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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcttgatctatgtactagcatctcatgatctggaactttgctttcttgtttttaacagtttttttgtatttaaacttgaggttttgtgtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAGGCTGTATTACTCTCTGCCACTGAGGCTGCTGAGATGATTCTTAGAGTTG

Basic information

species Vitis vinifera
transcript Vv18s0001g00480.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 11
-------atatcttgatctatgtactagcatctcatgatctggaactttgctttcttgtttttaacagtttttttgtatttaaacttgaggttttgtgtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAGGCTGTATTACTCTCTGCCACTGAGGCTGCTGAGATGATTCTTAGAGTTG
        || |||| | |||||  |||  ||| |  |       || |||| |||  ||| |  | |  |     || ||   | || | | |  |    ||| |||| ||||| ||||| |||| |||||| |  |||||||||||||| ||||| |||||||| || ||| | || ||||| ||||||||||| ||||||||||
caggattttaccttggtttatgt--tag--tcttagaaaagtatcctgtgctctctattttctgtctggctaacc-tactttggcctgtgctgtatttc--tggaagGTTGGAGACATGGCTGAACGGGGGATATGCGAAGCATTCAAAGTCAAGCAAGCTGTATTGCTATCTTCAACAGAGGCAGCTGAGATGATCCTTAGAGTTG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 11
-atatcttgatctatgtactagcatctcatgatctggaactttgctttcttgtttttaacagtttttttg---tatttaaacttgaggttttgtgtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAGGCTGTATTACTCTCTGCCACTGAGGCTGCTGAGATGATTCTTAGAGTTG
 |    || | |||||   |   |  || ||     | |   ||   ||||  | ||  | ||||   |    || ||  ||   | ||| | | |  ||| |||| ||||| ||||| ||||  || || ||||||||||||||||| ||||| |||||||| || ||| | || ||||| ||||||||||| ||||||||||
caggctttta-ctatggtttgttag-tcttggaaaagtatcctgtgctctttctattttctgtttggctaacttactttgaccc-atgttgtatttc-tggtagGTTGGAGACATGGCTGAACGCGGAATATCTGAAGCATTCAAAGTCAAGCAAGCTGTATTGCTATCTTCAACAGAGGCAGCTGAGATGATCCTTAGAGTTG
















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|34545929|gb|CF514161.1|CF514161
EST:     AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|33404923|gb|CF210550.1|CF210550
EST:     AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|110361054|gb|EC924506.1|EC924506
EST:     AGCACCACAAGGAAGTAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|34544937|gb|CF513169.1|CF513169
EST:     AGCACCCCAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTTTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|351026682|gb|FQ436335.1|FQ436335
EST:     AGCACCACAAGGAAGTAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|110694929|gb|EE072362.1|EE072362
EST:     AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|352773729|gb|FQ472511.1|FQ472511
EST:     AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|110728449|gb|EE104025.1|EE104025
EST:     AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGGATTTCTGAAGCATTCAAAGTTAAGCC
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGG-ATTTCTGAAGCATTCAAAGTTAAGCA
EST: gi|110688180|gb|EE066436.1|EE066436
EST:     CGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: CGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|110387828|gb|EC952526.1|EC952526
EST:     AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|351017182|gb|FQ424611.1|FQ424611
EST:     AGCACCACAAGGAAGTAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|34543743|gb|CF511975.1|CF511975
EST:     AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
EST: gi|351015108|gb|FQ444397.1|FQ444397
EST:     AGCACCACAAGGAAGTAAGCCACGCAGGGATTGATGTCATCTCTGGTTCG                         GTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG
genomic: AGCACCACAAGGAAGAAAGCCACGCAGGGATTGATGTCATCTCTGGTTCGgtaagtaatg ... gtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtttttaacagtttttttgtatttaaacttgaggttttgtgtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAGGCTGTATTACTCTCTGCCACTGAGGCTGCTGAGATGATTCTTAGAGTTG
       ttttaac  putative branch site (score: 2)
      tttttaacagtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcttgatctatgtactagcatctcatgatctggaactttgctttcttgtttttaacagtttttttgtatttaaacttgaggttttgtgtgatggcagGTAGGAGATATGGCAGAACTGGGGATTTCTGAAGCATTCAAAGTTAAGCAGGCTGTATTACTCTCTGCCACTGAGGCTGCTGAGATGATTCTTAGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - -tatgtac
- - - - - - - - - - - - - catgatc