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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagatatttgtatttctatattgaagcttcttgcatgcagttgcttcttgatacttgtggtctcttaatggtaggaacaacattcatgttcatgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTCCAAAGAACCTCTCCATGGATGGTGCAGAATGGGTGGAGCTATTTGTTAG

Basic information

species Vitis vinifera
transcript Vv11s0016g05730.t01
intron # 2
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|110396128|gb|EC961805.1|EC961805
EST:     GGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAG                         GTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
genomic: GGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAGgtacatggat ... catgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
EST: gi|110689393|gb|EE065576.1|EE065576
EST:     TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAG                         GTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
genomic: TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAGgtacatggat ... catgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
EST: gi|349827156|gb|FQ421429.1|FQ421429
EST:     TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAG                         GTGTGGCTGCAACTAATGGAGAGGTCATATCTTCTGAGGATCCATCTGCTC
genomic: TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAGgtacatggat ... catgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
EST: gi|351027398|gb|FQ444647.1|FQ444647
EST:     TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAG                         GTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
genomic: TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAGgtacatggat ... catgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
EST: gi|110707354|gb|EE083682.1|EE083682
EST:     TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAG                         GTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
genomic: TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAGgtacatggat ... catgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
EST: gi|110688137|gb|EE066345.1|EE066345
EST:     TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAG                         GTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
genomic: TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAGgtacatggat ... catgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
EST: gi|110701421|gb|EE078969.1|EE078969
EST:     TGGTACTTCTGATGTAAGTCTGGAAACAAAAGTTCAACTTCAGTCACAAG                         GTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC
genomic: TGGTACTTCTGATGTAGGTCTGGAAACAAAAGTTCAACTTCAGTCACAAGgtacatggat ... catgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatacttgtggtctcttaatggtaggaacaacattcatgttcatgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTCCAAAGAACCTCTCCATGGATGGTGCAGAATGGGTGGAGCTATTTGTTAG
                 tcttaat  putative branch site (score: 3)
                 tcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagatatttgtatttctatattgaagcttcttgcatgcagttgcttcttgatacttgtggtctcttaatggtaggaacaacattcatgttcatgttgcagGTGTGGCTGCAACTAATGGAGAGGTCGTATCTTCTGAGGATCCATCTGCTCCAAAGAACCTCTCCATGGATGGTGCAGAATGGGTGGAGCTATTTGTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - -tgaagct
- - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcat