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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGGATTAAGCCCAAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgcttcctgttttccgattgccgtttcattaccatatgtatttgttagctttgtccttactgtaactattttttcccag

Basic information

species Oryza sativa
transcript LOC_Os02g10310.2
intron # 10
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|29660372|gb|CB656647.1|CB656647
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAATTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29672587|gb|CB668862.1|CB668862
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29612852|gb|CB617865.1|CB617865
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29657905|gb|CB654180.1|CB654180
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|86599975|gb|CI258315.1|CI258315
EST:     AGGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTGACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: A-GGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29671043|gb|CB667318.1|CB667318
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCANNNNNNNNTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|163929432|gb|EG713401.1|EG713401
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|117232667|gb|CT861058.1|CT861058
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29637362|gb|CB642371.1|CB642371
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88904130|gb|CI006363.1|CI006363
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29672144|gb|CB668419.1|CB668419
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88691997|gb|CI735572.1|CI735572
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29643533|gb|CB648540.1|CB648540
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGGTTA-TGGATGCA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTG-TTAATGGATGCA
EST: gi|29636552|gb|CB641561.1|CB641561
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29636597|gb|CB641606.1|CB641606
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|86496229|gb|CI138862.1|CI138862
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29664840|gb|CB661115.1|CB661115
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88690598|gb|CI734677.1|CI734677
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88223961|gb|CI223810.1|CI223810
EST:     AGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|86433902|gb|CI094245.1|CI094245
EST:     GAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: GAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|27548667|gb|CA766758.2|CA766758
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGGATTAAGCCCAAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgcttcctgttttccgattgccgtttcattaccatatgtatttgttagctttgtccttactgtaactattttttcccag

- - - - - - -  AAGGAG
- - - - - - - -  GGAGCA
- - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - GCAAAG