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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaagaactatctcctaatgttatctaaatgtttgttttcattgattggttaattctaggttccccccctcaatgctaaagattgtttttctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTCTATTATGGAGATTGCAGCAAGTATGCTGAGGATTCCAGGGTATTTAATG

Basic information

species Vitis vinifera
transcript Vv13s0019g05240.t01
intron # 3
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|30327358|gb|CD010620.1|CD010620
EST:     AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAG                         TGTCTTGACATAGGTCTTCCTCCTGNAAATGATCCTCTTCCATTGAATTTC
genomic: AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAGgtttgtgatt ... ctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
EST: gi|32269108|gb|CD718267.1|CD718267
EST:     AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAG                         TGTCTTGACATAGGTCTTCCTCCTGANAATGATCCTCTTCCATTGAATTTC
genomic: AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAGgtttgtgatt ... ctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
EST: gi|110700080|gb|EE077708.1|EE077708
EST:     AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAG                         TGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
genomic: AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAGgtttgtgatt ... ctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
EST: gi|161715241|gb|FC068704.1|FC068704
EST:     AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAG                         TGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
genomic: AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAGgtttgtgatt ... ctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
EST: gi|32248038|gb|CD713857.1|CD713857
EST:     AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAG                         TGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
genomic: AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAGgtttgtgatt ... ctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
EST: gi|32269553|gb|CD718712.1|CD718712
EST:     AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAG                         TGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
genomic: AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAGgtttgtgatt ... ctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
EST: gi|161705821|gb|FC057098.1|FC057098
EST:     AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAG                         TGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC
genomic: AAGTTGTAGCTGGTCATGAACCCTCTGATGAAGCTGTTGATCTTGAGAAGgtttgtgatt ... ctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttaattctaggttccccccctcaatgctaaagattgtttttctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTCTATTATGGAGATTGCAGCAAGTATGCTGAGGATTCCAGGGTATTTAATG
                            tgctaaa  putative branch site (score: 2)
                                     ttgtttttctttttcc  putative PPT
                                    attgtttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaagaactatctcctaatgttatctaaatgtttgttttcattgattggttaattctaggttccccccctcaatgctaaagattgtttttctttttccagTGTCTTGACATAGGTCTTCCTCCTGAAAATGATCCTCTTCCATTGAATTTCTATTATGGAGATTGCAGCAAGTATGCTGAGGATTCCAGGGTATTTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
caaagaa
- - - - - -ctcctaa
- - - - - - - - - - - - - - - - - - - - - tgattgg