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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcttttataagatcagttcactttgaaacaaatcaaactgttgcataataatcgattattttttttaatttgtgtgcacccatggtcttaaatataatttctcattgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG

Basic information

species Oryza sativa
transcript LOC_Os06g09370.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09370.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G116785_T03 (Zea mays), 3'ss of exon 3
gtgagttcttt---tataagatcagttcactttgaaacaaatcaaactgttgcataataatc---gattattttttttaatt---tgtgtgcacccatggtcttaaatataatttctcattgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG----------------------------------
||||| | |||   ||| |||||||| |||||     ||||   ||  ||||||||||  |     ||| ||| |||   ||   | | || |  |      || | |||||||||  | | |||||||||||||| |||||||||||||||| |||||||||||||| || |  ||||||||||| |||||||||                                  
gtgaggtttttatttatgagatcagtccacttgagggcaaactgaagagttgcataatgtttttgaattgtttgtttcgcttgcttttatgaaggctaaagtttgactataatttcctaatctgctgcagCTTCGCAGAGAGAAAATTTCAGATAGGATGAAAAATCTGCAGGATCTTGTCCCAAATTCCAATAAGGTACTTTTTTTGGAGGGTGGGGGTGGGTTGACTT

upper sequence: LOC_Os06g09370.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G116785_T01 (Zea mays), 3'ss of exon 3
gtgagttcttt---tataagatcagttcactttgaaacaaatcaaactgttgcataataatc---gattattttttttaatt---tgtgtgcacccatggtcttaaatataatttctcattgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG
||||| | |||   ||| |||||||| |||||     ||||   ||  ||||||||||  |     ||| ||| |||   ||   | | || |  |      || | |||||||||  | | |||||||||||||| |||||||||||||||| |||||||||||||| || |  ||||||||||| |||||||||
gtgaggtttttatttatgagatcagtccacttgagggcaaactgaagagttgcataatgtttttgaattgtttgtttcgcttgcttttatgaaggctaaagtttgactataatttcctaatctgctgcagCTTCGCAGAGAGAAAATTTCAGATAGGATGAAAAATCTGCAGGATCTTGTCCCAAATTCCAATAAG

upper sequence: LOC_Os06g09370.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G024530_T01 (Zea mays), 3'ss of exon 5
gtgagttctt--ttataagatcagttcactttgaaacaaatcaaactgttgcataataatc--gattattttttttaatttg---tgtgcacccatggtcttaaatataatttctcattgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG
||||||| ||  ||||  ||||||| ||| |     ||||   ||  ||| ||||||| |   || |  ||| |||   |||   | || | | ||    || | || ||||||  ||  || ||||||||||| |||| ||||||||||| |||||||||||||| ||||  |||||||| || || ||||||
gtgagtttttctttatgtgatcagtccacctcagtgcaaacagaagagttacataatatttttgaattatttgtttggcttgcattatgtatc-ataagtttgactacaatttcatat-atgttgcagCTTCGCAGAGAAAAAATTTCAGATAGGATGAAAAATCTACAAGATCTTGTCCCGAATTCTAATAAG

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|87012724|gb|CI295168.1|CI295168
EST:     AAGGGCTCGCCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGG                         CTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
genomic: AAGGGCTCG-CCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGGgtgagttctt ... tgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
EST: gi|88980643|gb|CI026705.1|CI026705
EST:     CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGG                         CTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
genomic: CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGGgtgagttctt ... tgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
EST: gi|218483231|gb|FG956163.1|FG956163
EST:     CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGG                         CTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
genomic: CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGGgtgagttctt ... tgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
EST: gi|86498321|gb|CI140954.1|CI140954
EST:     CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGG                         CTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
genomic: CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGGgtgagttctt ... tgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
EST: gi|5039098|gb|AU071208.1|AU071208
EST:     CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGG                         CTTCG-CGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
genomic: CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGGgtgagttctt ... tgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
EST: gi|218482847|gb|FG953463.1|FG953463
EST:     CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGG                         CTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
genomic: CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGGgtgagttctt ... tgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
EST: gi|58603374|gb|CK013902.1|CK013902
EST:     CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGG                         CTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC
genomic: CAAGGGCTCGCCGTGGACAGGCAACTGATCCTCACAGTATTGCTGAACGGgtgagttctt ... tgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttaatttgtgtgcacccatggtcttaaatataatttctcattgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG
  ttttaat  putative branch site (score: 3)
                                     tttctcatt  putative PPT
                         tcttaaatataatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcttttataagatcagttcactttgaaacaaatcaaactgttgcataataatcgattattttttttaatttgtgtgcacccatggtcttaaatataatttctcattgtgctgcagCTTCGCCGAGAGAAAATTTCAGAAAGGATGAAAAATCTCCAAGTCCTTGTCCCAAACTCCAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG