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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttaatactattcattagttagtagatatatcagtatttttttcttctcaacaccatcaaatttacatgttcaattttaattagttattcgtttgcagTTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCAGTTTTTTACAGGATGAATATGATGCAGAAACCACCGGTGTACTGCCACC

Basic information

species Oryza sativa
transcript LOC_Os01g43870.1
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|33676393|gb|CF304632.1|CF304632
EST:     TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATG                         TTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCA
genomic: TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATGgtaaagtccg ... tcgtttgcagTTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCA
EST: gi|88359907|gb|CI617818.1|CI617818
EST:     TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTAATCAAAATG                         TTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCA
genomic: TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATGgtaaagtccg ... tcgtttgcagTTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCA
EST: gi|88364965|gb|CI616384.1|CI616384
EST:     TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATG                         TTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGC
genomic: TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATGgtaaagtccg ... tcgtttgcagTTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGC
EST: gi|88347839|gb|CI635932.1|CI635932
EST:     TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATG                         TTTGCTCTACTTCTGAAGTATCA
genomic: TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATGgtaaagtccg ... tcgtttgcagTTTGCTCTACTTCTGAAGTATCA
EST: gi|88390836|gb|CI611062.1|CI611062
EST:     TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATG                         TTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCA
genomic: TGCACTCGATAGAACAGCGGTGGGGTCAACACTTCTAAGTCATCAAAATGgtaaagtccg ... tcgtttgcagTTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcaacaccatcaaatttacatgttcaattttaattagttattcgtttgcagTTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCAGTTTTTTACAGGATGAATATGATGCAGAAACCACCGGTGTACTGCCACC
                               ttttaat  putative branch site (score: 3)
                                            ttcgttt  putative PPT
            atcaaatttacatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttaatactattcattagttagtagatatatcagtatttttttcttctcaacaccatcaaatttacatgttcaattttaattagttattcgtttgcagTTTGCTCTACTTCTGAAGTATCAGGGGGAAACTTTGGAATCGCTGAAGTCAGTTTTTTACAGGATGAATATGATGCAGAAACCACCGGTGTACTGCCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG