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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatattgttatcaaaggttatatacataatataaaatggtaatgcagaatgatataaatttgcttgtggctcatagaactaatatgccttattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGGTCATGTTTGAAAGAAACGGCTTCTGCTCCAAAGGATTAGAAAGAAAGTA

Basic information

species Vitis vinifera
transcript Vv06s0004g02660.t01
intron # 6
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|29783231|gb|CB349270.2|CB349270
EST:     TCACTCAACTGACTGTGATTGGAGAGTGGTCAACCCGATGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCT
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCT
EST: gi|110726802|gb|EE102900.1|EE102900
EST:     TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAAATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
EST: gi|37185470|gb|CF604823.1|CF604823
EST:     TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
EST: gi|28970321|gb|CB349354.1|CB349354
EST:     TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
EST: gi|110428655|gb|EC995132.1|EC995132
EST:     TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
EST: gi|32459062|gb|CD800236.1|CD800236
EST:     TCACTCAACTGACCGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
EST: gi|30129190|gb|CB914529.1|CB914529
EST:     TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
EST: gi|351026098|gb|FQ428110.1|FQ428110
EST:     TCACTCAACTGACTGTCAATCGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
EST: gi|32457906|gb|CD799080.1|CD799080
EST:     TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAG                         GCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG
genomic: TCACTCAACTGACTGTCAATGGAGAGTGGTCAACCCCAAGGGTTCATGAGgtaaggctat ... tattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaatgatataaatttgcttgtggctcatagaactaatatgccttattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGGTCATGTTTGAAAGAAACGGCTTCTGCTCCAAAGGATTAGAAAGAAAGTA
                                aactaat  putative branch site (score: 2)
                                          ccttatt  putative PPT
       atataaatttgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatattgttatcaaaggttatatacataatataaaatggtaatgcagaatgatataaatttgcttgtggctcatagaactaatatgccttattgaacagGCAATGCAGATCTGTCTCGAAGCTTGCTCAAAGCTTGCCAAGATCATAAGGTCATGTTTGAAAGAAACGGCTTCTGCTCCAAAGGATTAGAAAGAAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - -ataaaat
- - - - - - - - - - - - - - - - - - - - - - -cagaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcct