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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggttaaattacagtttttttttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA

Basic information

species Vitis vinifera
transcript Vv16s0050g00610.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g38520.2 (Oryza sativa), 3'ss of exon 2
----atggttaaattacagtttttttttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcatt---cagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
    ||| ||  ||  | | ||| | |||  |  |||  |      |||   |  || |  |   |||   ||       |  || | || |  ||| | |   |||||| ||| |||||||||    || || ||||||||||||||||| |||||||| ||||| || ||||||||| | ||||||||||||||||||||||| |
ttcaatgatttgatc-ctgctttatattatctgctttgcagt----ttactggccattatttcctattgcatttgc--acttaccttgttggcatgttaatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCTGGATTTGCTCCCTATGAGAAGCGTATCACTGAGCTTCTCAAAGTTGGCA

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g62350.1 (Oryza sativa), 3'ss of exon 2
atggttaaattacagtttttttttaattatttttt----aagattgttatatggaataaa-gtgtc---attatgttcattggttacc-cctttttgggtgtcatt-cagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
           | || ||| ||||  |   ||  |    || |  |  |||    |||   |  ||    |||| ||| ||  |||     ||||   || | ||| |||||||  | |||||| ||  |||| || |||  |||||| ||||| ||||  || ||||| |||||||||||  |||||||||||||||| || ||||| |
----------cagagatttcttttgctgtcttcctgatgaatacggccatacaccatagctgcttcctatttatattctttcattaatatgttttcttgtcttattgcagAAAAGTACCAAGAGAGTGAATTTTGTCAGGGGCTTGATTAGGGAGGTTGTGGGATTTGCTCCATATGAGAAACGAATCACTGAGCTTCTGAAGGTTGGAA

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G850966_T03 (Zea mays), 3'ss of exon 2
atggttaaattacagtttttttttaattattttttaagattgt---tatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
   ||  |  || |   ||     || |||    ||   ||     | | || | |  | |||  |     || ||  || |   || ||   |||  |||||||| | |  ||||||||   | | || |||  | ||||||| || |||||||| ||||| || ||||||||| | |||||||||||||| || ||||| |
-ctgtacatgtaaatgattagcacaagtatgcggtagatttacatatctttgcacttgattgttttctgtgtccttcattccaagttattt--tgttgttcagAAATCAACGAAGAGGGTGTCTATGGTCAGGGGCCTGATCAGAGAGGTTGCTGGGTTTGCTCCTTATGAGAAGCGTATCACTGAGCTTCTGAAGGTTGGCA

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G850966_T01 (Zea mays), 3'ss of exon 3
atggttaaattacagtttttttttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
                                       |  | | |  |  |   | ||  |  |  | ||  |   |   |   || |     ||| |||     |||||      | |  | | | |  |||| | || |||      |   |  ||  |    | |  ||||     |||       | |  ||| 
-------------------------------------cctgatcagagaggttgctgggtt-tgctccttatgagaagcgtatcactgAGC----TTCTGAAGGTTGGCAAGGACAAGCGTGCCCTGAAG--CTTGCTAAGAGAAAGCTTGGAACTCACAAGAGGGCAAAGAAGAA-----GAGAGAGGAGATGGCGGG-

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G29990.3 (Glycine max), 3'ss of exon 2
atggttaaattacagttttttttta-attattttttaagattgttatatggaataaagtgtcattatgtt-cat-tggttac--ccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
     ||| | |   |  |    || |  | |  ||||||  |  ||  | ||    || |   ||| ||  || |||| |      | | | | |   |  |||||||| ||||||||||| || || || |||||| | || || || ||||||||||||||||| ||||| ||| | || |||||| | || || |||||||
-----taattcatcctcatccactatagaaataattaagaaaggcatcagaaactttgtttttatatcttatatgtggtcataatattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G37840.1 (Glycine max), 3'ss of exon 2
atggttaaattacagtttttttttaatta---ttttttaagattgttatatggaataaagtgtcattatgttcat-tggt--tacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
    ||||||||   |  | | ||   ||    |  ||||||    || |  || |    | | ||    |  || ||||  ||    | | | | |   |  |||||||| ||||||||||| || || || |||||| | || || || ||||||||||||||||| ||||| ||| | || |||||| | || || |||||||
----ttaaattatgatgctgtattggataaaaataattaagaca--tacagagattttgtttttatatcttatatgtggtcctaaaattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G37600.2 (Arabidopsis thaliana), 3'ss of exon 1
atggttaaattacagttttttt-ttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttggg--tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
   ||||| ||   ||||||||  |   | |||   |||| | | || |     |   ||  | |   ||  |           |||||    | |  || ||||||| |||||||||  |   ||| |||| ||  |||| |||||||| |||||  | || || ||||||||||||||||||||||||||||| |||||||
---gttaagttggtgtttttttactctctgtttcacaagagtttcatttcactgactttggtaattcatttctcaagagttttgttttgatatttttgtttagAAAACGAGCAAGAGGACCATATTCATAAGAAAACTGATTAGGGAAGTAGCTGGAATGGCTCCTTATGAGAAGAGAATCACTGAGCTTCTCAAGGTTGGGA

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G53740.1 (Arabidopsis thaliana), 3'ss of exon 2
-atggttaaattacagtttttttttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
 || | ||  |     || |||  | || ||||||   |    |  | | |       |||   |   |      ||       |||   |  |   ||||||||| |||||||||      ||  | || |||||||| | |||||||||||||   || || |||||||||||||||||||||||| | ||        
gatagctatctcttgattatttcgttatgattttt-gtggcaatcttcttgctgtgtttgtttatgcatctgagtgtggtattgtttcttgatttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCTGGTCAAGCTCCCTATGAGAAGAGAATCACTGAGCTTTTGAAG-------

upper sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G53740.2 (Arabidopsis thaliana), 3'ss of exon 2
-atggttaaattacagtttttttttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
 || | ||  |     || |||  | || ||||||   |    |  | | |       |||   |   |      ||       |||   |  |   ||||||||| |||||||||      ||  | || |||||||| | |||||||||||||   || || |||||||||||||||||||||||| | || ||||| |
gatagctatctcttgattatttcgttatgattttt-gtggcaatcttcttgctgtgtttgtttatgcatctgagtgtggtattgtttcttgatttgctcagAAAACGAGCAAGAGGACAATCTTTATCAGAAACTTGATAAAGGAAGTTGCTGGTCAAGCTCCCTATGAGAAGAGAATCACTGAGCTTTTGAAGGTTGGTA

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|110429139|gb|EC995628.1|EC995628
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110385689|gb|EC950235.1|EC950235
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110422139|gb|EC988452.1|EC988452
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|87584541|gb|DY473667.1|DY473667
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110424794|gb|EC991167.1|EC991167
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|37189943|gb|CF609292.1|CF609292
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|87586274|gb|DY474608.1|DY474608
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110692581|gb|EE071987.1|EE071987
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110692560|gb|EE071942.1|EE071942
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110693783|gb|EE070314.1|EE070314
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|83277254|gb|DV941262.1|DV941262
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110405321|gb|EC970861.1|EC970861
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110706538|gb|EE082152.1|EE082152
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|33405067|gb|CF210694.1|CF210694
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110405586|gb|EC971129.1|EC971129
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110419315|gb|EC985532.1|EC985532
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
EST: gi|110732418|gb|EE107685.1|EE107685
EST:     ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGA                         AAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT
genomic: ATATTGTAACCAAGAAAGAATTACCTCCACGCCCATCGGATAGGAAAGGAgtaagttaat ... tgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA
     aataaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggttaaattacagtttttttttaattattttttaagattgttatatggaataaagtgtcattatgttcattggttacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - ggaataa