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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtacacggagatattttcttcctcccacctcctcctcctcctccttttgctgccctttcacaactgacaagctctctctctctctctcttctctctttgggggtggttcttggtgcagAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT

Basic information

species Oryza sativa
transcript LOC_Os09g13870.1
intron # 1
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|88363440|gb|CI618001.1|CI618001
EST:     GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGG                         AGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG
genomic: GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGGgtgggtacac ... cttggtgcagAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG
EST: gi|88732308|gb|CI755485.1|CI755485
EST:     GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGG                         AGCCGATCTGCGGCGGTGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG
genomic: GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGGgtgggtacac ... cttggtgcagAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG
EST: gi|13896471|gb|AU182807.1|AU182807
EST:     GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGG                         AGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG
genomic: GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGGgtgggtacac ... cttggtgcagAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG
EST: gi|88350748|gb|CI619006.1|CI619006
EST:     GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGG                         AGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG
genomic: GCCGGCGGCGGGGACGACCCGGCCCGCGATCGCGACGCCGAGCATTGCGGgtgggtacac ... cttggtgcagAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgacaagctctctctctctctctcttctctctttgggggtggttcttggtgcagAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT
 aactgac  putative branch site (score: 2)
                                           ttctt  putative PPT
















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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtacacggagatattttcttcctcccacctcctcctcctcctccttttgctgccctttcacaactgacaagctctctctctctctctcttctctctttgggggtggttcttggtgcagAGCCGATCTGCGGCGGCGGCGGGTGTGGGGGGCTCGAGGAGCCGCTGGTCGGGAAGAGGAGGAGGAGGAAGAACGGCCGCCCT

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