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Annotation of Drosophila splice junctions by RNA-seq

experiment: Annotation of Drosophila splice junctions by RNA-seq project: The Drosophila Transcriptome PI: Sue Celniker Labs: Brenton Graveley
For the final scoring of the junctions all of the developmental RNA-Seq data was aligned to a bowtie index containing both the genome and the 79,514 splice junctions. For single reads, the alignments were performed with the following parameters to report uniquely mapped reads [-m 1 -v 2 -y --best]. For paired-end reads, the data was aligned using the following parameters [-m 10 -v 10 -y --best] after which spa was used to to identify unique instances of mate-pairs in which both reads map on the same chromosome, within 200 kb of one another and oriented towards one another. The remaining reads were further filtered to identify cases in which there were multiple potential mapping positions of a mate pair within 200 kb of one another. In this case, the closest of multiple mate pair mapping positions was retained. Finally, for mate pairs in which only one read could be mapped, if the remaining read was mapped uniquely, it was retained. Junctions were scored using both the total number of reads and the entropy score.

All features generated by this experiment:
Feature Export
ExonRegion ? 3005431 Expression Levels 3491140
This represents 128976 unique ExonRegions
TAB CSV GFF3 (for UCSC) SEQ
Intron ? 1745570 Expression Levels 1745570
This represents 79498 unique Introns
TAB CSV GFF3 (for UCSC) SEQ
TranscriptRegion ? 1745570
This represents 79498 unique TranscriptRegions
TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse track by chromosome
There are 30 Computational Annotation submissions for this experiment:
DCC id Name Embargoed until Features, GBrowse and Data Files
modENCODE_2688

Splice Junction Annotation Embryo 0-2h embargo expired
? ExonRegion: 72033   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  81890   export: TAB   CSV
? Intron: 40945   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  40945   export: TAB   CSV
? TranscriptRegion: 40945   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: Transcript_regions_2688


1 files Download data files
modENCODE_2689

Splice Junction Annotation Embryo 2-4h embargo expired
? ExonRegion: 79145   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  90494   export: TAB   CSV
? Intron: 45247   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  45247   export: TAB   CSV
? TranscriptRegion: 45247   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2690

Splice Junction Annotation Embryo 4-6h embargo expired
? ExonRegion: 87725   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  102262   export: TAB   CSV
? Intron: 51131   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  51131   export: TAB   CSV
? TranscriptRegion: 51131   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2716

Splice Junction Annotation Adult Female, eclosion + 30d embargo expired
? ExonRegion: 94880   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  109386   export: TAB   CSV
? Intron: 54693   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  54693   export: TAB   CSV
? TranscriptRegion: 54693   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2700

Splice Junction Annotation Larvae L1 embargo expired
? ExonRegion: 99968   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  115886   export: TAB   CSV
? Intron: 57943   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  57943   export: TAB   CSV
? TranscriptRegion: 57943   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2715

Splice Junction Annotation Adult Male, eclosion + 5d embargo expired
? ExonRegion: 113254   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  132734   export: TAB   CSV
? Intron: 66367   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  66367   export: TAB   CSV
? TranscriptRegion: 66367   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2699

Splice Junction Annotation Embryo 22-24h embargo expired
? ExonRegion: 103551   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  121478   export: TAB   CSV
? Intron: 60739   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  60739   export: TAB   CSV
? TranscriptRegion: 60739   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2702

Splice Junction Annotation Larvae L3 12hr post-molt embargo expired
? ExonRegion: 95839   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  108610   export: TAB   CSV
? Intron: 54305   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  54305   export: TAB   CSV
? TranscriptRegion: 54305   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2717

Splice Junction Annotation Adult Male, eclosion + 30d embargo expired
? ExonRegion: 107108   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  123352   export: TAB   CSV
? Intron: 61676   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  61676   export: TAB   CSV
? TranscriptRegion: 61676   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2701

Splice Junction Annotation Larvae L2 embargo expired
? ExonRegion: 102104   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  119108   export: TAB   CSV
? Intron: 59554   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  59554   export: TAB   CSV
? TranscriptRegion: 59554   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2704

Splice Junction Annotation Larvae L3, light blue gut PS3-6 embargo expired
? ExonRegion: 103464   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  118434   export: TAB   CSV
? Intron: 59217   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  59217   export: TAB   CSV
? TranscriptRegion: 59217   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2703

Splice Junction Annotation Larvae L3, dark blue gut PS1-2 embargo expired
? ExonRegion: 96971   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  109070   export: TAB   CSV
? Intron: 54535   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  54535   export: TAB   CSV
? TranscriptRegion: 54535   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2706

Splice Junction Annotation White Prepupae embargo expired
? ExonRegion: 108156   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  126754   export: TAB   CSV
? Intron: 63377   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  63377   export: TAB   CSV
? TranscriptRegion: 63377   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2705

Splice Junction Annotation Larvae L3, clear gut PS7-9 embargo expired
? ExonRegion: 106379   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  123276   export: TAB   CSV
? Intron: 61638   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  61638   export: TAB   CSV
? TranscriptRegion: 61638   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2692

Splice Junction Annotation Embryo 8-10h embargo expired
? ExonRegion: 91314   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  106118   export: TAB   CSV
? Intron: 53059   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  53059   export: TAB   CSV
? TranscriptRegion: 53059   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2708

Splice Junction Annotation White Prepupae, WPP + 24hr embargo expired
? ExonRegion: 108863   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  127136   export: TAB   CSV
? Intron: 63568   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  63568   export: TAB   CSV
? TranscriptRegion: 63568   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2691

Splice Junction Annotation Embryo 6-8h embargo expired
? ExonRegion: 88150   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  102394   export: TAB   CSV
? Intron: 51197   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  51197   export: TAB   CSV
? TranscriptRegion: 51197   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2707

Splice Junction Annotation White Prepupae, WPP + 12hr embargo expired
? ExonRegion: 110747   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  130150   export: TAB   CSV
? Intron: 65075   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  65075   export: TAB   CSV
? TranscriptRegion: 65075   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2694

Splice Junction Annotation Embryo 12-14h embargo expired
? ExonRegion: 100453   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  118746   export: TAB   CSV
? Intron: 59373   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  59373   export: TAB   CSV
? TranscriptRegion: 59373   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2710

Splice Junction Annotation Pupae, WPP + 3d embargo expired
? ExonRegion: 109995   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  128818   export: TAB   CSV
? Intron: 64409   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  64409   export: TAB   CSV
? TranscriptRegion: 64409   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2693

Splice Junction Annotation Embryo 10-12h embargo expired
? ExonRegion: 95781   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  112036   export: TAB   CSV
? Intron: 56018   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  56018   export: TAB   CSV
? TranscriptRegion: 56018   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2709

Splice Junction Annotation Pupae, WPP + 2d embargo expired
? ExonRegion: 111845   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  131436   export: TAB   CSV
? Intron: 65718   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  65718   export: TAB   CSV
? TranscriptRegion: 65718   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2696

Splice Junction Annotation Embryo 16-18h embargo expired
? ExonRegion: 102806   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  120942   export: TAB   CSV
? Intron: 60471   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  60471   export: TAB   CSV
? TranscriptRegion: 60471   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2712

Splice Junction Annotation Adult Female, eclosion + 1d embargo expired
? ExonRegion: 100047   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  116150   export: TAB   CSV
? Intron: 58075   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  58075   export: TAB   CSV
? TranscriptRegion: 58075   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2695

Splice Junction Annotation Embryo 14-16h embargo expired
? ExonRegion: 98124   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  113894   export: TAB   CSV
? Intron: 56947   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  56947   export: TAB   CSV
? TranscriptRegion: 56947   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2711

Splice Junction Annotation Pupae, WPP + 4d embargo expired
? ExonRegion: 108143   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  125296   export: TAB   CSV
? Intron: 62648   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  62648   export: TAB   CSV
? TranscriptRegion: 62648   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2714

Splice Junction Annotation Adult Female, eclosion + 5d embargo expired
? ExonRegion: 94701   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  109366   export: TAB   CSV
? Intron: 54683   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  54683   export: TAB   CSV
? TranscriptRegion: 54683   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2698

Splice Junction Annotation Embryo 20-22h embargo expired
? ExonRegion: 99128   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  114664   export: TAB   CSV
? Intron: 57332   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  57332   export: TAB   CSV
? TranscriptRegion: 57332   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2713

Splice Junction Annotation Adult Male, eclosion + 1d embargo expired
? ExonRegion: 111928   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  130816   export: TAB   CSV
? Intron: 65408   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  65408   export: TAB   CSV
? TranscriptRegion: 65408   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files
modENCODE_2697

Splice Junction Annotation Embryo 18-20h embargo expired
? ExonRegion: 102829   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  120444   export: TAB   CSV
? Intron: 60222   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  60222   export: TAB   CSV
? TranscriptRegion: 60222   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]


1 files Download data files