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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaggagtgattttaaatgaatttatcaatttttatctacattgtttaactagtaagttgtaactagccaaatgacatgtacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT

Basic information

species Vitis vinifera
transcript Vv08s0007g00530.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 3'ss of exon 5
atgaggagtgattttaaatgaatttatcaatttttatctacattgt----ttaactagtaagttgtaactagccaaatgacatgtacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT
   || |   |   | | || | ||   |  |   |     |||||    | ||  || |  ||| | | |  || |     |  | || | |     |  |||||||||||| ||||| |||| ||| |||||  | ||||| || |||||||| |||||||||||| |  | |||||||||||||  || ||||| ||    
-aaagaacaaaccctcagtgcagttgaaatctggaagaattattgtaacttgaatcaggagattgcatcga--catactcttttcattt-tgtttttaatgcagGGCTGGAGGATTACAGGATAAAGATGGTGGTGTGCGGGAGTTGCTTGTTGGGAAGGATGATGAGATCTTGAAGACAGAAACAAAAACTATTACCAGAGCA

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G39930.2 (Glycine max), 3'ss of exon 5
-------atgaggagtgattttaaatgaatttatcaatttttatctacattgtttaactagtaagttgtaactagccaaatgacatgtacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT
         |    | | ||||  |||||  |    | |||| | |   || ||    |  ||| || |      |||  |  | |    ||||||  | ||  ||||||||| ||||| ||||| | ||| || ||  | |||||| ||||||| || |||||||||||||||||  |||| ||||| || ||||| |||||   |
tagtttggagtaaggggcttttttatgaacatgctgagttttttttttctttttctttttttaattttt------ccatctttcctcactttctata-ctgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAACTAGATCT

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G15960.1 (Glycine max), 3'ss of exon 5
-----------atgaggagtgattttaaatgaatttatcaatttttatctacattgtttaactagtaagttgtaactagccaaatgacatgtacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT
            | |||||   |||||  ||||  |  | | |||| | |    |  ||   |  ||| || |      |||  |  | |    ||||||  | ||  ||||||||| ||||| ||||| | ||| || ||  | |||||| ||||||| || |||||||||||||||||  |||| ||||| || ||||| | |||   |
aatagtttagagtcaggagctttttta--tgaacatgccgagtttttttttttcttctttttt--taactttt------ccatgtttcctcactttctata-ctgagccagGGCTGGTGGCTTGCAAGACAAAGATGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAAGTAGATCT

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G37660.1 (Arabidopsis thaliana), 3'ss of exon 5
atgaggagtgattttaaatgaatttatcaatttttatctacatt--gtttaactagtaagttgtaactagccaaatgacatg-tacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT
                   | |  | | | | ||||  | |||   ||  || | | ||      | ||  |  ||       || | || |   |||  ||||||||||||  | || || |  || |||||||| || ||||||||||| || || ||||| ||||| ||| ||||||||||||| || ||  | ||   |
-------------------gtaacttttattgtttacttgcatccggtacaaattgcaatggcggaatattctcatcttgcaatattgctct--tggattcagGGCTGGAGGTCTGCAGGACAAGGACGGTGGCATTCGAGAATTACTTGTGGGAAAAGATGACGAGCTACTTGAGACAGAAACAAGAACAATCGCAAGAGCT

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|349811666|gb|FQ409663.1|FQ409663
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|349810529|gb|FQ402772.1|FQ402772
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|28959045|gb|CB339524.1|CB339524
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|351016336|gb|FQ446196.1|FQ446196
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|349821239|gb|FQ404371.1|FQ404371
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|28959215|gb|CB339608.1|CB339608
EST:     ANNGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|22008555|gb|BQ793589.1|BQ793589
EST:     AATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|110700744|gb|EE077667.1|EE077667
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|110385557|gb|EC950093.1|EC950093
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|110731770|gb|EE106470.1|EE106470
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|352786365|gb|FQ478974.1|FQ478974
EST:     AA-GCTGAACAGTATTTATCGGACTCTGGAATACCTTACACAATTATAAA                         GGCTGGAGGCTTACAAGATAGAGAAGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGG
EST: gi|45771772|gb|CN007624.1|CN007624
EST:     AAAGCTGAGCAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|351023663|gb|FQ448214.1|FQ448214
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|352790186|gb|FQ481385.1|FQ481385
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|110419625|gb|EC985868.1|EC985868
EST:     ACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: ACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|351051751|gb|FQ449565.1|FQ449565
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|351054211|gb|FQ450293.1|FQ450293
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|351028714|gb|FQ433144.1|FQ433144
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|110692043|gb|EE070833.1|EE070833
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
EST: gi|351055225|gb|FQ440564.1|FQ440564
EST:     AAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTACACAATTATAAG                         GGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG
genomic: AAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTACACAATTATAAGgtacatctaa ... gcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactagtaagttgtaactagccaaatgacatgtacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT
             ttgtaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaggagtgattttaaatgaatttatcaatttttatctacattgtttaactagtaagttgtaactagccaaatgacatgtacttctatggcggaaacagGGCTGGAGGCTTACAAGATAGAGAAGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - -aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacatg