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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatgattagccaaggctatggcaactcgagattcttttgattttcctttctctgtttatgggttgttgattaatagccgcgtttttttgcttaatcagAAAAGGAGGCATCCGACAAAAGAAAATTAGTGAGCAAATGGCATCCTACAACGAAGGGTACACTTAGGAGGAACTACAGAGTTCCCTCCAAATCTGAAGG

Basic information

species Vitis vinifera
transcript Vv06s0004g00940.t01
intron # 3
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|110690479|gb|EE067613.1|EE067613
EST:     TGGTGATCTGGGGTTCTCTAAGTGGCTTGAGAGCTTACAAAGAAATCCAG                         AAAAGGAGGCATCCGACAAAAGAAAATTAGTGAGCAAATGGCATCCTACAA
genomic: TGGTGATCTGGGGTTCTCTAAGTGGCTTGAGAGCTTACAAAGAAATCCAGgtttgtgggt ... gcttaatcagAAAAGGAGGCATCCGACAAAAGAAAATTAGTGAGCAAATGGCATCCTACAA
EST: gi|329112211|gb|JG391679.1|JG391679
EST:     GTTCTCTAAGTGGCTTGAGAGCTTACAAAGAAATCCAG                         AAAAGGAGGCATCCGACAAAAGAAAATTAGTGAGCAAATGGCATCCTACAA
genomic: GTTCTCTAAGTGGCTTGAGAGCTTACAAAGAAATCCAGgtttgtgggt ... gcttaatcagAAAAGGAGGCATCCGACAAAAGAAAATTAGTGAGCAAATGGCATCCTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttctctgtttatgggttgttgattaatagccgcgtttttttgcttaatcagAAAAGGAGGCATCCGACAAAAGAAAATTAGTGAGCAAATGGCATCCTACAACGAAGGGTACACTTAGGAGGAACTACAGAGTTCCCTCCAAATCTGAAGG
                        gattaat  putative branch site (score: 3)
                                      tttttttgctt  putative PPT
                                      tttttttgcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatgattagccaaggctatggcaactcgagattcttttgattttcctttctctgtttatgggttgttgattaatagccgcgtttttttgcttaatcagAAAAGGAGGCATCCGACAAAAGAAAATTAGTGAGCAAATGGCATCCTACAACGAAGGGTACACTTAGGAGGAACTACAGAGTTCCCTCCAAATCTGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - -ttagcca
- - - - - - - - - tatggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggttgt