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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtctttgcctcagtttatcttatagcatttctgttttatagttctcaagaaaaattttagttctcctgatggtttagttgtgcatttcctttgtgcagAAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATGGCACAGCGGGAGGAAGTGATTAAGAGGACAGTATATGTGTCTGACATTG

Basic information

species Vitis vinifera
transcript Vv16s0098g01040.t01
intron # 2
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|110720783|gb|EE097005.1|EE097005
EST:     TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGG                         AAGAAGGAACA-TTATAATCAGAAGCGGAGAATCAACAGCCGAAACAGCAT
genomic: TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGGgtatggtttt ... ctttgtgcagAAGA-GGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCAT
EST: gi|110709689|gb|EE085367.1|EE085367
EST:     TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGG                         G
genomic: TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGGgtatggtttt ... ctttgtgcag-
EST: gi|110709689|gb|EE085367.1|EE085367
EST:     TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGG                         G
genomic: TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGGgtatggtttt ... ctttgtgcag-
EST: gi|110698581|gb|EE076239.1|EE076239
EST:     TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGG                         AAGAGGA-CAATTATAATCAGAAGCGGAGAATCA-CAGCCGAAC-AGCATG
genomic: TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGGgtatggtttt ... ctttgtgcagAAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATG
EST: gi|110731191|gb|EE109131.1|EE109131
EST:     TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGG                         AAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATG
genomic: TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGGgtatggtttt ... ctttgtgcagAAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATG
EST: gi|30132916|gb|CB918255.1|CB918255
EST:     TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGG                         AAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATG
genomic: TTGTATTGCAGGCTAATTTTGGCAATGCAAATGGGAATGCTGGTAGACGGgtatggtttt ... ctttgtgcagAAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaagaaaaattttagttctcctgatggtttagttgtgcatttcctttgtgcagAAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATGGCACAGCGGGAGGAAGTGATTAAGAGGACAGTATATGTGTCTGACATTG
                    tcctgat  putative branch site (score: 3)
                                       catttccttt  putative PPT
      aaaaattttagttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtctttgcctcagtttatcttatagcatttctgttttatagttctcaagaaaaattttagttctcctgatggtttagttgtgcatttcctttgtgcagAAGAGGAACAATTATAATCAGAAGCGGAGAATCAACAGCCGAACCAGCATGGCACAGCGGGAGGAAGTGATTAAGAGGACAGTATATGTGTCTGACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - -tgcctca
- - - - - - - - - - - - - gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - aagaaaa