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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaactttctaatctgaggaaataagggacttggtgctttgtattcagtagcataaaaaatatgctatatagattttgtgttgaattgtaaggttaaagcgttgcattattcttctggacttcctgatatgattgtttggagtttattaaagtattgtgctttatctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTACTGGTTCACTGAGAATTGGAGCTGAGTTTCTGGCAAGGCATTACTACCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g03720.t01
intron # 4
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|71856755|gb|DT005810.1|DT005810
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161707491|gb|FC057730.1|FC057730
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|110707578|gb|EE084139.1|EE084139
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161709257|gb|FC060537.1|FC060537
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161719485|gb|FC066421.1|FC066421
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161719323|gb|FC068275.1|FC068275
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|18458020|gb|BM436298.1|BM436298
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|351043366|gb|FQ451418.1|FQ451418
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|351041433|gb|FQ447560.1|FQ447560
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161705960|gb|FC056683.1|FC056683
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|351032771|gb|FQ462485.1|FQ462485
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161716797|gb|FC067211.1|FC067211
EST:     GCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: GCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|30126137|gb|CB911476.1|CB911476
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|71857156|gb|DT006211.1|DT006211
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|351036480|gb|FQ457193.1|FQ457193
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|71859825|gb|DT008880.1|DT008880
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|71854888|gb|DT003943.1|DT003943
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|349819864|gb|FQ404532.1|FQ404532
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|71879610|gb|DT028665.1|DT028665
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161709194|gb|FC060110.1|FC060110
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|352778302|gb|FQ465612.1|FQ465612
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCCAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|161708734|gb|FC057910.1|FC057910
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|352776536|gb|FQ474838.1|FQ474838
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|37183728|gb|CF603082.1|CF603082
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|349816215|gb|FQ403711.1|FQ403711
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|71861868|gb|DT010923.1|DT010923
EST:     CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCCATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: CTGGCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
EST: gi|27586682|gb|CB009377.1|CB009377
EST:     GCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAG                         CCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC
genomic: GCAGAGTTCAATAAATTGAGCGCTAAACTCATTTTTGGTGCTGACAGgtatgaaact ... ctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgatatgattgtttggagtttattaaagtattgtgctttatctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTACTGGTTCACTGAGAATTGGAGCTGAGTTTCTGGCAAGGCATTACTACCAG
 tcctgat  putative branch site (score: 3)
                                       ctttatct  putative PPT
                    agtttattaaagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaactttctaatctgaggaaataagggacttggtgctttgtattcagtagcataaaaaatatgctatatagattttgtgttgaattgtaaggttaaagcgttgcattattcttctggacttcctgatatgattgtttggagtttattaaagtattgtgctttatctggcaacagCCCGGCTATCCAAGAAAATAGAGTAGCTACTGTCCAGGGTTTGTCTGGTACTGGTTCACTGAGAATTGGAGCTGAGTTTCTGGCAAGGCATTACTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA