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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaataataattgaattgtatttattctggttagccgttagtggacttttgccaaattgatttacgatcttagaaaaatcccatgttttttctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAAGGTGGTCCTGAAACTTTCCGAGGAGTTTTCATCCGCGCTCCTGCAATCC

Basic information

species Vitis vinifera
transcript Vv06s0004g03000.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|352794338|gb|FQ481569.1|FQ481569
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351032258|gb|FQ460515.1|FQ460515
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|352799005|gb|FQ480854.1|FQ480854
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|349829976|gb|FQ420236.1|FQ420236
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351027188|gb|FQ440056.1|FQ440056
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|352790573|gb|FQ478212.1|FQ478212
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351039932|gb|FQ464970.1|FQ464970
EST:     TAGTTGGGGGCCTTGACTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|122689691|gb|EC942857.1|EC942857
EST:     TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351038808|gb|FQ464674.1|FQ464674
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|349814306|gb|FQ398746.1|FQ398746
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351039369|gb|FQ461236.1|FQ461236
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|122690972|gb|EC965184.1|EC965184
EST:     TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAATTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|349824064|gb|FQ417451.1|FQ417451
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351036688|gb|FQ457401.1|FQ457401
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|349815212|gb|FQ400367.1|FQ400367
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351046692|gb|FQ453308.1|FQ453308
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351041568|gb|FQ455784.1|FQ455784
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351037793|gb|FQ464234.1|FQ464234
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|349828753|gb|FQ418488.1|FQ418488
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
EST: gi|351033877|gb|FQ462286.1|FQ462286
EST:     TAGTTGGGGGCCTTGATTGTACAGTCCACCGGAACTTCTTTGGCAGTCAG                         ATTCAGAGTTTTGAGACAGAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA
genomic: TAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAGgtaatgatat ... tctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgccaaattgatttacgatcttagaaaaatcccatgttttttctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAAGGTGGTCCTGAAACTTTCCGAGGAGTTTTCATCCGCGCTCCTGCAATCC
         aattgat  putative branch site (score: 4)
                                 tcccatgttttttctt  putative PPT
                                     atgttttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataataattgaattgtatttattctggttagccgttagtggacttttgccaaattgatttacgatcttagaaaaatcccatgttttttctttttcagATTCAGAGTTTTGAGACACAGCTTTCTGTACCTGAACTTGCAGCCAAGGAAGGTGGTCCTGAAACTTTCCGAGGAGTTTTCATCCGCGCTCCTGCAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - aattgaa
- - - - - - - - - - - - - -tggttag
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaattga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccatgt