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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAGTTTCTTTCCAAAGCACTCCAAGACCACCAGCAGCACTACTACGACAACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaacagcttttcagttctctcgtgagcttgttcttgaaacatgtttatacttgggattagaaacatggaaacaaactgatggaagcactgaactgaaaattactcttttgttgctttataag

Basic information

species Oryza sativa
transcript LOC_Os01g53880.1
intron # 2
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|33655776|gb|CF278390.1|CF278390
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGGAAGGAACTT
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGG-AAGGAACTT
EST: gi|29675173|gb|CB671448.1|CB671448
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
EST: gi|699717|gb|D46008.1|D46008
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGNCACAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
EST: gi|4715020|gb|AU056137.1|AU056137
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGGCAAGGGCAGGATGTGGGAAGGAACTT
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGG-CAAGGGCAGGATGTGGGAAGGAACTT
EST: gi|29672642|gb|CB668917.1|CB668917
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
EST: gi|29679027|gb|CB675302.1|CB675302
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
EST: gi|66913500|gb|CX100348.1|CX100348
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
EST: gi|58658772|gb|CK047452.1|CK047452
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCA
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCA
EST: gi|58695140|gb|CK083827.1|CK083827
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
EST: gi|29675175|gb|CB671450.1|CB671450
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGGATGTGGGAAGGAACTTG
EST: gi|33655772|gb|CF278386.1|CF278386
EST:     AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACGAAACAGAAG                         GTTATAACGACCAGAAGCAGCAGGCGAGGGCAGGGATGTGGGAAGGAACTT
genomic: AACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaaca ... gctttataagGTTATAACGACCAGAAGCAGCAGGCAAGGGCAGG-ATGTGGGAAGGAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTAGTTTCTTTCCAAAGCACTCCAAGACCACCAGCAGCACTACTACGACAACTGGAGCAAAGAGGGGATTCATAGACACAGTTGAGGACAAAACAGAAGgtaacaaacagcttttcagttctctcgtgagcttgttcttgaaacatgtttatacttgggattagaaacatggaaacaaactgatggaagcactgaactgaaaattactcttttgttgctttataag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG