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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacacatacgttcttgatgcaatgttgtgctgttcttgcgaattactgcgtttgtgcactaatcgattgatgcgtgatgtcttgtcctttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG

Basic information

species Oryza sativa
transcript LOC_Os03g13790.1
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|88362353|gb|CI608744.1|CI608744
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88328977|gb|CI658625.1|CI658625
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|117217875|gb|CT845173.1|CT845173
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|29628330|gb|CB633341.1|CB633341
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88373410|gb|CI614746.1|CI614746
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGGGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGGGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88351778|gb|CI617503.1|CI617503
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|58689184|gb|CK077871.1|CK077871
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88409790|gb|CI571047.1|CI571047
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88730127|gb|CI753742.1|CI753742
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88351022|gb|CI620682.1|CI620682
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88352611|gb|CI624550.1|CI624550
EST:     ACGCCAAGAGGAACAAAATTTTTTCAAGTGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: ACGCCAAGAGGAACAAAATTTTTTCAA-TGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|29621639|gb|CB626650.1|CB626650
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|29630702|gb|CB635711.1|CB635711
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|86904162|gb|CI304596.1|CI304596
EST:     CACGCCAAGAGGAACAAAATTTTTTCACTGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88344650|gb|CI637259.1|CI637259
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|58612137|gb|CK039849.1|CK039849
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88387482|gb|CI583000.1|CI583000
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|87023602|gb|CI286353.1|CI286353
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88573702|gb|CI665471.1|CI665471
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88450057|gb|CI572188.1|CI572188
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88337044|gb|CI628130.1|CI628130
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88412252|gb|CI573528.1|CI573528
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
EST: gi|88370989|gb|CI595101.1|CI595101
EST:     CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAG                         AATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
genomic: CACGCCAAGAGGAACAAAATTTTTTCAATGCGCTGCGCCAAGTAGGGAAGgtaagacaca ... tttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgcgtttgtgcactaatcgattgatgcgtgatgtcttgtcctttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG
                                     tcttgtccttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacacatacgttcttgatgcaatgttgtgctgttcttgcgaattactgcgtttgtgcactaatcgattgatgcgtgatgtcttgtcctttgtgtcagAATTTTGAGAAGATTACGCTGCGTGTCCAGAGCAAAAGCAAAGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA