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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAGTGTGCAGTTCAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcgatcataccattaccttctgggaaaattattttatggcaaattgggttttttgatcttgttggttagagcgggttgatgtcattggtttcc...

Basic information

species Vitis vinifera
transcript Vv09s0002g02560.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g46430.2 (Oryza sativa), 5'ss of exon 2
TCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAGTGTGCAGTTCAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgt-attagtcgatcat---accattacc--ttctgggaaaattattttatggcaaattgggttttttgatcttgttggttagagcgggttgatgtcattggtttcc
  || ||| || |||||| ||||||||||  |||  ||||  |||||||||| ||| |||  |||||| || ||||| ||| |||||||||||||||||||| | |||||| |  |   | |||| |    | |  ||     |           |||  |  | |  |   || ||  | | | |   ||||||  || ||    
AACTGCTTCCTGGTGAAGCAGTTCGGGAATAGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTGTACAATGTCCACTCCTACAAGCACTCTGgtcagtagtcgcttcttgcaacattgctggctttttgatggaaaccaagcatttcattcagcatctgcaaagtgctgacttgggtga--tgatgtgttttgtaag-

upper sequence: Vv09s0002g02560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os02g57540.1 (Oryza sativa), 5'ss of exon 2
TCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAGTGTGCAGTTCAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgt-attagtcga---tcataccattac---cttctgg-gaaaattattttatggcaaattgggttttttgatcttgttggttagagcgggttgatgtcattggtttcc
  || ||| ||||||||| |||| || ||| |||  ||||  |||||||||| ||| |||  |||||| || ||||| ||  |||||||||||||||||||| | |||| |    ||  | | | ||   |||  |  | |||||||    | |  | |  |  |||   || |  |    ||| |  | |   |    |  |     
AACTGCTTCCTCGTGAAGCAGTTTGGAAACAGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTGTACAATGTTCACTCCTACAAGCACTCTGgtcagtagttgcttctcgcaacgtcacaggctttagatgcaaattatgcctttg--attcagcctttgcaatgtcctgacatagtgttgttgtgttctgtaag-----

upper sequence: Vv09s0002g02560.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G088060_T04 (Zea mays), 5'ss of exon 2
TCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAGTGTGCAGTTCAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcgatcataccattaccttctgggaaaattattttatggcaaattgggttttttgatcttgttggttag-----agcgggttgatgtcattggtttcc------------------
  |||||| || |||||| |||| || |||||||  ||||  |||||||||| ||| |||  |||||| |||||||| ||  ||||||||||| ||||||||||  |  | ||    | | |  ||||||    ||     ||  | | |     || | |||||||  |  | |      |  |  ||  |||     ||||                    
AACTCCTTCCTGGTGAAGCAGTTTGGCAACGGCAATGCCAAGGTGCAGTTCACCAAGGAGCCCAACAACCTCTACAATGTACACTCCTACAAGTACTCTGgtat--gctgctc---tcctcagtttctggattgatctgcctacagaacacc---ttatgtgatcttagtaataaacaataaatgattttgtgttgaccgttttgcctgtttttttgtttcag

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|71877453|gb|DT026508.1|DT026508
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|37188885|gb|CF608234.1|CF608234
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|30126857|gb|CB912196.1|CB912196
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|37187461|gb|CF606814.1|CF606814
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|30137111|gb|CB922449.1|CB922449
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|71866381|gb|DT015436.1|DT015436
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|30127339|gb|CB912678.1|CB912678
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|77581630|gb|DV219763.1|DV219763
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|110365315|gb|EC928109.1|EC928109
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|30136063|gb|CB921401.1|CB921401
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|71869153|gb|DT018208.1|DT018208
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|37187417|gb|CF606770.1|CF606770
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|37187689|gb|CF607042.1|CF607042
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|71855040|gb|DT004095.1|DT004095
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|71871612|gb|DT020667.1|DT020667
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|71860821|gb|DT009876.1|DT009876
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|71868068|gb|DT017123.1|DT017123
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|110393499|gb|EC958782.1|EC958782
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|110707611|gb|EE084204.1|EE084204
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|71866729|gb|DT015784.1|DT015784
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|30133884|gb|CB919223.1|CB919223
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|37188785|gb|CF608134.1|CF608134
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
EST: gi|29782791|gb|CB348407.2|CB348407
EST:     CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTG                         GGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG
genomic: CAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcg ... gatgtactagGGTTGGCAAACCACAAAACAGTTACTATTCAAGGAGGCAAAGATAATGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAGTGTGCAGTTCAGCAAAGAGAGCAACAATCTCTACAACGTCAACTCCTACAAGCACTCTGgtattagtcgatcataccattaccttctgggaaaattattttatggcaaattgggttttttgatcttgttggttagagcgggttgatgtcattggtttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaaaa