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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttacctctgttcatctttttaacgtaggacaatgttcagtttagatttgcagaactttgatgtttgctttaatttgttgttaatacagATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAGAGATGACGATTGTGCCATATGTGCCAGATACAGTTACCTACTGTGGCGA

Basic information

species Oryza sativa
transcript LOC_Os01g05510.3
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|86882171|gb|CI325687.1|CI325687
EST:     CACAGTCAAAATATCAG                         ATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG
genomic: CACAGTCAAAATATCAGgtttacctct ... gttaatacagATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG
EST: gi|87027264|gb|CI269939.1|CI269939
EST:     AGAGCTGCCTATCTCATGTCCCAGTCTTCTTTGCACAGTCAA--TATCAG                         ATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG
genomic: AGAGCTGCCTATCTCATGTCCCAGTCTTCTTTGCACAGTCAAAATATCAGgtttacctct ... gttaatacagATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG
EST: gi|88843164|gb|CI372064.1|CI372064
EST:     TTGCACAGTCAAAATATCAG                         ATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG
genomic: TTGCACAGTCAAAATATCAGgtttacctct ... gttaatacagATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG
EST: gi|86873537|gb|CI329915.1|CI329915
EST:     AGTCAAAATATCAG                         ATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG
genomic: AGTCAAAATATCAGgtttacctct ... gttaatacagATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagtttagatttgcagaactttgatgtttgctttaatttgttgttaatacagATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAGAGATGACGATTGTGCCATATGTGCCAGATACAGTTACCTACTGTGGCGA
                                            tgttaat  putative branch site (score: 3)
                                  tttaatttgttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttacctctgttcatctttttaacgtaggacaatgttcagtttagatttgcagaactttgatgtttgctttaatttgttgttaatacagATGATCCAGAGTATCGTGCGTCTAAGGCACTCACTGCAAAGAGAGAACCAGAGATGACGATTGTGCCATATGTGCCAGATACAGTTACCTACTGTGGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG