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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattgaacacacttctcatcatatggttttatcgaaacaagcaacatttatctgattttgtccccacgatctgaatactgaccgtctcaatactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGGCTCACAGAATACGACGGTGAGGAGGCGCTCCGGGCCATCCGCGTCGCCC

Basic information

species Oryza sativa
transcript LOC_Os04g52606.1
intron # 9
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|87022891|gb|CI269827.1|CI269827
EST:     GACAAGATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: GACAAGATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|88453643|gb|CI682945.1|CI682945
EST:     GATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: GATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|88453850|gb|CI687081.1|CI687081
EST:     GATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: GATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|86479836|gb|CI122469.1|CI122469
EST:     CAAACTATGATGATGCTCTTGAAGAAGACAAGATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: CAAACTATGATGATGCTCTTGAAGAAGACAAGATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|88664520|gb|CI698863.1|CI698863
EST:     GATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: GATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|88501759|gb|CI695068.1|CI695068
EST:     GATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: GATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|86482166|gb|CI124799.1|CI124799
EST:     CAAACTATGATGATGCTCTTGAAGAAGACAAGATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: CAAACTATGATGATGCTCTTGAAGAAGACAAGATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|88665086|gb|CI708695.1|CI708695
EST:     GATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: GATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
EST: gi|88453623|gb|CI682290.1|CI682290
EST:     GATTTATATTTTCGAATGG                         GCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG
genomic: GATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGG

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: 34 (upstream exon), 43 (downstream exon)
Score: 2

TGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGCCGACCAAACTATGATGATGCTCTTGAAGAAGACAAGATTTATATTTTCGAATGGgtaagctcag ... atactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGGCTCACAGAATACGACGGTGAGGAGGCGCTCCGGGCCATCCGCGTCGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttatctgattttgtccccacgatctgaatactgaccgtctcaatactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGGCTCACAGAATACGACGGTGAGGAGGCGCTCCGGGCCATCCGCGTCGCCC
                               tactgac  putative branch site (score: 2)
                                              tactttc  putative PPT
                                            aatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattgaacacacttctcatcatatggttttatcgaaacaagcaacatttatctgattttgtccccacgatctgaatactgaccgtctcaatactttcagGCCTGGGAGCTGTACGAGAACAACTACCCTCTGGGCGTCGTAGACCCAAGGCTCACAGAATACGACGGTGAGGAGGCGCTCCGGGCCATCCGCGTCGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - -gaacaca
- - - - - - - - - - - - - - - - - - - caagcaa