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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGTTGTCATCCAAATCTTTATGGCAAGAGAACTGTTCTGTCTACTCAGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtaccagtttactatccatagattgatggaatgttgttgtttcatggaaagctctcctgagtgttctgctactgattatttgaagctaatgtttattttgtaatattgaccaagttactttggatgctttatattacatttgatatttacttattctcagatttttttactcag

Basic information

species Vitis vinifera
transcript Vv00s0598g00010.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0598g00010.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G32660.2 (Glycine max), 5'ss of exon 3
TGGTGGTTGTCATCCAAATCTTTATGGCAAGAGAACTGTTCTGTCTACTCAGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtaccagtttactatccatagattgatggaatgttgttgtttcatggaaagctct---cctgagtgttctgctactgattatttgaagctaatgtttattttgtaatattgac-caagttactttggatgctttatattacatttgatatttacttattctcagatttttttactcag
|||||||||| ||||||||||| |||||||| || ||||||  ||||||||||| | |||||||||| || || || ||||| || |||||||||||||||||  |  |  | || | ||  ||   |    |  |||  |  | |||||||   | ||     || ||   || |  ||   |  |  | ||   | |   ||  ||||   ||||||  |  | | ||  |                                                   
TGGTGGTTGTTATCCAAATCTTCATGGCAAGGGAGCTGTTCAATCTACTCAGGAGAGCTCATGAAGATAGGCAGCTGCCAGGATTTAGGCTATTAAATTGgtatctacat-aattcattactcacgcagctgtacaataattct-tttcatgattaactaatggccagaacctttttttaaaaaaaaaataaataaatttagtaacttgt--cattgacatatatcatttcag---------------------------------------------------

upper sequence: Vv00s0598g00010.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 3
TGGTGGTTGTCATCCAAATCTTTATGGCAAGAGAACTGTTCTGTCTACTCAGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtaccagtttactatccatagattgatggaatgttgttgtttcatggaaagctctcctgagtgttctg--ctactgattatttgaagctaatgtttattttgtaatattgac-caagttactttggatgctttatattacatttgatatttacttattctcagatttttttactcag
|||||||||| ||||||||||| |||||||| || || |||  ||||||||||| | |||||||||| || || || ||||| || |||||||||||||||||  |  || | || | ||  |||  |    |  |||  |  | |||||||   | ||      | ||  | |  |   |  || ||| ||   |||  | | |       ||||||  |  | | ||  |                                                   
TGGTGGTTGTTATCCAAATCTTCATGGCAAGGGAGCTTTTCAATCTACTCAGGAGAGCTCATGAAGATAGGCAGCTGCCAGGATTTAGGCTATTAAATTGgtatctacac-aattcattactcatgcagcagtacaataatcct-tttcatgattaact------aatggccagaacctttttttttttaaaaaaaatagtaactc---gtcattgacatatatcatttcag---------------------------------------------------
















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|71863603|gb|DT012658.1|DT012658
EST:     AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTG                         GCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
genomic: AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtac ... ttttactcagGCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
EST: gi|161711012|gb|FC058615.1|FC058615
EST:     GCTATTAAATTG                         GCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
genomic: GCTATTAAATTGgtaagtgtac ... ttttactcagGCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
EST: gi|71864214|gb|DT013269.1|DT013269
EST:     AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTG                         GCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
genomic: AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtac ... ttttactcagGCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
EST: gi|37188422|gb|CF607771.1|CF607771
EST:     AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTG                         GCACTTTTTCTTCA
genomic: AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtac ... ttttactcagGCACTTTTTCTTCA
EST: gi|110722646|gb|EE099052.1|EE099052
EST:     AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTG                         GCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
genomic: AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtac ... ttttactcagGCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
EST: gi|71864173|gb|DT013228.1|DT013228
EST:     AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTG                         GCACTTTTTCTTCACAGCAATGCTA
genomic: AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtac ... ttttactcagGCACTTTTTCTTCACAGCAATGCTA
EST: gi|32269792|gb|CD718951.1|CD718951
EST:     AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTG                         GCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA
genomic: AGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtac ... ttttactcagGCACTTTTTCTTCACAGCAATGCTATTTGTATATGGCCGCATTCTCAGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGTTGTCATCCAAATCTTTATGGCAAGAGAACTGTTCTGTCTACTCAGGAAAACTCATGAAGACAGTCATCTCCCAGGTTTCAGGCTATTAAATTGgtaagtgtaccagtttactatccatagattgatggaatgttgttgtttcatggaaagctctcctgagtgttctgctactgattatttgaagctaatgtttattttgtaatattgaccaagttactttggatgctttatattacatttgatatttacttattctcagatttttttactcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA