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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttttttttttgatagtctctcttctggtttacaattattttttacttggcattagtatctaatttttttttttttttttttgtgcttatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG

Basic information

species Vitis vinifera
transcript Vv00s0220g00110.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|349818318|gb|FQ409093.1|FQ409093
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|352786516|gb|FQ479125.1|FQ479125
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351035256|gb|FQ458613.1|FQ458613
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351034594|gb|FQ457951.1|FQ457951
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351012893|gb|FQ430456.1|FQ430456
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351031526|gb|FQ459783.1|FQ459783
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351046895|gb|FQ454505.1|FQ454505
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351043332|gb|FQ451384.1|FQ451384
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351040114|gb|FQ425200.1|FQ425200
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351044506|gb|FQ443037.1|FQ443037
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|352795642|gb|FQ480230.1|FQ480230
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|349822000|gb|FQ408329.1|FQ408329
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGGCATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351017801|gb|FQ436154.1|FQ436154
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351032123|gb|FQ460380.1|FQ460380
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351054122|gb|FQ450204.1|FQ450204
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
EST: gi|351039410|gb|FQ461277.1|FQ461277
EST:     CAAGTAAACGGGCAGAG                         ATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA
genomic: CAAGTAAACGGGCAGAGgtaattcaaa ... tatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttggcattagtatctaatttttttttttttttttttgtgcttatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG
               atctaat  putative branch site (score: 3)
                     tttttttttttttttt  CT-rich tract
              tatctaattttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttttttttttgatagtctctcttctggtttacaattattttttacttggcattagtatctaatttttttttttttttttttgtgcttatatttcagATCATGTGGTTAGTAGACATCTTCAGAGCAAAAATTGTTGACATTTCAGAACATTCATTGACCATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - -tctctct
- - - - - - - - - - - - - - - - - - - - - - - tacttgg