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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttctattctgtagttgtttctatagtatttatgaaaaagaaagatgtcctatagatctttgctcaaacggagcattcaatgttcctcttgtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTTGCAAATAGG

Basic information

species Vitis vinifera
transcript Vv02s0236g00140.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G47100.1 (Arabidopsis thaliana), 3'ss of exon 3
gttctattctgtagttgtttctatagtatttatgaaaaagaaagatgtcctatagatctttgctcaaacggagcattcaatgttcct------cttgtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTTGCAAATAGG
  |  ||||  |   | ||| ||| |  ||  | | ||| |  |||||  | | |  |    ||   |    |      || |||        ||||| ||||||||||||||||||| | ||| | ||||||||||||||||| || ||| | ||||| ||||||
--ttaattccat---tttttatattggtttgcttataaaaattgatgttttcttggcccactcttggatattgttacttattttctcgaccaacttgt-tatgcagGAAGAGTTTCAACTTGCTTTGTTCAAGAACAGAAAGAAAGAAAATTTGTTTGCCAATAGG
















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|352789785|gb|FQ478600.1|FQ478600
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|27581540|gb|CB004235.1|CB004235
EST:     AGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: AGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|27580184|gb|CB002879.1|CB002879
EST:     AGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: AGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|349822445|gb|FQ412709.1|FQ412709
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|71873772|gb|DT022827.1|DT022827
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|349820979|gb|FQ408687.1|FQ408687
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|349819279|gb|FQ412173.1|FQ412173
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|71872712|gb|DT021767.1|DT021767
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|349826413|gb|FQ417910.1|FQ417910
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|110418331|gb|EC984477.1|EC984477
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTT-ATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|349832733|gb|FQ422257.1|FQ422257
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|30131430|gb|CB916769.1|CB916769
EST:     GATGATGGGTTAATAAACAAG                         GAAGAGTTTCCATTGGCTCTATTCCAGAACAGAAAGAAGGAGAATCTCTTT
genomic: GATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|110382953|gb|EC947286.1|EC947286
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|161708395|gb|FC056127.1|FC056127
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|351019013|gb|FQ426512.1|FQ426512
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|71863154|gb|DT012209.1|DT012209
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|351055152|gb|FQ440491.1|FQ440491
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAACCAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|71864022|gb|DT013077.1|DT013077
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|71877098|gb|DT026153.1|DT026153
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|351014198|gb|FQ434787.1|FQ434787
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|349815321|gb|FQ400476.1|FQ400476
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|351038650|gb|FQ464516.1|FQ464516
EST:     TATTCAAGAGCATTAGTAGTTCTGTAATTGATGATGGGTTAATAACCAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|34549400|gb|CF517632.1|CF517632
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
EST: gi|110699550|gb|EE076647.1|EE076647
EST:     TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAG                         GAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT
genomic: TATTCAAGAGCATTAGCAGTTCTGTAATTGATGATGGGTTAATAAACAAGgtaatctgta ... gtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcctatagatctttgctcaaacggagcattcaatgttcctcttgtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTTGCAAATAGG
                                     ttcctcttgt  CT-rich tract
                                           ttgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctattctgtagttgtttctatagtatttatgaaaaagaaagatgtcctatagatctttgctcaaacggagcattcaatgttcctcttgtatatgcagGAAGAGTTTCAATTGGCTCTATTCAAGAACAGAAAGAAGGAGAATCTCTTTGCAAATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattca