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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcactaaatgatattaatttcttctgtggtacatttgcactaaagttgatgcacagttattacatggtatgtttcttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGAGAAAGATGCTCTTGACAGTGACTCGCAACGATACACAACAGCTTCTACC

Basic information

species Oryza sativa
transcript LOC_Os11g36070.3
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|29688057|gb|CB684332.1|CB684332
EST:     CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
EST: gi|66923674|gb|CX110522.1|CX110522
EST:     CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
EST: gi|24468830|gb|CA305779.1|CA305779
EST:     CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
EST: gi|29626154|gb|CB631165.1|CB631165
EST:     CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
EST: gi|86503375|gb|CI146008.1|CI146008
EST:     CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: CACAATATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
EST: gi|29614178|gb|CB619191.1|CB619191
EST:     TATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: TATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
EST: gi|29688058|gb|CB684333.1|CB684333
EST:     TATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: TATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
EST: gi|3759781|gb|C97039.1|C97039
EST:     TATTCCAAATGAACNTCCTGCTACATTGCCACCTCGAGATTCAAG                         AGAGTCCCAGCACANTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA
genomic: TATTCCAAATGAACATCCTGCTACATTGCCACCTCGAGATTCAAGgtcagcacta ... cttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatttgcactaaagttgatgcacagttattacatggtatgtttcttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGAGAAAGATGCTCTTGACAGTGACTCGCAACGATACACAACAGCTTCTACC
                                        tgtttctt  CT-rich tract
                           ttattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagcactaaatgatattaatttcttctgtggtacatttgcactaaagttgatgcacagttattacatggtatgtttcttaatgcagAGAGACCCAGCACACTTATTCATTGTCCAATGAGAATGTTAATCATAGGGAGAAAGATGCTCTTGACAGTGACTCGCAACGATACACAACAGCTTCTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG