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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattactctcttttggaattctctagcttgtactactattcaagttgctcatagtattacatgtttctgaactaattggatttgctcaacacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAGGTTCTGTATATTGCTGCAGTTCGAG

Basic information

species Vitis vinifera
transcript Vv01s0011g04970.t01
intron # 5
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|110711442|gb|EE087923.1|EE087923
EST:     TTTGGGATCTAACATCATCAACGGCTGTAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGACAAGAATCAG
genomic: TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|110712942|gb|EE088427.1|EE088427
EST:     GGGGATCTA-CATCATNCA-CGGCTATAGCTTCACTACCCAAAGGAAA-T                         GATGAGGTTTTTGCATTCTGCAGATT
genomic: GGG-ATCTAACATCAT-CAACGGCTATAGCTTCACTACCCAA-GGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATT
EST: gi|110698023|gb|EE075561.1|EE075561
EST:     TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGAATTTCTCAAACTAACGTCAAGAATCAG
genomic: TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|110713391|gb|EE089281.1|EE089281
EST:     TGGGGATCTA-CATCATNCA-CGGCTATAGCTTC-CTACC-AAGGAAAAT                         GATGAGGTTTTTGCAT-CTGCAGATTT-CTCAA
genomic: TTGGGATCTAACATCAT-CAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAA
EST: gi|110377427|gb|EC942492.1|EC942492
EST:     TTTGGGATCTAACATCATCAACGGCTGTAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAAAGACAAGAATCAG
genomic: TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|110360943|gb|EC924388.1|EC924388
EST:     TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
genomic: TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|71876936|gb|DT025991.1|DT025991
EST:     CGGCTATAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
genomic: CGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|33402110|gb|CF207737.1|CF207737
EST:     TACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
genomic: TACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|110404868|gb|EC970393.1|EC970393
EST:     TTTGGGATCTAACATCATCAACGGCTGTAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGACAAGAATCAG
genomic: TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|110711776|gb|EE088641.1|EE088641
EST:     TTTGGGATCTAACATCATCAACGGCTGTAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGACAAGAATCAG
genomic: TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG
EST: gi|110380366|gb|EC945626.1|EC945626
EST:     TTTGGGATCTAACATCATCAACGGCTGTAGCTTCACTACCCAAGGAAAAT                         GATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAAAGACAAGAATCAN
genomic: TTTGGGATCTAACATCATCAACGGCTATAGCTTCACTACCCAAGGAAAATgtaagaaatt ... acacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgctcatagtattacatgtttctgaactaattggatttgctcaacacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAGGTTCTGTATATTGCTGCAGTTCGAG
                          aactaat  putative branch site (score: 2)
       atagtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattactctcttttggaattctctagcttgtactactattcaagttgctcatagtattacatgtttctgaactaattggatttgctcaacacatccagGATGAGGTTTTTGCATTCTGCAGATTTTCTCAAACTAACGTCAAGAATCAGGTTCTGTATATTGCTGCAGTTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - -cttttgg
- - - - - - - - - - - ctctagc
- - - - - - - - - - - - - - - - - - -ctattca
- - - - - - - - - - - - - - - - - - - - - - - - gctcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaat