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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatttctctctattttcgtgatgttctttctgtctgtgaaagctctcaacgtgtttcttttgttaatgtttctcttcctggattttgattcattttttcatcttacgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCAT

Basic information

species Vitis vinifera
transcript Vv06s0004g03000.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|352794338|gb|FQ481569.1|FQ481569
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351032258|gb|FQ460515.1|FQ460515
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|352799005|gb|FQ480854.1|FQ480854
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACGGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|349829976|gb|FQ420236.1|FQ420236
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351027188|gb|FQ440056.1|FQ440056
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|352790573|gb|FQ478212.1|FQ478212
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351039932|gb|FQ464970.1|FQ464970
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|122689691|gb|EC942857.1|EC942857
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351038808|gb|FQ464674.1|FQ464674
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|349814306|gb|FQ398746.1|FQ398746
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351039369|gb|FQ461236.1|FQ461236
EST:     GGCTGTGGGCGTTTTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|349824064|gb|FQ417451.1|FQ417451
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351036688|gb|FQ457401.1|FQ457401
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|349815212|gb|FQ400367.1|FQ400367
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351046692|gb|FQ453308.1|FQ453308
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351041568|gb|FQ455784.1|FQ455784
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351037793|gb|FQ464234.1|FQ464234
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACGGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|349828753|gb|FQ418488.1|FQ418488
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
EST: gi|351033877|gb|FQ462286.1|FQ462286
EST:     GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAG                         CGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC
genomic: GGCTGTGGGCGTTCTCGCTCTACAGGGGTCTTTTAACGAACACATAGCAGgcatttctct ... cgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaatgtttctcttcctggattttgattcattttttcatcttacgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCAT
                                       atcttac  putative branch site (score: 3)
                                ttttttcatcttac  CT-rich tract
                     attttgattcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatttctctctattttcgtgatgttctttctgtctgtgaaagctctcaacgtgtttcttttgttaatgtttctcttcctggattttgattcattttttcatcttacgtttcgcagCGCTGAGGAAACTGGGGGTTAAGGGTGTGGAGATAAGGAAGCCAGAACAGCTGGAGCAAGTGGGCTCCCTTATCATCCCTGGTGGAGAGAGCACCACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA