595   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
MRNA: 39418   export: TAB   CSV GFF3 SEQ    create LIST
Transcript: 3055   export: TAB   CSV GFF3 SEQ    create LIST
StopCodon: 39433   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
FivePrimeUTR: 60196   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
StartCodon: 39559   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
ThreePrimeUTR: 37615   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: Celniker_GINORMOUS


63 files Download data files
modENCODE_4056


Related to: modENCODE_2980
modENCODE_3083
modENCODE_3084
modENCODE_3085
modENCODE_3086
modENCODE_3087

Analysis of Novel Drosophila Transcripts via Interspecific Comparison embargo expired
Exon: 1320   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Gene: 1105   export: TAB   CSV GFF3 SEQ    create LIST
Transcript: 1105   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: OLIVER_CUFFLINKS_Genes
OLIVER_NOVEL_Genes


66 files Download data files