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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagaaaattacaggacttttctcttgattgttgtgttgattcaattatgttttattgaaacctccatgtaggcatcttcattctatttgattttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG

Basic information

species Vitis vinifera
transcript Vv02s0236g00140.t01
intron # 6
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 6
lower sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 6
agagaaaatta-caggacttttctcttgattgttgtgttgattcaattatgttttattgaaacctccatg----taggcatcttcattctatttgattttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG
 | | |  ||  || | | | | |||| |     |||||  | || |  | |  |||| |    |   ||    ||  ||| ||  || |  |   || || |||||||| |||||||||||||||||||| | ||| || || ||||||||||| |||||   ||| || | ||| ||||| |||
ggtgtattttgtcatggcatctatcttca-----gtgtttgtgcactcctatcctattaattttttagtgggcttattcatttttcttttggtgatttctgacagGTCAAGCAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCAGATGATGTCATAGAAACAATTCTTGACAAG

upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G15900.1 (Glycine max), 3'ss of exon 4
-agagaaaattacaggacttttctcttgattgttgtgttgattcaattatgttttattgaaacctccatgtaggcatcttcattctatttgatttt-ggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG
  |      || || | | | | |||| | ||||       | | ||  | ||   ||  |     | | |   ||| ||  || | | ||||||    ||||||||  ||||||||||||||||||| | ||| || || ||||||||||| |||||   ||| || | ||| ||||| |||
gtgtatttttttcatggcatctatcttcagtgtttgtgcactcctatcctattaatttttagtgggcttatt--catttttcttttttgtgatttccaacagGTCAAGGAAATGTTAATTGCACTTCTTTTTGAGTCGGATATGAAGTTGGCAGATGATGTCATAGAAACAATTCTTGACAAG

upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 5
----------------agagaaaattacaggacttttctcttgattgttgtgttgat--tcaattatgtttta-ttgaaacctccatgtaggcatcttcattctatttgattt--tggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG
                ||     | |||  | | |      |  |||   ||||  |    | | || ||||| || | | ||      ||  ||| | | |  || |||| |  | ||||||||| |||||||| || || ||||| || ||||||||||||||  |||||||||||||||| ||||||||||| ||||||
gtaatactaacttgcaagctttgaatactagtcatgatagatctttgccatgttcttgagtattcatcttttacttaataactttgca-agaaatcgttaatgaatgtgatatatttgcagGTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCTGATGAAACCATAGAGATAATACTCGATAAG

upper sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G47100.1 (Arabidopsis thaliana), 3'ss of exon 6
---agagaaaattacaggacttttctcttgattgttgtgt------tgattcaa-----ttatgttttattgaaac--ctccatgtaggcatcttcat-----tctatttgattttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG
   |   |   |   |   |||  |  |  |||             || |||||     ||  || |||| ||  |  |  ||| ||    |  ||||     | |||  | ||||||||||| || || ||||| ||||||||||| || ||||||||||||||  |||||||||| || || ||||| ||||||||| ||
gtaaacaatggtcctatatcttcacattccattcccaaacaatctatgtttcaaagactttcagtattatggattctgcatcatctataagtaatcataattgtgtatgcgtttttggcagGTGAAGCAGATGTTGATTGCACTTCTCTGCGAATCTGAAATGAAACTGGCTGATGATACAATAGAGATGATACTTGATCAG

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|32246390|gb|CD712209.1|CD712209
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|352789785|gb|FQ478600.1|FQ478600
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|27581540|gb|CB004235.1|CB004235
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|27580184|gb|CB002879.1|CB002879
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|349822445|gb|FQ412709.1|FQ412709
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|71873772|gb|DT022827.1|DT022827
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTCCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|349820979|gb|FQ408687.1|FQ408687
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|349819279|gb|FQ412173.1|FQ412173
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|349826413|gb|FQ417910.1|FQ417910
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|110418331|gb|EC984477.1|EC984477
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|32245760|gb|CD711579.1|CD711579
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|349832733|gb|FQ422257.1|FQ422257
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|30131430|gb|CB916769.1|CB916769
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|110382953|gb|EC947286.1|EC947286
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|351019013|gb|FQ426512.1|FQ426512
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|351055152|gb|FQ440491.1|FQ440491
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGNAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|33401878|gb|CF207505.1|CF207505
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTCCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|71877098|gb|DT026153.1|DT026153
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTCCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|351014198|gb|FQ434787.1|FQ434787
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|349815321|gb|FQ400476.1|FQ400476
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|110716343|gb|EE091242.1|EE091242
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|351038650|gb|FQ464516.1|FQ464516
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|30297304|gb|CB974098.1|CB974098
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GACAAACAAATGTTAATTGCACTCCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|34549400|gb|CF517632.1|CF517632
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTCCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|110699550|gb|EE076647.1|EE076647
EST:     CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
EST: gi|45770983|gb|CN006835.1|CN006835
EST:     CATTCAAGCTCTATGATCTGGATAGCACAGGATTCATTGAGCGGCAAGAG                         GTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT
genomic: CATTCAAGCTCTATGATTTGGATAGCACAGGATTCATTGAGCGGCAAGAGgtaccttgct ... attttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgttttattgaaacctccatgtaggcatcttcattctatttgattttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG
                                        atttgat  putative branch site (score: 5)
                                   attctatttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagaaaattacaggacttttctcttgattgttgtgttgattcaattatgttttattgaaacctccatgtaggcatcttcattctatttgattttggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- agaaaat
- - - - - -caggact
- - - - - - - - - - - - - - -tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaggca