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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgggtccaatggcacatcaggaaaactatgccccttttgctattagttgatgacaaaaattttttgtcagtcctgaaatatttcatttttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAACTTGACCAAACTTCAGCAATT

Basic information

species Oryza sativa
transcript LOC_Os05g17604.3
intron # 4
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|29682357|gb|CB678632.1|CB678632
EST:     TCTGGACTACTTCCAAAGGAACTAGGAAACCTCACCAATCTTCTTTCATT                         GGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
genomic: TCTGGACTACTTCCAAAGGAACTAGGAAACCTCACCAATCTTCTTTCATTgtaagaaatc ... tttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
EST: gi|29627199|gb|CB632210.1|CB632210
EST:     GAACTAGGAAACCTCACCAATCTTCTTTCATT                         GGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
genomic: GAACTAGGAAACCTCACCAATCTTCTTTCATTgtaagaaatc ... tttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
EST: gi|29680539|gb|CB676814.1|CB676814
EST:     GAACTAGGAAACCTCTTCAATCTTCTTTCATT                         GGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
genomic: GAACTAGGAAACCTCACCAATCTTCTTTCATTgtaagaaatc ... tttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
EST: gi|29622647|gb|CB627658.1|CB627658
EST:     TCTGGACTACTTCCAAAGGAACTAGGAAACCTCACCAATCTTCTTTCATT                         GGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
genomic: TCTGGACTACTTCCAAAGGAACTAGGAAACCTCACCAATCTTCTTTCATTgtaagaaatc ... tttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
EST: gi|29624375|gb|CB629386.1|CB629386
EST:     TCTGGACTACTTCCAAAGGAACTAGGAAACCTCACCAATCTTCTTTCATT                         GGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA
genomic: TCTGGACTACTTCCAAAGGAACTAGGAAACCTCACCAATCTTCTTTCATTgtaagaaatc ... tttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttgatgacaaaaattttttgtcagtcctgaaatatttcatttttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAACTTGACCAAACTTCAGCAATT
  agttgat  putative branch site (score: 5)
                                      tttcatttttcattt  putative PPT
                               tgaaatatttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgggtccaatggcacatcaggaaaactatgccccttttgctattagttgatgacaaaaattttttgtcagtcctgaaatatttcatttttcatttagGGGCATTAGCTCAGACAATTTTACAGGAAGTCTTCCAGAAGAACTGGGTAACTTGACCAAACTTCAGCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC