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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCGCTTTTTCAATGATGAGGTCCATCTGGATTTAAAGCATTCAAAAACAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattggctcatgtttattgttaaacgttcccacataaataaaaaatttccaagtcatttttcctcttgtatcctatttatcctatttgtagatgtttctgaagttatgttaagaactcatgaaactgcttttgttttcag

Basic information

species Vitis vinifera
transcript Vv19s0027g01660.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G00460.1 (Glycine max), 5'ss of exon 3
AGCTCGCTTTTTCAATGATGAGGTCCATCTGGATTTAAAGCATTCAAAAACAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattggctcatgtttattgttaaacgttcc---cacataaataaaaaatttccaagtcattt--ttcctcttgtatcctatttatcctatttgtagatgtttctgaagttatgttaagaactcatgaaactgcttttgttttcag
|||||| ||||||| ||||||  | ||| | ||||| |||||||| || || ||||| ||||||||||| ||||| ||||||||||| |||||||| |||||||     | |  |||     ||| |  |||||   |   | | |  | |||    ||  | |    |   ||||   |     || |  | |||||   |||||                                           
AGCTCGGTTTTTCAGTGATGAAATTCATATTGATTTGAAGCATTCCAAGACTGGAACAGTTGCCATGGCAAGTGCTGGAGAGAATCTGAATGCTTCACAGgtatggcatgttt-tgtggcaggttgagggttcctttcctgttattttagaatagttaatacgtaaaataaatcttcagttactattgttttgtttgtttctgttttcag---------------------------------------

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA15G28380.1 (Glycine max), 5'ss of exon 3
AGCTCGCTTTTTCAATGATGAGGTCCATCTGGATTTAAAGCATTCAAAAACAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattggctcatgtttattgttaaacgttcccacataaataaaaaatttccaagtcatttttcctcttgtatcctatttatcctatttgtagatgtttctgaagttatgttaagaactcatgaaactgcttttgttttcag
|||||| ||||||| ||||||  | ||| | ||| | |||||||| || || ||||| ||| ||||||| ||||| ||||||||||| ||||| || |||||||        |||||||| ||  |             |  |  |   || |         |||||| || | |   | |  |   ||  ||| |      | || ||    | |  | |  |     || || ||||| |||
AGCTCGGTTTTTCAGTGATGAAATTCATATTGATCTGAAGCATTCCAAGACTGGAACAGTTTCCATGGCAAGTGCTGGAGAGAATCTGAATGCATCACAGgtatgg------catgtttagtggcagg---------gcaggttgatggttcc---------tttcctgttattttggaatagttg-atacgtaaaa-----taaattttcagttactattgttttgtttgtttctgtttgcag

upper sequence: Vv19s0027g01660.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G53720.1 (Arabidopsis thaliana), 5'ss of exon 4
AGCTCGCTTTTTCAATGATGAGGTCCATCTGGATTTAAAGCATTCAAAAACAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattggctcatgtttattgttaaacgttcccacataaataaaaaatttccaagtcatttttcctcttgtatcctatttatcctatttgtagatgtttctgaagttatgttaagaactcatgaaactgcttttgttttcag
 ||||| |||| ||| |||||| | ||||| |||||||| |||||||| || || |||||||| ||||| ||||  ||||||||||| |||||||| ||||||   ||   |||| |||     | ||  || | |  |  || |||  | |       |    |  ||| ||   | || | ||||   |||  |  |||||    |  | | |                             
GGCTCGTTTTTACAAAGATGAGATTCATCTTGATTTAAAACATTCAAAGACCGGCACTGTTGCAATGGCCAGTGGTGGAGAGAATCTCAATGCTTCCCAGgtaagcttaa-tcatttttgcc--tgaa--ttactaagtttatgaaatctcttgggaaaagaaatgttctggtgatcgatatgtcct-catgtgaacttttctattctcttttcag----------------------------

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|351013338|gb|FQ425043.1|FQ425043
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351056299|gb|FQ454160.1|FQ454160
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351019880|gb|FQ439697.1|FQ439697
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|349829098|gb|FQ419630.1|FQ419630
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351021566|gb|FQ429670.1|FQ429670
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|349828467|gb|FQ417209.1|FQ417209
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351029259|gb|FQ436653.1|FQ436653
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACCACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351015245|gb|FQ445529.1|FQ445529
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|352786284|gb|FQ478895.1|FQ478895
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351014040|gb|FQ434192.1|FQ434192
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|349824097|gb|FQ417484.1|FQ417484
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351014258|gb|FQ434847.1|FQ434847
EST:     CAGGAACTGTTGCCATGTCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351019573|gb|FQ439390.1|FQ439390
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351030963|gb|FQ438999.1|FQ438999
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351030959|gb|FQ438995.1|FQ438995
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351015056|gb|FQ444345.1|FQ444345
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351052152|gb|FQ450722.1|FQ450722
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|351036687|gb|FQ457400.1|FQ457400
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAGGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
EST: gi|349832490|gb|FQ421051.1|FQ421051
EST:     CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAG                         TTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT
genomic: CAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattgg ... ttgttttcagTTCTATTTCACGCTGCGTGATGATCTAGACTACCTGGATGGAAAGCATACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCGCTTTTTCAATGATGAGGTCCATCTGGATTTAAAGCATTCAAAAACAGGAACTGTTGCCATGGCTAGTGCAGGAGAGAATCTTAATGCTTCTCAGgtataattggctcatgtttattgttaaacgttcccacataaataaaaaatttccaagtcatttttcctcttgtatcctatttatcctatttgtagatgtttctgaagttatgttaagaactcatgaaactgcttttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA