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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatcattcgagcaatttatttccctgtgcattatatactactagtatatgtgaagctaatgctcattgatatatatatctgggaattcgatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC

Basic information

species Oryza sativa
transcript LOC_Os01g45550.1
intron # 3
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|58675818|gb|CK064505.1|CK064505
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|88246655|gb|CI246504.1|CI246504
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|86434306|gb|CI094649.1|CI094649
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|88225519|gb|CI225435.1|CI225435
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|89179874|gb|CI044153.1|CI044153
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|89194724|gb|CI117161.1|CI117161
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCCTTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|87015309|gb|CI275499.1|CI275499
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|89164996|gb|CI102084.1|CI102084
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|86482461|gb|CI125094.1|CI125094
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|86505347|gb|CI147980.1|CI147980
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|86477474|gb|CI120107.1|CI120107
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|86535239|gb|CI175445.1|CI175445
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|109712580|gb|CI105188.1|CI105188
EST:     CGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|89163486|gb|CI100376.1|CI100376
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|89183756|gb|CI046321.1|CI046321
EST:     CGATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|88222283|gb|CI222239.1|CI222239
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|86592538|gb|CI253219.1|CI253219
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|86486031|gb|CI128664.1|CI128664
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|89175799|gb|CI042820.1|CI042820
EST:     CTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
EST: gi|88246381|gb|CI246230.1|CI246230
EST:     CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAG                         GCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT
genomic: CAATCGCCATCGGACTCCGCGGGACGCTCCTGCACGTCGCCATTGTTCAGgtaactatgg ... gatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatatgtgaagctaatgctcattgatatatatatctgggaattcgatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC
                   tcattgatatatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatcattcgagcaatttatttccctgtgcattatatactactagtatatgtgaagctaatgctcattgatatatatatctgggaattcgatttgatagGCGGCTCTACCACAAGGGATTGTGCCTTTTGTTTTTGCAAAAGAATACAATGTCCACCCGGCCATCCTGAGCACAGC

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