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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcggccatgtgtatatattatttggtttattgactattgactatttggtatattattttgggtttgaatttcctgactgaaaggtgaaaatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAACAGATAGCATTTGATAATTTGGAAAAATTCCAGGCAGAAGCACGACTTA

Basic information

species Vitis vinifera
transcript Vv00s0283g00020.t01
intron # 16
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|27584247|gb|CB006942.1|CB006942
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
EST: gi|30253044|gb|CB970595.1|CB970595
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
EST: gi|30135435|gb|CB920773.1|CB920773
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
EST: gi|71869579|gb|DT018634.1|DT018634
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
EST: gi|254914692|gb|GR906793.1|GR906793
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGT
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGT
EST: gi|71869623|gb|DT018678.1|DT018678
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
EST: gi|110715593|gb|EE093818.1|EE093818
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
EST: gi|71872847|gb|DT021902.1|DT021902
EST:     CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAG                         GAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA
genomic: CTTTGATTGATGTGGAAGCTGAATCCAGTATAAATGCTGCAATGTTGAAGgtttgaaacc ... aatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtatattattttgggtttgaatttcctgactgaaaggtgaaaatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAACAGATAGCATTTGATAATTTGGAAAAATTCCAGGCAGAAGCACGACTTA
                           tcctgac  putative branch site (score: 2)
                                               tttttc  putative PPT
     tatattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcggccatgtgtatatattatttggtttattgactattgactatttggtatattattttgggtttgaatttcctgactgaaaggtgaaaatttttcagGAAGGGCTTGCTACTGTAGAGAAAAGAAAGAGATGGGACCCCAAGGAAAAACAGATAGCATTTGATAATTTGGAAAAATTCCAGGCAGAAGCACGACTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtttg