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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgataatatttgctgtatagttttgcttttatttcatatgccatcatgatatcaattgcttctccttacaacttttgtattattttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTAGATTTCCGTTTTATTTGTGGGGGCAAAGCCACATTGCGATGCCTGATCT

Basic information

species Oryza sativa
transcript LOC_Os02g13990.3
intron # 7
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|29681479|gb|CB677754.1|CB677754
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88201604|gb|CI201959.1|CI201959
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86500192|gb|CI142825.1|CI142825
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCCATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86545114|gb|CI185320.1|CI185320
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88227188|gb|CI228301.1|CI228301
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86500747|gb|CI143380.1|CI143380
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86421117|gb|CI057106.1|CI057106
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88223253|gb|CI223102.1|CI223102
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86536011|gb|CI176217.1|CI176217
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|29645677|gb|CB650684.1|CB650684
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86503360|gb|CI145993.1|CI145993
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCCATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|89196166|gb|CI397168.1|CI397168
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88321409|gb|CI535361.1|CI535361
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCTCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88225868|gb|CI225784.1|CI225784
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|55409763|gb|CV722139.1|CV722139
EST:     CCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: CCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|5005007|gb|AU068324.1|AU068324
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88223197|gb|CI223046.1|CI223046
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86426359|gb|CI071456.1|CI071456
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88830705|gb|CI078149.1|CI078149
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88252358|gb|CI350786.1|CI350786
EST:     ATGGGGCGGATGAGAAGAACCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|89178382|gb|CI391561.1|CI391561
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86505850|gb|CI148483.1|CI148483
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88460872|gb|CI553008.1|CI553008
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|116875219|gb|EC365727.1|EC365727
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|88450626|gb|CI547126.1|CI547126
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86541745|gb|CI181951.1|CI181951
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86496623|gb|CI139256.1|CI139256
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86540436|gb|CI180642.1|CI180642
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAG                         GGTTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|86500143|gb|CI142776.1|CI142776
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCCATTGAAGAG                         GATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA
EST: gi|66915896|gb|CX102744.1|CX102744
EST:     ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAATAG                         GATTGAAGGCATATGCACACCCTGATATAATCTGGCACCAAGTTGGTGTTA
genomic: ATGGGGCGGATGAGAAGAAGCAAAATGAAGAAAGCACCCCAATTGAAGAGgtaatgataa ... attttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgccatcatgatatcaattgcttctccttacaacttttgtattattttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTAGATTTCCGTTTTATTTGTGGGGGCAAAGCCACATTGCGATGCCTGATCT
                          tccttac  putative branch site (score: 2)
                                           ttattttc  putative PPT
                             ttacaacttttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgataatatttgctgtatagttttgcttttatttcatatgccatcatgatatcaattgcttctccttacaacttttgtattattttcacagGATTGAAGGCATATGCACACACTGATATAATCTGGCACCAAGTTGGTGTTAGATTTCCGTTTTATTTGTGGGGGCAAAGCCACATTGCGATGCCTGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG