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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCTGTCAAAAAGTACATACAGAAGGATCAACAGAGTGGTAGCAGAATTATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaactaatctctattgtgtattattttactttgtggttttgaaatgaacaagttttcattttaaaacagtttctggaaaaaaccattatcgagttc...

Basic information

species Vitis vinifera
transcript Vv08s0007g08110.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA03G29600.1 (Glycine max), 5'ss of exon 2
GCCTCTGTCAAAAAGTACATACAGAAGGATCAACAGAGTGGTAGCAGAATTATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgta-ttaact--aatct--ctattgtgtattattttactttgtggttttgaaatgaacaagttttcattttaaaacagtttctggaaaaaaccattatcgagttc
|||  |||| ||||||   ||||||||||||||| | || ||||||||  | || ||||| |||||||| ||||||||||||||||||||||| ||||||||  || |||   |||   || || | || || ||| |||| ||||| ||   || | ||  ||  | ||   ||  | || |     ||   |  ||    || 
GCCGGTGTCGAAAAGTTTGTACAGAAGGATCAACCGGGTAGTAGCAGAGCTCTTGTGGCTGGAGCTTGTATGGCTTATTGATTGGTGGGCAGGAGTTAAGgtgcttcactcggatccaacttttctctaataattttctttttggttctgtt-tggataaacttctactt---aattgattttaacgtaagttaaaattacctt-

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G32420.1 (Glycine max), 5'ss of exon 2
GCCTCTGTCAAAAAGTACATACAGAAGGATCAACAGAGTGGTAGCAGAATTATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtatt-aactaatctcta--ttgtgtattattttactttgtggttttgaaatgaacaagttttcattttaaaacagtttctggaaaaaaccattatcgagttc
|||  |||| || | |   |||||| |||||||| | || || || ||| | || ||||| || ||||| ||||||||||||||||||||||| |||||||| || |||||   || |  || | | | |||||  || ||  | ||   || ||   ||| ||  |  | |    |    | ||||||  |  |    || |
GCCGGTGTCCAAGAATTTGTACAGACGGATCAACCGGGTAGTGGCGGAACTCTTGTGGCTGGAACTTGTATGGCTTATTGATTGGTGGGCAGGAGTTAAGgtgtttaactatgatccaacttttttctaattttctttcgttctgtttggataaa---gttctcgatcaacactcataggagaaaaaaataaaaacttcgtac

upper sequence: Vv08s0007g08110.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G12560.2 (Glycine max), 5'ss of exon 2
GCCTCTGTCAAAAAGTACATACAGAAGGATCAACAGAGTGGTAGCAGAATTATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaactaatctctattgtgtattattttactttgtggttttgaaatga-acaagttttcattttaaaacagtttctggaaaaaaccattatcgagttc------
|||  |||| || | |   ||| |  |||| ||||| ||||| || ||  |  | ||||| ||||| |||||| |||||||||||||||| || ||||||||      |||| ||| |||| |  || || |  |||| | |||||  |          |  | |  ||    || | |       |    | | | | |       
GCCGGTGTCGAAGAATCTGTACCGGCGGATGAACAGGGTGGTGGCGGAGCTGCTCTGGCTGGAGCTCGTGTGGATTATTGATTGGTGGGCCGGTGTTAAGgt-----ttaatttctcttgtct--tagttaatgttgttgatttgagttattgttctcctctagtgcaaggtggtgtttattttttagttgttttgtgctttgcttg

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|110685332|gb|EE063631.1|EE063631
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACATTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|30252575|gb|CB970126.1|CB970126
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|71862495|gb|DT011550.1|DT011550
EST:     CTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: CTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|71864165|gb|DT013220.1|DT013220
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|161706024|gb|FC056715.1|FC056715
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|71866396|gb|DT015451.1|DT015451
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|71874295|gb|DT023350.1|DT023350
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|161717359|gb|FC065274.1|FC065274
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|33405255|gb|CF210882.1|CF210882
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|110696361|gb|EE072411.1|EE072411
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACATTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|110708022|gb|EE085087.1|EE085087
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|161715416|gb|FC068047.1|FC068047
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
EST: gi|77578022|gb|DV217773.1|DV217773
EST:     TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAG                         ATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG
genomic: TATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaacta ... ctgactgcagATCCAACTGTACACAGATCCAGAAACGTTTCGCTTAATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCTGTCAAAAAGTACATACAGAAGGATCAACAGAGTGGTAGCAGAATTATTATGGCTCGAGCTTGTGTGGCTTATTGATTGGTGGGCAGGGGTTAAGgtattaactaatctctattgtgtattattttactttgtggttttgaaatgaacaagttttcattttaaaacagtttctggaaaaaaccattatcgagttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa