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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttatgttagcttggaacaagcaaatgtttttttcttcaaaagaattcacttcttcaacctaccttcttacaaggtattgcattcaaattttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTTCCTTAGCAATCATGATCTTGATGCCAGTCCTCCCATAATAAAACTTATC

Basic information

species Vitis vinifera
transcript Vv12s0059g00750.t01
intron # 11
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|27583171|gb|CB005866.1|CB005866
EST:     AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAG                         GAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
genomic: AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAGgtttgttcta ... ttttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
EST: gi|46910391|gb|CN545766.1|CN545766
EST:     AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAG                         GAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
genomic: AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAGgtttgttcta ... ttttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
EST: gi|30129079|gb|CB914418.1|CB914418
EST:     AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAG                         GAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
genomic: AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAGgtttgttcta ... ttttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
EST: gi|51052564|gb|CO819624.1|CO819624
EST:     AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAG                         GAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
genomic: AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAGgtttgttcta ... ttttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
EST: gi|110418797|gb|EC984974.1|EC984974
EST:     AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAG                         GAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
genomic: AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAGgtttgttcta ... ttttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
EST: gi|30329365|gb|CD012627.1|CD012627
EST:     AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAG                         GAGTTTGCCACATTTATCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
genomic: AGGCTTCTATGGCTGAGCCCCGTGCACAGACAGCTTTGGCACATCTTCAGgtttgttcta ... ttttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
EST: gi|110423979|gb|EC990332.1|EC990332
EST:     GCCCCGTGCACAGACAGCTTTGGCACATCTTCAG                         GAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT
genomic: GCCCCGTGCACAGACAGCTTTGGCACATCTTCAGgtttgttcta ... ttttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcacttcttcaacctaccttcttacaaggtattgcattcaaattttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTTCCTTAGCAATCATGATCTTGATGCCAGTCCTCCCATAATAAAACTTATC
                     ttcttac  putative branch site (score: 2)
                                             ttttttgc  putative PPT
                                      attcaaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttatgttagcttggaacaagcaaatgtttttttcttcaaaagaattcacttcttcaacctaccttcttacaaggtattgcattcaaattttttgcagGAGTTTGCCACATTTCTCCGTGTACTTGGTTGCTATCCTATGGATTCCTTTCCTTAGCAATCATGATCTTGATGCCAGTCCTCCCATAATAAAACTTATC

- - - - - - - -ggaacaa
- - - - - - - - - - - gcaaatg
- - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattca