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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttcctctaccctttcattttcttcccttttatttatttttgagtatttcgattcgatttcgatgtgaaataaaaaataaaatcaaatcaaaatgattcgatttgtgatcttgttttgatatttgatataatagtggatttgaatttgaatttgattttaccggtggtggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGGAACATTACCAGAACTTGGGGTAGCAAATTAGCAATGGAATGGTGGGATA

Basic information

species Vitis vinifera
transcript Vv18s0001g09290.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|110363248|gb|EC926824.1|EC926824
EST:     AGTGAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGTGAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110719699|gb|EE095054.1|EE095054
EST:     GAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: GAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110723607|gb|EE101109.1|EE101109
EST:     AGTGAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGTGAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110426654|gb|EC993072.1|EC993072
EST:     AGTGAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGTGAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110717841|gb|EE094049.1|EE094049
EST:     AGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110408597|gb|EC974233.1|EC974233
EST:     AGTGAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGACCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGTGAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110411766|gb|EC977489.1|EC977489
EST:     AGTGAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGTGAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110404810|gb|EC970334.1|EC970334
EST:     GAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: GAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110364916|gb|EC928517.1|EC928517
EST:     GTGAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: GTGAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110723241|gb|EE100327.1|EE100327
EST:     AGTGAGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGTGAGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110699923|gb|EE077375.1|EE077375
EST:     AAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|110710686|gb|EE087040.1|EE087040
EST:     AGAGAGAGAAAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AGAGAGAGAAAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|30137140|gb|CB922478.1|CB922478
EST:     AAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|87586872|gb|DY474969.1|DY474969
EST:     AAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
EST: gi|27585632|gb|CB008327.1|CB008327
EST:     AAAGTGTCGCCAAA                         GTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG
genomic: AAAGTGTCGCCAAAgtcagttcct ... tggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatataatagtggatttgaatttgaatttgattttaccggtggtggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGGAACATTACCAGAACTTGGGGTAGCAAATTAGCAATGGAATGGTGGGATA
                           atttgat  putative branch site (score: 5)
               atttgaatttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttcctctaccctttcattttcttcccttttatttatttttgagtatttcgattcgatttcgatgtgaaataaaaaataaaatcaaatcaaaatgattcgatttgtgatcttgttttgatatttgatataatagtggatttgaatttgaatttgattttaccggtggtggtgtacagGTCATCTTCTTCTTCTGATCTCTCTCTTCAGGCTGAAGCGGAGGAGGGCGGAACATTACCAGAACTTGGGGTAGCAAATTAGCAATGGAATGGTGGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG