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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctacatcggtaaatggacacatgctttcggccctttgccaattgacatgtcctctatgtgtggacacttaccaatgtactttactgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07880.1
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|29662011|gb|CB658286.1|CB658286
EST:     GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
EST: gi|427667|gb|D23801.1|D23801
EST:     GGTCGTATAGAGCTATTGATGTTACCTATGCACTATTGANGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
EST: gi|86429643|gb|CI076324.1|CI076324
EST:     GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
EST: gi|29633318|gb|CB638327.1|CB638327
EST:     GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
EST: gi|86600858|gb|CI356615.1|CI356615
EST:     ACTCTTGAAGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: ACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
EST: gi|86832776|gb|CI345190.1|CI345190
EST:     ACCTATGCACTCTTGAAGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: ACCTATGCACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
EST: gi|29663728|gb|CB660003.1|CB660003
EST:     GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
EST: gi|86492716|gb|CI135349.1|CI135349
EST:     GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACG                         GCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
genomic: GGTCGTATAGAGCTATTGATGTTACCTATGCACTCTTGAAGAACATAACGgtatgctcta ... tgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgacatgtcctctatgtgtggacacttaccaatgtactttactgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG
                         cacttac  putative branch site (score: 2)
                                       ctttact  putative PPT
                                     tacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctacatcggtaaatggacacatgctttcggccctttgccaattgacatgtcctctatgtgtggacacttaccaatgtactttactgttgtgtagGCTATCAAAGAGAACTTCCGTATTACAAGTGATGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA