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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatgggaggagtcaaaaattaactcagccatattctttataaaggtattttgtttactaataagtaatgactaccaattatccctttttcttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGGGAATACTCATTCTGCTGTTCCTGTTAACTATGGTGGCTATAACCCTGTA

Basic information

species Oryza sativa
transcript LOC_Os04g51370.1
intron # 16
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|14980796|gb|BI305474.1|BI305474
EST:     GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAG                         TTACAGAGCAGACCANNNNNNNCACGCATCTTCTCGTGGGTCGCTTGGAGG
genomic: GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAGgtattcaatg ... cttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGG
EST: gi|27546452|gb|CA767254.2|CA767254
EST:     GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAG                         TTACAGAGCAGACCANNNNNNNCACGCATCTTCTCGTGGGTCGCTTGGAGG
genomic: GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAGgtattcaatg ... cttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGG
EST: gi|88829825|gb|CI004863.1|CI004863
EST:     TCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAG                         TTACAGAGCAGACCANNNNNNNCACGCATCTTCTCGTGGGTCGCTTGGAGG
genomic: TCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAGgtattcaatg ... cttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGG
EST: gi|86482408|gb|CI125041.1|CI125041
EST:     GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAG                         TTACAGAGCAGACCANNNNNNNCACGCATCTTCTCGTGGGTCGCTTGGAGG
genomic: GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAGgtattcaatg ... cttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGG
EST: gi|14981599|gb|BI306277.1|BI306277
EST:     GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAG                         TTACAGAGCAGACCANNNNNNNCACGCATCTTCTCGTGGGTCGCTTGGAGG
genomic: GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAGgtattcaatg ... cttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGG
EST: gi|86477310|gb|CI119943.1|CI119943
EST:     GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAG                         TTACAGAGCAGACCANNNNNNNCACGCATCTTCTCGTGGGTCGCTTGGAGG
genomic: GTCCAAAGCCACATTTTCATGGGCTCGAACCCTTTACCAGCAGGCGAAAGgtattcaatg ... cttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttgtttactaataagtaatgactaccaattatccctttttcttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGGGAATACTCATTCTGCTGTTCCTGTTAACTATGGTGGCTATAACCCTGTA
          tactaat  putative branch site (score: 1)
                          ctaccaattatccctt  putative PPT
        tttactaataagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatgggaggagtcaaaaattaactcagccatattctttataaaggtattttgtttactaataagtaatgactaccaattatccctttttcttttttcagTTACAGAGCAGACCATTTTTTTCACGCATCTTCTCGTGGGTCGCTTGGAGGGAATACTCATTCTGCTGTTCCTGTTAACTATGGTGGCTATAACCCTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG