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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagtctgttttagtcttagcttccctaaacttacatttaagtttataccttttgatcatatgaacactgcatcactcattgattatggttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCAAGAGTGACTAATGAGGCTGTCCAAAAGGCT

Basic information

species Vitis vinifera
transcript Vv08s0056g01570.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|110400294|gb|EC966852.1|EC966852
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|161708072|gb|FC055712.1|FC055712
EST:     GTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGT-AGCTCAGGCTTCAAGGAAGTCCTCCCC
genomic: GTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCC-TCAGCTCAGGCTTCAAGGAAGTCCTCCCC
EST: gi|110429998|gb|EC996518.1|EC996518
EST:     GTGAATGCCTTGGCCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: GTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|352773499|gb|FQ472281.1|FQ472281
EST:     TGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGGTCACAAAGAGGAG                         GCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAG-AAGTCCTCCCCA
genomic: TGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGG-TCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|32246818|gb|CD712637.1|CD712637
EST:     CCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: CCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|110698652|gb|EE076398.1|EE076398
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|110402853|gb|EC963625.1|EC963625
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|110688611|gb|EE067363.1|EE067363
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|156735832|gb|EV239953.1|EV239953
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAA                         GCATTCTTCTCTGACAATGCCGT-AGCTCAGGCTTCAGGGA-GTCCTCCCC
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCC-TCAGCTCAGGCTTCAAGGAAGTCCTCCCC
EST: gi|33408742|gb|CF214369.1|CF214369
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|161721618|gb|FC070828.1|FC070828
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCGCAAAGAGGAG                         GCATTCTTCTCTGACAATGCCGCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCA
EST: gi|110719746|gb|EE095143.1|EE095143
EST:     TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAG                         GCATTCTTCTCCGACAATGCCGT-AGCTCAGGCTTCAAGGAAGTCCTCCCC
genomic: TTGTTGAAGTGAATGCCTTGGCCAAGGCATTGGCTGGTCACAAAGAGGAGgtatcctttg ... ttattttcagGCATTCTTCTCTGACAATGCC-TCAGCTCAGGCTTCAAGGAAGTCCTCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataccttttgatcatatgaacactgcatcactcattgattatggttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCAAGAGTGACTAATGAGGCTGTCCAAAAGGCT
                                 cattgat  putative branch site (score: 4)
                                             ttattttc  putative PPT
                                      attatggttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagtctgttttagtcttagcttccctaaacttacatttaagtttataccttttgatcatatgaacactgcatcactcattgattatggttattttcagGCATTCTTCTCTGACAATGCCTCAGCTCAGGCTTCAAGGAAGTCCTCCCCAAGAGTGACTAATGAGGCTGTCCAAAAGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
tcaagtc
- - - - - - - - - - -cttccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactcat