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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtagcaagtagcaactcacgcagcttcggttggagcgagatcttcttggctatcagctggttcctgttttcatttgagaatttctactgggctctatgaaaattctgattgttttgggtggtgaaatttttgtctgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATCTTCACTCATCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g70520.1
intron # 1
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|29612788|gb|CB617801.1|CB617801
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|29620623|gb|CB625634.1|CB625634
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|58587977|gb|CF986285.1|CF986285
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACGTC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|88420750|gb|CI564586.1|CI564586
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|88313076|gb|CI592360.1|CI592360
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|88454325|gb|CI569897.1|CI569897
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|29619009|gb|CB624021.1|CB624021
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|58593808|gb|CF992116.1|CF992116
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|117242417|gb|CT842994.1|CT842994
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCTTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|29614528|gb|CB619541.1|CB619541
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|58609911|gb|CK037944.1|CK037944
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
EST: gi|88454346|gb|CI569918.1|CI569918
EST:     GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAG                         TATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC
genomic: GGGATTTCCCGGAGGATTTCGTCTTCGGATCCGCCACCTCGTCGTACCAGgtagtagcaa ... tgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctctatgaaaattctgattgttttgggtggtgaaatttttgtctgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATCTTCACTCATCAAG
             ttctgat  putative branch site (score: 3)
                                     tttttgtct  putative PPT
     tatgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtagcaagtagcaactcacgcagcttcggttggagcgagatcttcttggctatcagctggttcctgttttcatttgagaatttctactgggctctatgaaaattctgattgttttgggtggtgaaatttttgtctgtctggtagTATGAGGGTGGTTTTGATGAGGATGGTAGGAGCCCAAGCAACTGGGACATCTTCACTCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA