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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgagcagagtatgattattcttctgtttctagatgacttataaatgtcttccagttagctatatcaaatgttgttctgatctgaattataatatttcaatcagAGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG

Basic information

species Vitis vinifera
transcript Vv05s0020g01800.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|110360502|gb|EC923659.1|EC923659
EST:     ACTACGAAAGGGCAGTTTCACTGTGATGACTGTGGGATCTGTAG                         AGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG
genomic: ACTACGAAAGGGCAGTTTCACTGTGATGACTGTGGGATCTGTAGgttagtgagc ... tttcaatcagAGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG
EST: gi|161721536|gb|FC069746.1|FC069746
EST:     ACTACGAAAGGGCAGTTTCACTGTGATGACTGTGGGATCTGTAG                         AGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG
genomic: ACTACGAAAGGGCAGTTTCACTGTGATGACTGTGGGATCTGTAGgttagtgagc ... tttcaatcagAGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG
EST: gi|161716059|gb|FC067162.1|FC067162
EST:     ACTACGAAAGGGCAGTTTCACTGTGATGACTGTGGGATCTGTAT                         AGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG
genomic: ACTACGAAAGGGCAGTTTCACTGTGATGACTGTGGGATCTGTAGgttagtgagc ... tttcaatcagAGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagttagctatatcaaatgttgttctgatctgaattataatatttcaatcagAGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG
                         ttctgat  putative branch site (score: 3)
                              atctgaattataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgagcagagtatgattattcttctgtttctagatgacttataaatgtcttccagttagctatatcaaatgttgttctgatctgaattataatatttcaatcagAGTTGGAGGTCGTGATAAATTCTTTCACTGCAAGAAGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT