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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGAGGATTATGTTAAGGCCATCAAAGAGGAAATCAACAAGGTTGTCAAGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctcttctctatgctctagcatgggtttttaagattcaaattccttgtttttctgttgaaagaacaatggttctaattctgcctactgtttggatgtttcttaatatag

Basic information

species Vitis vinifera
transcript Vv08s0056g01570.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g01570.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: EFJ28889 (Selaginella moellendorffii), 5'ss of exon 8
TGAGGAGGATTATGTTAAGGCCATCAAAGAGGAAATCAACAAGGTTGTCAAGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctcttctctatgctctagcatgggtttttaagattcaaattccttgtttttctgttgaaagaacaatggttctaattctgcctactgtttggatgtttcttaatatag
 ||||| || || || | ||||||||||   ||||||  ||  ||||| ||||||||||| || ||||||||||| || |||||||| || ||||| |||||  ||    ||    |   || |  |  | | |  ||  | ||   ||||| ||   | |                                                      
CGAGGAAGAGTACGTGACGGCCATCAAATCTGAAATCGCCAGCGTTGTGAAGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtagga----tttggcagattccataactgatct--aatctacattgtcctttttcgccag------------------------------------------------------

upper sequence: Vv08s0056g01570.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: EFJ05611 (Selaginella moellendorffii), 5'ss of exon 8
TGAGGAGGATTATGTTAAGGCCATCAAAGAGGAAATCAACAAGGTTGTCAAGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctcttctctatgctctagcatgggtttttaagattcaaattccttgtttttctgttgaaagaacaatggttctaattctgcctactgtttggatgtttcttaatatag
 ||||| || || || ||||||||||||   |||||   ||  ||||| ||||||||||| || ||||||||||| || |||||||| || ||||| |||||  ||  | |     || |  |||| ||    | |||  | ||   ||||| ||   | |                                                      
CGAGGAAGAGTACGTGAAGGCCATCAAATCTGAAATTGCCAGCGTTGTGAAGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtagga--tttggcagattccatagc-tga---tctaatctacattgtcctttttcgccag------------------------------------------------------
















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|110400294|gb|EC966852.1|EC966852
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|71886245|gb|DT035300.1|DT035300
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|294965861|gb|GW837344.1|GW837344
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110374362|gb|EC939061.1|EC939061
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110404481|gb|EC969603.1|EC969603
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110429998|gb|EC996518.1|EC996518
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110426553|gb|EC992966.1|EC992966
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110376456|gb|EC941522.1|EC941522
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110403691|gb|EC969387.1|EC969387
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|161721696|gb|FC070122.1|FC070122
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110381130|gb|EC946448.1|EC946448
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110383670|gb|EC948053.1|EC948053
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110698652|gb|EE076398.1|EE076398
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110402853|gb|EC963625.1|EC963625
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|29785954|gb|CB343329.2|CB343329
EST:     TGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: TGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110422645|gb|EC988972.1|EC988972
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110690135|gb|EE066968.1|EE066968
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|33408742|gb|CF214369.1|CF214369
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|161721618|gb|FC070828.1|FC070828
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|110719746|gb|EE095143.1|EE095143
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTG
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTG
EST: gi|110687537|gb|EE065057.1|EE065057
EST:     TGATATTGACGTGCTCGTCCATGGTGAACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
genomic: TGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC
EST: gi|33409401|gb|CF215028.1|CF215028
EST:     AGCTCCAGGAAGAACTTGATATTGACGTGCTCGTCCATGGTGGACCTGAG                         AGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCCGGTTTTGCCTTC
genomic: AGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctc ... cttaatatagAGGAACGATATGGTCGAGTACTTTGGAGAGCAGTTGTCTGGTTTTGCCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGAGGATTATGTTAAGGCCATCAAAGAGGAAATCAACAAGGTTGTCAAGCTCCAGGAAGAACTTGATATTGATGTGCTCGTCCATGGTGAACCTGAGgtgtgagctcttctctatgctctagcatgggtttttaagattcaaattccttgtttttctgttgaaagaacaatggttctaattctgcctactgtttggatgtttcttaatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC