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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctcaatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA

Basic information

species Vitis vinifera
transcript Vv02s0025g01580.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 3
agatgcatgccttttttttagcatgtttcttgtgatgt-tactgtttatatgcaactctgttcaaatgtcttcactgatttctaattt--ctcaat-atttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
  |  | |     | | ||   | |||  || |    | ||| | ||  | ||   ||  ||||  |  | ||||||||||   ||||   | ||| ||||||||| || |||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||||||||| || |  ||    || |||||||||||||| |
-aacaccttgaagtgtcttgtgaggttgattataccttctacagctttgacgc---tccattcagctcacctcactgattttgtatttaattgaatgatttcagCTCGTGTTTTCATCTTCAGCAACTGTATATGGTTGGCCAAAGGAGGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 3
agatgcatgccttttttttagcatgtt-tcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctcaat--atttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
  |    |  || |  | |  | || | | |||   |||        ||  |  || |  |   | | | || ||||||||   ||||||  |   |||||||||||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||| |||||||||||  | |  ||  |||| ||||||||||||||||
--accttttactctcctatcccctgctattttgaagtgtcttgtggaattggttacgcaatctgattat-ttaactgattttatatttcttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGGTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctc--aat-atttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
   |       | | || | | ||   |   |   |  |  | |||   ||   ||    ||  ||   || ||||||||   ||||||   ||| |||||||||||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||| |||||||||||  | |  ||  |||| ||||||||||||||||
---ttttgaagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 3
agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctc--aat-atttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
  |  | |     | | ||     |||  || |    |  ||     | |||  |||  |||   |    ||||||||||   |||| |   ||| ||||||||| || || || || ||||| ||||| ||||||||||||||||| |||||||| |||||||||||||| || |  ||    || |||||||||||||| |
-aacaccttgaagtgtcttgcggggttgattatacctt--ctagcgctttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 3
---agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgt--cttcactgatttctaatttctcaatatt--tcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
   | || |     |  | | ||       | || || | || || | | ||||  | | |||   | ||   | | | | |  | |   |  |  || |   ||||||||| ||||| || || |||||||| ||||| ||||||||||||||||| |||||||||||||  || || | ||     | ||| |||||||| || |
gtaaaatccccttttggtctgtattgcagatttt-tggtattcct-tatgtatgtgagtatgtgacagtgaaacatgatttaactttctctcattgatctcaatcagCTTGTATTTTCTTCGTCCGCTACTGTGTATGGCTGGCCAAAGGAGGTTCCTTGTACAGAAGAGTCTCCCCTGTCTGGAATGAGTCCTTATGGACGGACAA

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 3
------agatgcatgccttttttttagcatgtttcttgtgatgt---tactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctcaatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
         | | | ||| | | ||    |  ||      |  |   | |  ||| |  |    |||  |   || || | | ||  || ||  | |||  | || |||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || || || ||||  ||  | | |||  | || |||||||| || || |
gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttgagtttgtcttgtttgatctcattattggctttta-ctactctgttttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctcaatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
  ||| ||   ||     || ||       |  ||    | | ||  | |||     || |||| | || | | |   | ||  || |||  | || |||||||| |||||||||||||| ||||| ||||| |  ||||| || ||||| |||||||| ||||| ||  | | ||||   || |||||||||||||| |
gtatgtataatttgccacta-cacaacaagttcgaatccatttttactttgc----ttgatcaattctcatgattagctactt-ttactctgt-ttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA

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:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110719820|gb|EE095280.1|EE095280
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110718272|gb|EE094913.1|EE094913
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGNNNNNNNCATCATCAGCTACTGTTTATGGTCGGCCAAAGGAGGTTCC
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTG-TTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCC
EST: gi|110731724|gb|EE106396.1|EE106396
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110720256|gb|EE096017.1|EE096017
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110720916|gb|EE097257.1|EE097257
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110697145|gb|EE073879.1|EE073879
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|161708830|gb|FC060896.1|FC060896
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGG
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGG
EST: gi|110718494|gb|EE095391.1|EE095391
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110720332|gb|EE096162.1|EE096162
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110727068|gb|EE103430.1|EE103430
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTT-CATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110728721|gb|EE104535.1|EE104535
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110732185|gb|EE107249.1|EE107249
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|71860637|gb|DT009692.1|DT009692
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|71883897|gb|DT032952.1|DT032952
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110727091|gb|EE103475.1|EE103475
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|30125545|gb|CB910884.1|CB910884
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGGCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110708350|gb|EE085791.1|EE085791
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|71861707|gb|DT010762.1|DT010762
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110718330|gb|EE095043.1|EE095043
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110719030|gb|EE096543.1|EE096543
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|110709164|gb|EE084386.1|EE084386
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|71856066|gb|DT005121.1|DT005121
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
EST: gi|30126470|gb|CB911809.1|CB911809
EST:     TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAG                         CTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA
genomic: TTGGCACAATTACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAAAAGgtattatctc ... aatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgcaactctgttcaaatgtcttcactgatttctaatttctcaatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
                                 ttctaat  putative branch site (score: 2)
                                       tttctca  CT-rich tract
                               atttctaatttctcaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctcaatatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - -catgcct
- - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - -tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttcac