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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctaatcattaaggtaacctcaagaaggattatattgccttctagtaaatgaaatctctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAGGTGCAATTGCTGGAATATCGATTGGTGCCTCAGTTGTAGGATTAGCAGC

Basic information

species Oryza sativa
transcript LOC_Os08g10320.3
intron # 17
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|29630668|gb|CB635677.1|CB635677
EST:     TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTACTCCTACTGTGCGAGACGGTGTACCCAAA-GGCAAAGT
genomic: TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcctaa ... tctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGT
EST: gi|58688732|gb|CK077419.1|CK077419
EST:     TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG
genomic: TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcctaa ... tctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG
EST: gi|29620863|gb|CB625874.1|CB625874
EST:     TATTCAAGGTTACTATGGGCCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGCAG
genomic: TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcctaa ... tctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG
EST: gi|29630198|gb|CB635207.1|CB635207
EST:     TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG
genomic: TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcctaa ... tctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG
EST: gi|29623048|gb|CB628059.1|CB628059
EST:     TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG
genomic: TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcctaa ... tctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG
EST: gi|29615848|gb|CB620860.1|CB620860
EST:     TATTCAAGGTTACTATGGGCCATTGATCTCAGCATTAAGCATCACTCCAA                         ATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGCAG
genomic: TATTCAAGGTTACTACGGGCCATTGATCTCAGCATTAAGCATCACTCCAAgtaagcctaa ... tctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtaacctcaagaaggattatattgccttctagtaaatgaaatctctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAGGTGCAATTGCTGGAATATCGATTGGTGCCTCAGTTGTAGGATTAGCAGC
 aggtaac  putative branch site (score: 3)
                                           tctctgtttc  putative PPT
                                  taaatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctaatcattaaggtaacctcaagaaggattatattgccttctagtaaatgaaatctctgtttcagATTTTACTCCTACTGTGCGAAACGGTGTACCCAAAAGGAAAAGTAAAGTAGGTGCAATTGCTGGAATATCGATTGGTGCCTCAGTTGTAGGATTAGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA