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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttactaggagaagtctgggtaccaattttatgctgaaacaaacagaatagtaaggatccacaatcttttgtttgatttgtcaaataaatccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATCGTCTTGTCAGTGCTCCATACAAACTTGACTTCCTAAGAGAGAAAGACTC

Basic information

species Vitis vinifera
transcript Vv01s0011g06540.t01
intron # 2
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|110712325|gb|EE089814.1|EE089814
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|33409668|gb|CF215295.1|CF215295
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTTCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352777239|gb|FQ473872.1|FQ473872
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|110401076|gb|EC967670.1|EC967670
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352772780|gb|FQ473818.1|FQ473818
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352763773|gb|FQ473476.1|FQ473476
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352776787|gb|FQ472674.1|FQ472674
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|71856889|gb|DT005944.1|DT005944
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|37183516|gb|CF602870.1|CF602870
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352763853|gb|FQ474948.1|FQ474948
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCCGCGTGCCAG                         CTCACCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352767901|gb|FQ466110.1|FQ466110
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352763737|gb|FQ473440.1|FQ473440
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352773271|gb|FQ470858.1|FQ470858
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|161720918|gb|FC070322.1|FC070322
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|110374335|gb|EC939011.1|EC939011
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|32456765|gb|CD797939.1|CD797939
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTTTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352782274|gb|FQ470176.1|FQ470176
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352763919|gb|FQ465369.1|FQ465369
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|37184976|gb|CF604329.1|CF604329
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
EST: gi|352773525|gb|FQ472307.1|FQ472307
EST:     CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAG                         CTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC
genomic: CGAAACCTACCGGTATTTCGATCTTCCATTCTGCGTGCCAGgttttgatct ... ccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatagtaaggatccacaatcttttgtttgatttgtcaaataaatccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATCGTCTTGTCAGTGCTCCATACAAACTTGACTTCCTAAGAGAGAAAGACTC
                         gtttgat  putative branch site (score: 5)
                              atttgtcaaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttactaggagaagtctgggtaccaattttatgctgaaacaaacagaatagtaaggatccacaatcttttgtttgatttgtcaaataaatccaatggcagCTCATCTTAAAGAGAAGAAAGAAGCTCTTGGTGAGGTGTTGAATGGAGATCGTCTTGTCAGTGCTCCATACAAACTTGACTTCCTAAGAGAGAAAGACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - aggagaa
- - - - - - - - - ggtacca
- - - - - - - - - - - - - - -tatgctg
- - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa