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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTTTCTCTTCTCTCTCCGCCTCGCAGAGTCGCAGCGGAGGAGTTGCATAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcgttcctctcctcctcgatttggttgggctcgcgtcgctgactcggcggcggcggcggtggaggtggtggtggtggatttgggaggtggggg...

Basic information

species Oryza sativa
transcript LOC_Os11g06760.1
intron # 1
splice site 5'
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|4878454|gb|AU062753.1|AU062753
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|88339206|gb|CI633777.1|CI633777
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAACCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|88571169|gb|CI662542.1|CI662542
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|38474993|gb|CF959126.1|CF959126
EST:     CCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: CCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|218484821|gb|FG946766.1|FG946766
EST:     TAGGCGAAGCGGAGGAGGAGGCGGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|56157893|gb|C27653.2|C27653
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|25799906|gb|CA755867.1|CA755867
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|88305212|gb|CI652932.1|CI652932
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|88339833|gb|CI649090.1|CI649090
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|88309325|gb|CI655333.1|CI655333
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|29677609|gb|CB673884.1|CB673884
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
EST: gi|88338693|gb|CI644150.1|CI644150
EST:     TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAG                         GCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA
genomic: TAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcg ... caattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTTTTCTCTTCTCTCTCCGCCTCGCAGAGTCGCAGCGGAGGAGTTGCATAGACGAAGCGGAGGAGGAGGCAGCGAGGCGAGGCGAGCCCAATCGGAAGgtgcgattcgttcctctcctcctcgatttggttgggctcgcgtcgctgactcggcggcggcggcggtggaggtggtggtggtggatttgggaggtggggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG