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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag

Basic information

species Vitis vinifera
transcript Vv02s0025g01580.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA01G43540.2 (Glycine max), 5'ss of exon 4
TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag
 || |||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||||||||| || |  ||    || |||||||||||||| ||||||||  | ||    |     |       |   | ||||  |   |                 ||  | |    ||| ||      ||| ||                                                         
CGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTAAGgtatgactaggagtgtttgttggaaggtgaaacttggttttgatttgaattctgtgtgttcgccatctgatacgatgtttg----tttttcag--------------------------------------------------------

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA05G36850.1 (Glycine max), 5'ss of exon 4
TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttgggcaatgaacagaggcaatagtttcggttcag-gcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag
||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||| |||||||||||  | |  ||  |||| ||||||||||||||||||||    ||||     | |         ||| ||    ||    | |||||||  |      |   |  ||| |  |  |||     |||| ||                                                         
TGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCAAGgt----tttgcattttaatt-----tcataattataatttgttgaatactaacaa------tgatatctaatgaga--gtttttctcttttcag--------------------------------------------------------

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G02690.2 (Glycine max), 5'ss of exon 4
TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag
||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||| |||||||||||  | |  ||  |||| |||||||||||||||||||| |   ||    | |  | |     |||| |||  ||| |    |||| || ||  | ||      | | |  |  |||     |||| ||                                                         
TGTGTTCTCATCTTCAGCAACTGTATATGGGTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCAAGgttttgatttta-atttcataattataataattt--gttgaacagtactgaacaatgatatc-----tgatgaga--gtttttctcttttcag--------------------------------------------------------

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G01940.3 (Glycine max), 5'ss of exon 4
TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag
 || || || || ||||| ||||| ||||||||||||||||| |||||||| |||||||||||||| || |  ||    || |||||||||||||| ||||||||  | ||    |     |       |   | ||||  |   |                 ||  | |    ||| |||     ||| ||                                                         
CGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTAAGgtatgactaggagtgtttgttggtaggtgaaacttggttttgatttgaattctgtgttttcgccatctgatatgatgttta----tttttcag--------------------------------------------------------

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 5'ss of exon 4
TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttac-aatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag
||| ||||| || || |||||||| ||||| ||||||||||||||||| |||||||||||||  || || | ||     | ||| |||||||| || ||||||  |                    | | ||||  |       |||  ||||    || ||  |  |  ||   || || | |  | |||     |||||||  |||  |||                                     
TGTATTTTCTTCGTCCGCTACTGTGTATGGCTGGCCAAAGGAGGTTCCTTGTACAGAAGAGTCTCCCCTGTCTGGAATGAGTCCTTATGGACGGACAAAGgtactc--------------------agtcgttttcg-------atagcaaagtggaagcttttat-tgtagatttgattggtatttatactggaatgtttctcatttcgtag-------------------------------------

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G23920.1 (Arabidopsis thaliana), 5'ss of exon 4
TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgta-tgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag
||| |||||||||||||||||||| ||||| ||||| ||||||||||| || || || ||||  ||  | | |||  | || |||||||| || || ||||||   | ||  ||  |||  |  | |   ||      ||  |  ||| |   ||   |   |    || | | ||||  |   ||    |  || || || | || | | ||                                     
TGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAAAGgtagcacctttagcc-tgagtattgacccaagcccaccttgtg--atagtggtgatgaatgataataatcaggaaatgaatctgactgagattatttgcttgtgctgtgtaag-------------------------------------

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|110720449|gb|EE096391.1|EE096391
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110719820|gb|EE095280.1|EE095280
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110718272|gb|EE094913.1|EE094913
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110731724|gb|EE106396.1|EE106396
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110720256|gb|EE096017.1|EE096017
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGGTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110720916|gb|EE097257.1|EE097257
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110697145|gb|EE073879.1|EE073879
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110718494|gb|EE095391.1|EE095391
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110720332|gb|EE096162.1|EE096162
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110727068|gb|EE103430.1|EE103430
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGGAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110728721|gb|EE104535.1|EE104535
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110732185|gb|EE107249.1|EE107249
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|71860637|gb|DT009692.1|DT009692
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTG
EST: gi|71883897|gb|DT032952.1|DT032952
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110727091|gb|EE103475.1|EE103475
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110385299|gb|EC949809.1|EC949809
EST:     TCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: TCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110708350|gb|EE085791.1|EE085791
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|71861707|gb|DT010762.1|DT010762
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGT
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGT
EST: gi|110718330|gb|EE095043.1|EE095043
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110719030|gb|EE096543.1|EE096543
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|110709164|gb|EE084386.1|EE084386
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTACGGTTCAGATTCTGAATGG
EST: gi|30126470|gb|CB911809.1|CB911809
EST:     GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAG                         CTTGTTATTGAAGATATATGCCGTGATATTTAC
genomic: GTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttg ... atcctttcagCTTGTTATTGAAGATATATGCCGTGATATTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCAAGgtatgctttgggcaatgaacagaggcaatagtttcggttcaggcatactaaagaaacagattgcacataaaggaatggttagaacctttacaatctgtttcttctttattagcatctgttctaacaactgatgaggttgatcctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC