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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttggtatttttaagcaaataaatagaattaattcattttccttggtctttctttttgaaaattgcgtctttttgtgatactctctcaccttttgcagGTAATTACAAAGGAATCTCTTTTGACAGCACAG

Basic information

species Vitis vinifera
transcript Vv18s0001g11740.t01
intron # 1
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|161716630|gb|FC067824.1|FC067824
EST:     ACTTTCGTTTTGAGGGTGGGTGCCAGAATGAGAGTGCGCCATCCAGTAAG                         GTAATTACAAAGGAATCTCTTTTGACAGCACAG
genomic: ACTTTCGTTTTGAGGGTGGGTGCCAGAATGAGAGTGCGACATCCAGTAAGgtgaagtgtc ... ccttttgcagGTAATTACAAAGGAATCTCTTTTGACAGCACAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtctttctttttgaaaattgcgtctttttgtgatactctctcaccttttgcagGTAATTACAAAGGAATCTCTTTTGACAGCACAG
                                       ctctcac  putative branch site (score: 3)
                                   tactctctcacctttt  CT-rich tract
     tttctttttgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttggtatttttaagcaaataaatagaattaattcattttccttggtctttctttttgaaaattgcgtctttttgtgatactctctcaccttttgcagGTAATTACAAAGGAATCTCTTTTGACAGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - aaataaa
- - - - - - - - - - - - - agaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc