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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGTTCTTGAAACTGATGCAAATGTTATTGCGGGAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaattctcttgcttttcccctgcatttgagagaaaaatataaaatatttaaaaaatagtaacacaacctggagggcctctgttaccacttaccacccaatgaaaatgtaaatcctgttggctcatctcaatatatgctctaaataataaacttaattttccttttgcag

Basic information

species Vitis vinifera
transcript Vv10s0003g02760.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g02760.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G02270.3 (Glycine max), 5'ss of exon 5
AATTGTTCTTGAAACTGATGCAAATGTTATTGCGGGAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaattctcttgcttttcccctgcatttgagagaaaaatataaaatatttaaaaaatagtaacacaacctggagggcctctgttaccacttaccacccaatgaaaatgtaaatcctgttggctcatctcaatatatgctctaaataataaacttaattttccttttgcag
 ||  |||||||||||||| |||||||||| ||||| || ||||| ||| ||||| | ||||||||||||||||||||||| |||||| | ||    |  |     || | |  ||   | | || || ||  |    |||||   | |    | ||| ||       |||||| |                                                                                    
TATCATTCTTGAAACTGATCCAAATGTTATAGCGGGGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCTGAACAGgtattata----ttatatccctcactttaataccaaaaaagaaaattgaga--ttaaatttttgaggaataac-tgttttttttctgttgcag----------------------------------------------------------------------------------

upper sequence: Vv10s0003g02760.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA15G13190.2 (Glycine max), 5'ss of exon 4
---------------AATTGTTCTTGAAACTGATGCAAATGTTATTGCGGGAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaattctcttgcttttcccctgca-tttgagagaaaaatataaaatatttaaaaaatagtaacacaacctggagggcctctgttaccacttaccacccaatgaaaatgtaaatcctgttggctcatctcaatatatgctctaaataataaacttaattttccttttgcag
                ||  | |||||||||||| |||||||||| || || || ||||| ||| ||||| | |||||||||||||||||||| || ||||||  |||  ||  |  ||  | | || || ||| | |  |||| | |||||    || ||||  | ||  |   ||  |     ||||    | |       ||                                                                       
TCATATTTTGTGCAGTATCATACTTGAAACTGATCCAAATGTTATAGCTGGGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCCGAACAGgtatagtacatccttcactaatacgcttcactttaataccaaaaaagaaaatcgacaataaat--tcactta-tttgaggaataactgtatttattcctgttgcag----------------------------------------------------------------------

upper sequence: Vv10s0003g02760.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA15G13190.3 (Glycine max), 5'ss of exon 5
AATTGTTCTTGAAACTGATGCAAATGTTATTGCGGGAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaattctcttgcttttcccctgca-tttgagagaaaaatataaaatatttaaaaaatagtaacacaacctggagggcctctgttaccacttaccacccaatgaaaatgtaaatcctgttggctcatctcaatatatgctctaaataataaacttaattttccttttgcag
 ||  | |||||||||||| |||||||||| || || || ||||| ||| ||||| | |||||||||||||||||||| || ||||||  |||  ||  |  ||  | | || || ||| | |  |||| | |||||    || ||||  | ||  |   ||  |     ||||    | |       ||                                                                       
TATCATACTTGAAACTGATCCAAATGTTATAGCTGGGAAAGTTGCTAGTAATAGTATAGATTCTGGAGCTCCTTTGTCCGAACAGgtatagtacatccttcactaatacgcttcactttaataccaaaaaagaaaatcgacaataaat--tcactta-tttgaggaataactgtatttattcctgttgcag----------------------------------------------------------------------

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|71874497|gb|DT023552.1|DT023552
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|351019718|gb|FQ439535.1|FQ439535
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110373435|gb|EC937671.1|EC937671
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|30137194|gb|CB922532.1|CB922532
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110379625|gb|EC944835.1|EC944835
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110699583|gb|EE076708.1|EE076708
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110722790|gb|EE099364.1|EE099364
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110715992|gb|EE090583.1|EE090583
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|351018368|gb|FQ439180.1|FQ439180
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|351040188|gb|FQ425274.1|FQ425274
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110701897|gb|EE079989.1|EE079989
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110417687|gb|EC983761.1|EC983761
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|32250089|gb|CD715908.1|CD715908
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|77581566|gb|DV219730.1|DV219730
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|110686798|gb|EE064846.1|EE064846
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCCGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|349832724|gb|FQ422082.1|FQ422082
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|30256223|gb|CB972066.1|CB972066
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|32250057|gb|CD715876.1|CD715876
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
EST: gi|351043288|gb|FQ444009.1|FQ444009
EST:     GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAG                         ACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA
genomic: GAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaat ... ccttttgcagACAATAAGTCAAGCGCTGGCTACTGCTCGTGAGCATCTAGCGAGATCCCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTTCTTGAAACTGATGCAAATGTTATTGCGGGAAAGGTTGCAAGTCATAGTCTTGATTCTGGAGCTCCTTTGTCTGAGCAGgtactgtaattctcttgcttttcccctgcatttgagagaaaaatataaaatatttaaaaaatagtaacacaacctggagggcctctgttaccacttaccacccaatgaaaatgtaaatcctgttggctcatctcaatatatgctctaaataataaacttaattttccttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG