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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtaatgtactgcgggtagagaggtttggtttcatatcaaaaaggcttattgatcttgacagtttactgtgttacttgatcagGTTGCAGATCTACAGACAAGGAACTG

Basic information

species Oryza sativa
transcript LOC_Os04g45010.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88398288|gb|CI588176.1|CI588176
EST:     TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTGCAGATCTAAAGAC
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGAC
EST: gi|88427074|gb|CI602035.1|CI602035
EST:     TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTGCAGATCTACAGACAAGGAACTG
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGACAAGGAACTG
EST: gi|88415936|gb|CI594048.1|CI594048
EST:     TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTGCAGATCTACAGACAAGGAACTG
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGACAAGGAACTG
EST: gi|88414771|gb|CI604129.1|CI604129
EST:     TGAGCAGCTCTTCAAGGAGAGGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTGCAGATCTACAGACAAGGAACTG
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGACAAGGAACTG
EST: gi|88441198|gb|CI602220.1|CI602220
EST:     TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTGGAGATCTACAGACAAGGAACTG
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGACAAGGAACTG
EST: gi|88370488|gb|CI590066.1|CI590066
EST:     TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTTGCAGATCTACAGACAAGGAACTG
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTT-GCAGATCTACAGACAAGGAACTG
EST: gi|88294792|gb|CI604664.1|CI604664
EST:     TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTGCAGATCTACAGACAAGGAACTG
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGACAAGGAACTG
EST: gi|88370129|gb|CI585134.1|CI585134
EST:     TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG                         GTTGCAGATCTACAGACAAGGAACTG
genomic: TGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGACAAGGAACTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 66 (upstream exon), 26 (downstream exon)
Score: 14

ATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAGgtaatgtaat ... acttgatcagGTTGCAGATCTACAGACAAGGAACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcatatcaaaaaggcttattgatcttgacagtttactgtgttacttgatcagGTTGCAGATCTACAGACAAGGAACTG
                         tcttgac  putative branch site (score: 14)
     atatcaaaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtaatgtactgcgggtagagaggtttggtttcatatcaaaaaggcttattgatcttgacagtttactgtgttacttgatcagGTTGCAGATCTACAGACAAGGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA