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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgaataacttaacaaaagcaccaaaccttttcttcttccaaattcctgacaaaaaatccatgaagctttattcacttattatgcttctaatttgcagGTGGAAATGATACAGAAGCAAAATGATGAG

Basic information

species Oryza sativa
transcript LOC_Os06g10880.2
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|89193034|gb|CI050332.1|CI050332
EST:     CTGAGGTGGCAAAACTGAAGGAACAGAAGGCTGAATTGCAGAAAAAGCAG                         GTGGAAATGATACAGAAGCAAAATGATGAG
genomic: CTGAGGTGGCAAAACTGAAGGAACAGAAGGCTGAATTGCAGAAAAAGCAGgtatacctgc ... taatttgcagGTGGAAATGATACAGAAGCAAAATGATGAG
EST: gi|87029295|gb|CI276563.1|CI276563
EST:     CTGAGGTGGCAAAACTGAAGGAACAGAAGGCTGAATTGCAGAAAAAGCAG                         GTGGAAATGATACAGAAGCAAAATGATGAG
genomic: CTGAGGTGGCAAAACTGAAGGAACAGAAGGCTGAATTGCAGAAAAAGCAGgtatacctgc ... taatttgcagGTGGAAATGATACAGAAGCAAAATGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgacaaaaaatccatgaagctttattcacttattatgcttctaatttgcagGTGGAAATGATACAGAAGCAAAATGATGAG
                                          ttctaat  putative branch site (score: 2)
                                       tgcttct  CT-rich tract
                        tttattcacttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgaataacttaacaaaagcaccaaaccttttcttcttccaaattcctgacaaaaaatccatgaagctttattcacttattatgcttctaatttgcagGTGGAAATGATACAGAAGCAAAATGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA