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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGATAGCAAGGGCAGGGACTCCGATCGGGAGAGGGAGCGTGATAGAGAAGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccattgatttttctgctttggctctttttataagcatgttacgttttcctgatgttgcatgatgcccctccaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g27940.2
intron # 5
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|89184523|gb|CI047088.1|CI047088
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88833399|gb|CI076880.1|CI076880
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86486551|gb|CI129184.1|CI129184
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88365912|gb|CI545771.1|CI545771
EST:     CATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: CATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88297563|gb|CI550626.1|CI550626
EST:     GCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: GCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86260462|gb|CI066335.1|CI066335
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|38468717|gb|CF952848.1|CF952848
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|11564711|gb|AU165347.1|AU165347
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCNCCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89176294|gb|CI043315.1|CI043315
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88264164|gb|CI367938.1|CI367938
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88996496|gb|CI260000.1|CI260000
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86540778|gb|CI180984.1|CI180984
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGTACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89185574|gb|CI052100.1|CI052100
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|29660476|gb|CB656751.1|CB656751
EST:     AGCAGACGGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86485489|gb|CI128122.1|CI128122
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89186454|gb|CI048126.1|CI048126
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|29643647|gb|CB648654.1|CB648654
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89164932|gb|CI102020.1|CI102020
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86485638|gb|CI128271.1|CI128271
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86526544|gb|CI166750.1|CI166750
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGATAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89189792|gb|CI049331.1|CI049331
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89185769|gb|CI047638.1|CI047638
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|29636393|gb|CB641402.1|CB641402
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88421681|gb|CI556890.1|CI556890
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89187134|gb|CI047201.1|CI047201
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86253272|gb|CI058197.1|CI058197
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86431715|gb|CI085326.1|CI085326
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89163948|gb|CI101036.1|CI101036
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCACCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86425573|gb|CI070670.1|CI070670
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGGGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86526183|gb|CI166389.1|CI166389
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGATAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86823665|gb|CI258725.1|CI258725
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86495910|gb|CI138543.1|CI138543
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88298285|gb|CI561078.1|CI561078
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTTTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88833327|gb|CI076809.1|CI076809
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|10930981|gb|AU161255.1|AU161255
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88447869|gb|CI544976.1|CI544976
EST:     TAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: TAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89193634|gb|CI116267.1|CI116267
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86415439|gb|CI069842.1|CI069842
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86836074|gb|CI346142.1|CI346142
EST:     ACCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89161509|gb|CI099481.1|CI099481
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88840443|gb|CI079897.1|CI079897
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|89166659|gb|CI103945.1|CI103945
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|86486020|gb|CI128653.1|CI128653
EST:     AGCAGACAGGGATAGNCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
EST: gi|88957037|gb|CI095081.1|CI095081
EST:     AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAG                         GATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG
genomic: AGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccat ... tccaatgcagGATACTCTGACAAAGAGAAGTCAAGGCACCGCTCATCAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGATAGCAAGGGCAGGGACTCCGATCGGGAGAGGGAGCGTGATAGAGAAGCAGACAGGGATAGGCAGCGGAGACACCATTCTAAGGACAGAAGTTCAGgtattgccattgatttttctgctttggctctttttataagcatgttacgttttcctgatgttgcatgatgcccctccaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT