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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgcctgctttttttttttttgctatgtgtttctttatttctctaccgtttaaggtggtggcgcgtgagtggcgcgtgacggtgggtgtctgtgtttgtgttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTGGAGGGAGCTCAAGGTACTTGGCTAAGAAGTATGGGGCCAGTTGCCAAGG

Basic information

species Vitis vinifera
transcript Vv16s0039g01410.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 1
gttcgcctgctttttttttttttgctatgtgtttctt--tatttctctaccgtttaaggtggtggcgcgtgagtggcgcgtgacggtgggtgtctgtgtttgtgttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTGGAGGGAGCTCAAGGTACTTGGCTAAGAAGTATGGGGCCAGTTGCCAAGG
       |  || | |||  |||| |||    || ||  ||  | | ||    |||      ||  |  ||||| |   |  | | |   ||  |||| |||          || ||||  ||||| | |  ||||| ||| |||||||| ||||||||||||||||| |||||||| ||  | ||    || | ||| ||    |||     
------ttttttatctttggtttgttattcagttattgttacctttttaattattatacatatgaagt-tgagttg-atgccatg-taaatgattgtgattgaaaaaagAT-GAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGATTGGAGGAAGCTCAAGATATCTTGCCTCTAAATTTGGAGCTGAATGCAT---
















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|351051597|gb|FQ450149.1|FQ450149
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|37183670|gb|CF603024.1|CF603024
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTNGTGGGATT
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGT-GTGGGATT
EST: gi|71859120|gb|DT008175.1|DT008175
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|34547143|gb|CF515375.1|CF515375
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|28960633|gb|CB340324.1|CB340324
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|351032554|gb|FQ458919.1|FQ458919
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCTG                         AGGAGGGAGAGAAGGGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|46917781|gb|CN547110.1|CN547110
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGG
EST: gi|351057048|gb|FQ448565.1|FQ448565
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCTG                         AGGAGGGAGAGAAGGGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|352790125|gb|FQ481324.1|FQ481324
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCTG                         AGGAGGGAGAGAAGGGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|351033929|gb|FQ462984.1|FQ462984
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|351037069|gb|FQ465061.1|FQ465061
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCG                         AGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
EST: gi|351037494|gb|FQ460693.1|FQ460693
EST:     CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCTG                         AGGAGGGAGAGAAGGGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG
genomic: CGCTCAGATCCGAATGATCGAAGAGAGCCTCCGGTTCGCCGGAGTTTCCGgttcgcctgc ... gttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgcctgctttttttttttttgctatgtgtttctttatttctctaccgtttaaggtggtggcgcgtgagtggcgcgtgacggtgggtgtctgtgtttgtgttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTGGAGGGAGCTCAAGGTACTTGGCTAAGAAGTATGGGGCCAGTTGCCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT