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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctcaatggattctatcctctttggatgcacagccaaaagctaaatggtcatacatttttccatcaaatttgaaactctgtttattttctgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTGAAGACATGGTTGAGGATGATATTTCATCAAG

Basic information

species Vitis vinifera
transcript Vv11s0065g00450.t01
intron # 7
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|87584845|gb|DY473849.1|DY473849
EST:     TGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         AATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
EST: gi|110395278|gb|EC960936.1|EC960936
EST:     TGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         AATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
EST: gi|33405732|gb|CF211359.1|CF211359
EST:     TGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         AATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
EST: gi|110391622|gb|EC956610.1|EC956610
EST:     TGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         AATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
EST: gi|351028718|gb|FQ433148.1|FQ433148
EST:     TGATTCACGGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         AATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
EST: gi|22011495|gb|BQ796529.1|BQ796529
EST:     CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         T
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtag-
EST: gi|22011495|gb|BQ796529.1|BQ796529
EST:     CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         T
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtag-
EST: gi|110377829|gb|EC942921.1|EC942921
EST:     TGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         AATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
EST: gi|161716363|gb|FC068095.1|FC068095
EST:     TGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAG                         AATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG
genomic: CGATTCACAGTTATGCAACTCAGTGAACTACCACATCAATCGACCCTTAGgtatttggaa ... tgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtcatacatttttccatcaaatttgaaactctgtttattttctgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTGAAGACATGGTTGAGGATGATATTTCATCAAG
                               ctctgtttattttct  CT-rich tract
      atacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctcaatggattctatcctctttggatgcacagccaaaagctaaatggtcatacatttttccatcaaatttgaaactctgtttattttctgtcaagtagAATTCCTCGGTGAAGAAGAGCAGGATGTGTCAGGCCCAGTACAAATTTCTGAAGACATGGTTGAGGATGATATTTCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- ctcaatg
- - - - - - tctatcc
- - - - - - - - - - - - - - -cacagcc
- - - - - - - - - - - - - - - - - - aaaagcta
- - - - - - - - - - - - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcaa