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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaataaaaaaaaattcatatcggagttcagatttccactggtggaatcagggtttgagccacttctaaactattttgcatcatgaaaaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAAAACATGGATCTGTACATCCCCAGGAAATG

Basic information

species Vitis vinifera
transcript Vv05s0020g01480.t01
intron # 1
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|71858718|gb|DT007773.1|DT007773
EST:     AGCTTCTCTCGTCCTTCACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: AGCTTCTCTCGTCCTTCACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|30298272|gb|CB975066.1|CB975066
EST:     AGCTTCTCTCGTCCTTCACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: AGCTTCTCTCGTCCTTCACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|110722148|gb|EE098126.1|EE098126
EST:     CTCGTCCTTCACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: CTCGTCCTTCACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|32245894|gb|CD711713.1|CD711713
EST:     CACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: CACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|110697003|gb|EE073611.1|EE073611
EST:     CTCGTCCTTCACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: CTCGTCCTTCACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|110696043|gb|EE074748.1|EE074748
EST:     TTCACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: TTCACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|27582593|gb|CB005288.1|CB005288
EST:     CACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: CACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|27584673|gb|CB007368.1|CB007368
EST:     CACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: CACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
EST: gi|110688561|gb|EE067257.1|EE067257
EST:     CTCGTCCTTCACGTTTCCTG                         ATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA
genomic: CTCGTCCTTCACGTTTCCTGgtatgctttc ... aaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaatcagggtttgagccacttctaaactattttgcatcatgaaaaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAAAACATGGATCTGTACATCCCCAGGAAATG
                     ttctaaa  putative branch site (score: 2)
                                     atcatgaaaaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaaataaaaaaaaattcatatcggagttcagatttccactggtggaatcagggtttgagccacttctaaactattttgcatcatgaaaaaattacagATTTCGGTGTAGTCGCAAACACAAGGCAAAATGCAGAACGAAGAGGGTCAAAACATGGATCTGTACATCCCCAGGAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
aaaaaaa
- - - - - - - - - - - - - - - - - - -tccactg
- - - - - - - - - - - - - - - - - - - - - - - ggaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcatg