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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagcttaaacttctagccaaattggtggcttaaaagtagctaatgagaatatttttaggaacttaataatttaactgattctgtttgttgcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG

Basic information

species Vitis vinifera
transcript Vv04s0023g00140.t01
intron # 8
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|110356881|gb|EC920025.1|EC920025
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
EST: gi|110724761|gb|EE100872.1|EE100872
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
EST: gi|110712695|gb|EE087976.1|EE087976
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
EST: gi|71865271|gb|DT014326.1|DT014326
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
EST: gi|161715809|gb|FC065164.1|FC065164
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
EST: gi|30135371|gb|CB920709.1|CB920709
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
EST: gi|30129653|gb|CB914992.1|CB914992
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
EST: gi|161719832|gb|FC065768.1|FC065768
EST:     AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA                         GCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
genomic: AAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCAgtatgttgct ... gcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaatatttttaggaacttaataatttaactgattctgtttgttgcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG
                            aactgat  putative branch site (score: 3)
                                           ttgctttt  putative PPT
     tatttttaggaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagcttaaacttctagccaaattggtggcttaaaagtagctaatgagaatatttttaggaacttaataatttaactgattctgtttgttgcttttacagGCTTTGAATAAGTTTTTCGAGAATGTTTTACAG

- - - - - - - -agccaaa
- - - - - - - - - - - -tggtggc
- - - - - - - - - - - - - - - - aaaagta
- - - - - - - - - - - - - - - - - - - -gctaatg