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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttttatattatacagcacaaacgaacatcttgctgcatctatctatcagagaaggatagaaaacattttgattcatgattctttttttgttgagtagGTGAGGAAGTTGAGCAAATACGAAGAAGCAGCCACTCATTTGAGAATTTGAAGCTCCCTGAAAGGAAAATCTGCTTGAGTGGCCCAAATAAGCTCTCTGA

Basic information

species Oryza sativa
transcript LOC_Os01g05480.1
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|58610778|gb|CK038490.1|CK038490
EST:     AGCTCTTGAATGTGAAAGCAAGGCTTCTGTTGGATCTGTCTCTAGCAAAG                         GTGAGGAAGTTGAGCAAATACGAAGAAGCAGCCACTCATTTGAGAATTTGA
genomic: AGCTCTTGAATGTGAAAGCAAGGCTTCTGTTGGATCTGTCTCTAGCAAAGgtacacaaat ... tgttgagtagGTGAGGAAGTTGAGCAAATACGAAGAAGCAGCCACTCATTTGAGAATTTGA
EST: gi|88354627|gb|CI678670.1|CI678670
EST:     AGCTCTTGAATGTGAAAGCAAGGCTTCTGTTGGATCTGTCTCTAGCAAAG                         GTGAGGAAGTTGAGCAAATACGAAGAAGCAGCCACTCATTTGAGAAT
genomic: AGCTCTTGAATGTGAAAGCAAGGCTTCTGTTGGATCTGTCTCTAGCAAAGgtacacaaat ... tgttgagtagGTGAGGAAGTTGAGCAAATACGAAGAAGCAGCCACTCATTTGAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcagagaaggatagaaaacattttgattcatgattctttttttgttgagtagGTGAGGAAGTTGAGCAAATACGAAGAAGCAGCCACTCATTTGAGAATTTGAAGCTCCCTGAAAGGAAAATCTGCTTGAGTGGCCCAAATAAGCTCTCTGA
                       ttttgat  putative branch site (score: 4)
                                    ttctttttttgtt  putative PPT
             atagaaaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttttatattatacagcacaaacgaacatcttgctgcatctatctatcagagaaggatagaaaacattttgattcatgattctttttttgttgagtagGTGAGGAAGTTGAGCAAATACGAAGAAGCAGCCACTCATTTGAGAATTTGAAGCTCCCTGAAAGGAAAATCTGCTTGAGTGGCCCAAATAAGCTCTCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA