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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctagctataattcctctgttttattgtatgatttctttgatctgttgggttgtgatcgctgcaatttttgattccgtgttgtttcttttctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAAAATTGGGGTACTCGGCTCCAGTTGAACTGAGTCCTTATTAGATGTGGAG

Basic information

species Vitis vinifera
transcript Vv03s0038g02650.t01
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|71863859|gb|DT012914.1|DT012914
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGCAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|110699119|gb|EE075838.1|EE075838
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|294967291|gb|GW840166.1|GW840166
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|71858503|gb|DT007558.1|DT007558
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|71861861|gb|DT010916.1|DT010916
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGCAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|161707903|gb|FC055672.1|FC055672
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|110684787|gb|EE062462.1|EE062462
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGCAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|71864297|gb|DT013352.1|DT013352
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|161708312|gb|FC057026.1|FC057026
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|161718621|gb|FC068210.1|FC068210
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTC--GTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|156737705|gb|EV241826.1|EV241826
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGCAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|110730859|gb|EE108423.1|EE108423
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|110699744|gb|EE077009.1|EE077009
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA
EST: gi|161710423|gb|FC061118.1|FC061118
EST:     TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAG                         ACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAAGACGGAACAATTCAA
genomic: TTTTCCCAGATCTTCAGCTGTAGAGCGGCGCAGCTCACCAAATTGTAAAGgtgagatttt ... tctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgggttgtgatcgctgcaatttttgattccgtgttgtttcttttctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAAAATTGGGGTACTCGGCTCCAGTTGAACTGAGTCCTTATTAGATGTGGAG
                      ttttgat  putative branch site (score: 4)
                                   ttgtttcttttctgtt  putative PPT
                   aatttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctagctataattcctctgttttattgtatgatttctttgatctgttgggttgtgatcgctgcaatttttgattccgtgttgtttcttttctgttgtagACTTGTACTATTTCTTTGTCGTGTTGTCGAGTAGAGGACGGAACAATTCAAAATTGGGGTACTCGGCTCCAGTTGAACTGAGTCCTTATTAGATGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - cctctgt
- - - - - - - - - - - - - - - - - - - - - - - - gggttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattcc