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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatctgacctatttccagccttttgtgtactcattttttgttccactaaactttctagtcaaaaacattattatggacctggatgattttgatatattcacctttgtcttacatatgaataagcatggcgaactgatgaccaaccttttgtcttatcag

Basic information

species Vitis vinifera
transcript Vv14s0030g02020.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g02020.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 5
AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatctgacctatttccagccttttgtgtactcattttttgttccactaaactttctagtcaaaaacattattatggacctggatgattttgatatattcacctttgtcttacatatgaataagcatggcgaactgatgaccaaccttttgtcttatcag
|||| | || ||||| || || ||||||||||||||||| ||||||||||||||||| |  |  ||  | ||| | | | ||||  |  ||   ||||| |  | | |   |    || |  | |  |  || |||||| ||  |         ||| | |  ||||| |   || | |  ||| || |   |  | |  | |  |   |   | || | | |  |  | |  |                            
AGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTGgtatcaagtattgacacagtcta--cctcagaata-tcatttctttct---------tttgttgcaaaaaaaacatttcttggtctgcatcaaaatctttttcttagttcacttacagattttactttggcttgtcag---------------------------

upper sequence: Vv14s0030g02020.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatctgacctat--ttccagccttttgtgtactcattttttgttccactaaactttctagtcaaaaacattattatggacctggatgattttgatatattcacctttgtcttacatatgaataagcatggcgaactgatgaccaaccttttgtcttatcag
 |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||||||||||| ||| |  |||| |   |||||||||| ||| ||||| |||| |   |||| |  |||   |      ||  ||  ||  |||||| |||||  | |||   ||  |                                                                                               
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctttctgacaacacttgcccttgttcattgttc-actaacatctctttccaccag----------------------------------------------------------------------------------------------

upper sequence: Vv14s0030g02020.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G30360.1 (Glycine max), 5'ss of exon 5
AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatctgacctatttccagccttttgtgtactcattttttgttccactaaactttctagtcaaaaacattattatggacctggatgattttgatatattcacctttgtcttacatatgaataagcatggcgaactgatgaccaaccttttgtcttatcag
 |||||||||||||| ||||| |||| |||||| ||||| ||||| ||||||||||| ||||  ||    |||| |   |||||| ||| ||  ||||| || |             |||    ||| |||      |||||  | ||  |  |  | |  |    | |||  || || |  ||     || || | | |||    |||| |  ||||  ||||   ||||        | | |||| |  | | | |||||
GGAACTTGGAATTGGAATAGTACCATTCAGTCCCCTTGGCCGTGGATTTTTTGGTGGTAAGGGGGTCATAGAAAGTATACCTGCAGACAGTTATCTGgtatgaag------------ccaatagtttctgt------tttttaatacatca--cgatatgatatggatcatagttttgaaaatg-----ttatgttgttttc---cttgtttctcataacaata--tatggt-------taagcaacatcctttttcatcag

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|30252783|gb|CB970334.1|CB970334
EST:     TTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTG                         AGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
genomic: TTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatc ... gtcttatcagAGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
EST: gi|30252864|gb|CB970415.1|CB970415
EST:     TTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTG                         AGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
genomic: TTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatc ... gtcttatcagAGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
EST: gi|110425276|gb|EC991658.1|EC991658
EST:     TTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTG                         AGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
genomic: TTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatc ... gtcttatcagAGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
EST: gi|71875780|gb|DT024835.1|DT024835
EST:     TTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTG                         AGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
genomic: TTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatc ... gtcttatcagAGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA
EST: gi|33404078|gb|CF209705.1|CF209705
EST:     TTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCCG                         AGATTAAATCCTA
genomic: TTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatc ... gtcttatcagAGATTAAATCCTA
EST: gi|33404158|gb|CF209785.1|CF209785
EST:     TTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCCG                         AGATTAAATCCTAGGTTTCAAGGCGAGAACTTTGAAAAGAACAAGAACATA
genomic: TTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatc ... gtcttatcagAGATTAAATCCTAGGTTTCAAGGTGAGAACTTTGAAAAGAACAAGAACATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatctgacctatttccagccttttgtgtactcattttttgttccactaaactttctagtcaaaaacattattatggacctggatgattttgatatattcacctttgtcttacatatgaataagcatggcgaactgatgaccaaccttttgtcttatcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG