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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcattcttccaaagtattcagtcaattcgtatgaaaatctggaaaaatgttggcttgcttatttgtcctgaactgtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTTGTGGTTTGTTCTGTAAGGAAGCCTGACGAATTGAACTACAAACATATTT

Basic information

species Oryza sativa
transcript LOC_Os06g03760.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 11
gtaagtgcattcttccaaagtattcagtcaattcgtatgaaaatctggaaaaatgttggcttgcttatttgtcctga--actgtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTTGTGGTTTGTTCTGTAAG-GAAGCCTGACGAATTGAAC-TACAAACATATTT-----
|||||| |||| |    ||||  | ||||| |||  || || | ||  ||||    |      |   | |||  |    |||  ||||| |||||||| ||||||||||||| |||||||||||||||||||||||||||||||        |||||||| ||||  ||||| ||| | | ||    |    |      
gtaagt-cattttcatcaagtgcttagtca-ttcacattaacaactataaaagaaatcatgcacaactgtgttattcccactacttgtt-agGGATGGAGAAAGAGGAAACCAACAGGAAGATTCCAGCTCTCAAATTGATTTGC-------TCTGTAAGTGAAGTTTGACGGATTCATCATATGTGCCCCCTGAGTGG
















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|88974640|gb|CI022966.1|CI022966
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88488642|gb|CI425913.1|CI425913
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88508361|gb|CI435867.1|CI435867
EST:     ACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88514370|gb|CI441876.1|CI441876
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|89176031|gb|CI043052.1|CI043052
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88737037|gb|CI760545.1|CI760545
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|87019966|gb|CI299364.1|CI299364
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTTTAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88476562|gb|CI413833.1|CI413833
EST:     TGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: TGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88471869|gb|CI409140.1|CI409140
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|89184314|gb|CI046879.1|CI046879
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTGTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCCAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88447150|gb|CI531393.1|CI531393
EST:     TGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: TGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88762181|gb|CI771737.1|CI771737
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88486627|gb|CI423898.1|CI423898
EST:     CTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: CTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|89175363|gb|CI042384.1|CI042384
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|89176072|gb|CI043093.1|CI043093
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88519661|gb|CI447315.1|CI447315
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88907637|gb|CI090431.1|CI090431
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTNTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|15855078|gb|BI807890.1|BI807890
EST:     TGCGATACTCACACTCTTTTACTATGCCATATTT                         GGATGGCGAAAGAGGAAACCGACACGGAAGATTCCAGCTCTCAAATTGATT
genomic: TGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACA-GGAAGATTCCAGCTCTCAAATTGATT
EST: gi|88245030|gb|CI244879.1|CI244879
EST:     GGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: GGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88263197|gb|CI366971.1|CI366971
EST:     TTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: TTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88997561|gb|CI390227.1|CI390227
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88471943|gb|CI409214.1|CI409214
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|89163502|gb|CI100392.1|CI100392
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88460885|gb|CI553021.1|CI553021
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|86869332|gb|CI339056.1|CI339056
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|86484582|gb|CI127215.1|CI127215
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|5667175|gb|AU077435.1|AU077435
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88961963|gb|CI097116.1|CI097116
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTNTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88292088|gb|CI534882.1|CI534882
EST:     ACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|88284096|gb|CI405542.1|CI405542
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|89163461|gb|CI100351.1|CI100351
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTGTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
EST: gi|29679858|gb|CB676133.1|CB676133
EST:     ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT                         GGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT
genomic: ATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTgtaagtgcat ... gtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaaaatctggaaaaatgttggcttgcttatttgtcctgaactgtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTTGTGGTTTGTTCTGTAAGGAAGCCTGACGAATTGAACTACAAACATATTT
                                              tttgttc  CT-rich tract
             aaaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcattcttccaaagtattcagtcaattcgtatgaaaatctggaaaaatgttggcttgcttatttgtcctgaactgtttgttcagGGATGGCGAAAGAGGAAACCGACAGGAAGATTCCAGCTCTCAAATTGATTTGTGGTTTGTTCTGTAAGGAAGCCTGACGAATTGAACTACAAACATATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA