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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagttgcaatggttttattttaatttttgcttcatgggcctgatgcagttgtaatctttatgttttctgtgtttccaaacaatgctttgggactgttggctaaatttggttttatttggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTGAGAACTGGAGCAGCTGCAATGAAGACCATGCACAAAACAAC

Basic information

species Vitis vinifera
transcript Vv09s0002g02750.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|18459455|gb|BM437733.1|BM437733
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
EST: gi|18458659|gb|BM436937.1|BM436937
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
EST: gi|110710254|gb|EE086428.1|EE086428
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
EST: gi|30252607|gb|CB970158.1|CB970158
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
EST: gi|110687799|gb|EE065623.1|EE065623
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
EST: gi|110702629|gb|EE078765.1|EE078765
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
EST: gi|30297117|gb|CB973911.1|CB973911
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
EST: gi|37188108|gb|CF607459.1|CF607459
EST:     AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAG                         ATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG
genomic: AACAGCAAATTGAGCAGCTTGGAAATTTCCAATTGCGCATTCATGATCAGgttcagttgc ... ggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaaacaatgctttgggactgttggctaaatttggttttatttggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTGAGAACTGGAGCAGCTGCAATGAAGACCATGCACAAAACAAC
                         ggctaaa  putative branch site (score: 3)
                            taaatttggttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagttgcaatggttttattttaatttttgcttcatgggcctgatgcagttgtaatctttatgttttctgtgtttccaaacaatgctttgggactgttggctaaatttggttttatttggcatttcagATGATCCTGCTAGAAGGAGCGAAAGCCACAACTGAGACTGTTGATGCATTGAGAACTGGAGCAGCTGCAATGAAGACCATGCACAAAACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA