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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACAGCATGAACTCATCTTTGGTTGCTATAGTGTCAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttcttagcttggtttattcagtgtcacaaacaagaaagtgacaatcctcatcagatttttattttttattttattttttattattattatttttt...

Basic information

species Vitis vinifera
transcript Vv05s0020g03080.t01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 19
GTGACAGCATGAACTCATCTTTGGTTGCTATAGTGTCAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtga-tttcttagcttggtttattcagtgtcacaaacaagaaagtgacaatcctcatcagatttttatt-ttttattttattttttattattattatttttt
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GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgctgaccttagagagtagatattctg--caactgcacaactggtttctccaaactagcggaacattatattcttcttgcacctctttgccagtt
















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|71889597|gb|DT038652.1|DT038652
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|110414986|gb|EC980854.1|EC980854
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|46917646|gb|CN546975.1|CN546975
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|71882993|gb|DT032048.1|DT032048
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|46917526|gb|CN546855.1|CN546855
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|46918400|gb|CN547729.1|CN547729
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|71881187|gb|DT030242.1|DT030242
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|30129022|gb|CB914361.1|CB914361
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
EST: gi|71882474|gb|DT031529.1|DT031529
EST:     CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAG                         TATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC
genomic: CAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttctt ... gtgactgcagTATCAAGATTTAGGACAACTGTGCAATGACCCAAGAGTGAGGGCTGCTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACAGCATGAACTCATCTTTGGTTGCTATAGTGTCAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtgatttcttagcttggtttattcagtgtcacaaacaagaaagtgacaatcctcatcagatttttattttttattttattttttattattattatttttt

- - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaaa