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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttagaaatttctggtcacactgtttatctcctgtatcaacagagcatatatttaattaagtctatcgccactttctcatctgttctcattctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCGGCATGGATTCTGATGGCCCCCATACTTCACTTATACATGGTCTTCCTGA

Basic information

species Oryza sativa
transcript LOC_Os02g02350.1
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|58692095|gb|CK080782.1|CK080782
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88341129|gb|CI638685.1|CI638685
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88728791|gb|CI752301.1|CI752301
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|29666902|gb|CB663177.1|CB663177
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88396050|gb|CI595598.1|CI595598
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|29686687|gb|CB682962.1|CB682962
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88364006|gb|CI644632.1|CI644632
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88354817|gb|CI614095.1|CI614095
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88428577|gb|CI565045.1|CI565045
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|58594318|gb|CF992626.1|CF992626
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88570194|gb|CI661369.1|CI661369
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|25798904|gb|CA754865.1|CA754865
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
EST: gi|88354831|gb|CI614109.1|CI614109
EST:     CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATG                         GACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG
genomic: CAGATCCGACGCTTAAGCACCTTTCCGAGGTGTGATTTTTCCCCCCGATGgtattgtatc ... ttctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatatatttaattaagtctatcgccactttctcatctgttctcattctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCGGCATGGATTCTGATGGCCCCCATACTTCACTTATACATGGTCTTCCTGA
      atttaat  putative branch site (score: 4)
                        ccactttctcatctgt  putative PPT
     tatttaattaagtcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttagaaatttctggtcacactgtttatctcctgtatcaacagagcatatatttaattaagtctatcgccactttctcatctgttctcattctctttagGACAATTGATGACTTCTGAAATAAAGCACGGTGGAAAGCTATCCTGTAGCGGCATGGATTCTGATGGCCCCCATACTTCACTTATACATGGTCTTCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA