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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attactttttcatactttttacttggttgtttgaaaagaggcctgctgtgatattttaatccttatcttagtttctgctaattttcttccgtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAATGTATACTAGGTTGGCTGCCATGCCAAAGAAAGGTTAACTCCAGGGTGC

Basic information

species Oryza sativa
transcript LOC_Os02g42314.2
intron # 5
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|88278493|gb|CI399493.1|CI399493
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGAGTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88988696|gb|CI039115.1|CI039115
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|86872694|gb|CI341904.1|CI341904
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|300216021|gb|HO088647.1|HO088647
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88280311|gb|CI401509.1|CI401509
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|86905439|gb|CI285402.1|CI285402
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCT
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCT
EST: gi|86881474|gb|CI322565.1|CI322565
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88384445|gb|CI553937.1|CI553937
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88243713|gb|CI242835.1|CI242835
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88485512|gb|CI422783.1|CI422783
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|33655539|gb|CF278153.1|CF278153
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88550505|gb|CI478483.1|CI478483
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAGCCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|33655538|gb|CF278152.1|CF278152
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|9865086|gb|AU100836.1|AU100836
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|33807112|gb|CF329438.1|CF329438
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88506894|gb|CI434400.1|CI434400
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|87006784|gb|CI285818.1|CI285818
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCA
EST: gi|186892747|gb|FG124648.1|FG124648
EST:     TGCATTGATGGCCCATCCAGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88967252|gb|CI002446.1|CI002446
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|86415895|gb|CI029906.1|CI029906
EST:     ACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: ACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|89194948|gb|CI003412.1|CI003412
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88320430|gb|CI523173.1|CI523173
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88244898|gb|CI242749.1|CI242749
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|55409211|gb|CV721587.1|CV721587
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88258774|gb|CI361360.1|CI361360
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88564069|gb|CI494786.1|CI494786
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88270691|gb|CI385949.1|CI385949
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88564099|gb|CI494816.1|CI494816
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88506428|gb|CI433934.1|CI433934
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTNACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88459493|gb|CI519554.1|CI519554
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|25806709|gb|CA762670.1|CA762670
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCGAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88460200|gb|CI529275.1|CI529275
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|86527972|gb|CI168178.1|CI168178
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|86837261|gb|CI347731.1|CI347731
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88280941|gb|CI401991.1|CI401991
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         CCAACCTCCTGCGCTCAG-CNGACATCAGAGGCTATCAATCCATGGCAAGA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGC-GACATCAGAGGCTATCAATCCATGGCAAGA
EST: gi|86260810|gb|CI000258.1|CI000258
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88253294|gb|CI351920.1|CI351920
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|88849807|gb|CI001513.1|CI001513
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA
EST: gi|33689647|gb|CF317886.1|CF317886
EST:     TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAG                         GCAACCTCCTGCGCTCAGGCGACATCGGAGGCTATCAATCCATGGCAAGAA
genomic: TGCATTGATGGCCCATCCTGAACCAGACAGTCCACTTAACTGTGACTCAGgtagctccac ... gtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgatattttaatccttatcttagtttctgctaattttcttccgtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAATGTATACTAGGTTGGCTGCCATGCCAAAGAAAGGTTAACTCCAGGGTGC
                              tgctaat  putative branch site (score: 2)
                                    ttttcttccgt  CT-rich tract
     atattttaatccttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attactttttcatactttttacttggttgtttgaaaagaggcctgctgtgatattttaatccttatcttagtttctgctaattttcttccgtaaatatagGCAACCTCCTGCGCTCAGGCGACATCAGAGGCTATCAATCCATGGCAAGAATGTATACTAGGTTGGCTGCCATGCCAAAGAAAGGTTAACTCCAGGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - - - - - -cctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgct