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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctttgtttgtgtgactgtatgcacacttgcatgatacacttacctttattttattggatttttcccaaaggtattactgactatgtctttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTTGAGAGGATGCATGCACATTTAACTGCTGCGGTGGTTTCTAATGATTCCC

Basic information

species Vitis vinifera
transcript Vv17s0000g05800.t01
intron # 13
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|33402546|gb|CF208173.1|CF208173
EST:     AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAG                         GTTGTAACTGACTATAAAGACAATCAGCTACC-AGGGTGTTGGAAGCACTT
genomic: AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAGgtaattaaga ... ttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
EST: gi|110428757|gb|EC995236.1|EC995236
EST:     TTTTGGACCATTCCAG                         GTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
genomic: TTTTGGACCATTCCAGgtaattaaga ... ttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
EST: gi|110380514|gb|EC945785.1|EC945785
EST:     AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAG                         GTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
genomic: AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAGgtaattaaga ... ttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
EST: gi|26264607|gb|CA815670.1|CA815670
EST:     AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAG                         GTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
genomic: AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAGgtaattaaga ... ttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
EST: gi|27582713|gb|CB005408.1|CB005408
EST:     AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAG                         GTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
genomic: AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAGgtaattaaga ... ttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
EST: gi|351025255|gb|FQ434268.1|FQ434268
EST:     AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAG                         GTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
genomic: AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAGgtaattaaga ... ttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTT
EST: gi|110731235|gb|EE109223.1|EE109223
EST:     AGGATGGCAATTATGAGCTTGTTACAAGAGAAATTTTTGGACCATTCCAG                         GTTGTAACTGACTTATAAAGACAATCACCTACCCCGGGTGGTGGAAGC
genomic: AGGATGGCAATTATGAGCTTGTTACAAGAGAGATTTTTGGACCATTCCAGgtaattaaga ... ttgcccctagGTTGTAACTGACT-ATAAAGACAATCAGCTACCCAGGGTGTTGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattttattggatttttcccaaaggtattactgactatgtctttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTTGAGAGGATGCATGCACATTTAACTGCTGCGGTGGTTTCTAATGATTCCC
                               tactgac  putative branch site (score: 1)
                                          tctttgcccct  putative PPT
     ttttattggattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctttgtttgtgtgactgtatgcacacttgcatgatacacttacctttattttattggatttttcccaaaggtattactgactatgtctttgcccctagGTTGTAACTGACTATAAAGACAATCAGCTACCCAGGGTGTTGGAAGCACTTGAGAGGATGCATGCACATTTAACTGCTGCGGTGGTTTCTAATGATTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - -tgtgtga
- - - - - - - - - gtatgca
- - - - - - - - - - - - -cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgac