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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatattctcgaatgtgtttatatggtcgtcatcttacatgcatgtacaatgccctaagctgattaccaacttcttatttatggtttatggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG

Basic information

species Vitis vinifera
transcript Vv08s0056g00620.t01
intron # 4
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|349832600|gb|FQ421958.1|FQ421958
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCANGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110698903|gb|EE076929.1|EE076929
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|30133266|gb|CB918605.1|CB918605
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110423860|gb|EC990211.1|EC990211
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110723106|gb|EE100040.1|EE100040
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAAGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|351023437|gb|FQ432820.1|FQ432820
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCANGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110378220|gb|EC943340.1|EC943340
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|351013904|gb|FQ434056.1|FQ434056
EST:     TATACCTCCCACCACCTCCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGA
genomic: TATACCTCCCACCACCTCCC-AGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGA
EST: gi|110419865|gb|EC986119.1|EC986119
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACATCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGCGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110376043|gb|EC941082.1|EC941082
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110411460|gb|EC977174.1|EC977174
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACATCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGCGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110702891|gb|EE079258.1|EE079258
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACATCCTCTTCTG                         CTCAAGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGCGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|351017341|gb|FQ435693.1|FQ435693
EST:     GTATACCTCCCACCACCTCCCAATAGTGGTGATTCCCACAGCCCCTTCTG                         CTCAGGGAGG-GTGGTTTTG
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGG-AGGAGTGGTTTTG
EST: gi|110702889|gb|EE079256.1|EE079256
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACATCCTCTTCTG                         CTCAAGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGCGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|161718482|gb|FC066332.1|FC066332
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110687935|gb|EE065911.1|EE065911
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACATCCTCTTCTG                         CTCAGGANGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGCGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110411538|gb|EC977258.1|EC977258
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|32456707|gb|CD797881.1|CD797881
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGAAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|77587268|gb|DV222769.1|DV222769
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGT
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGT
EST: gi|110702890|gb|EE079257.1|EE079257
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACATCCTCTTCTG                         CTCAAGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGCGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|34361775|gb|CF403360.1|CF403360
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|110362618|gb|EC926164.1|EC926164
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
EST: gi|351015182|gb|FQ445466.1|FQ445466
EST:     GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTG                         CTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA
genomic: GTATACCTCCCACCACCTCCCAGTAGTGTTGATTCCCACAGCCTCTTCTGgtaaaaatct ... ggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacaatgccctaagctgattaccaacttcttatttatggtttatggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG
             agctgat  putative branch site (score: 4)
                              ttatttatggtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatattctcgaatgtgtttatatggtcgtcatcttacatgcatgtacaatgccctaagctgattaccaacttcttatttatggtttatggtttaacagCTCAGGAGGAGTGGTTTTGGCTTCACAGGACGGGAAGATAGTCTGTGAGAACACTCTGGATGCACGATTGGATGTTGTATTCCGACAGAAACTGCCTGAG

- - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - caatgcc