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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG

Basic information

species Vitis vinifera
transcript Vv13s0156g00180.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
         ||||| |||||| |  |  |  ||       |  ||  ||    | | | |  | || |||||           |||    | | ||  |||| |||||||||||||| ||||| |||||||||||||| ||  |||||||||| ||||| |||   ||||| ||
------gtaatgcc-actagattgat-catgattgctaccgttttatgtccatcttattggctaaaaagtgacaac-------attgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
----ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacag--tgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
    | || | | ||   |     | |  ||     | || |  |||| |     |     |  |  | |  |  | |    |      ||     ||| ||  |||| |||||||||||||| ||||| ||||||||||| || ||  | |||||||| ||||| |||   ||||| ||
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 3
ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctg--tggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
 |    || |    |  |  |||    |  |||  |  |  |  |  |  ||| | |     ||      ||||    | ||              |   |||| || ||||||||||| ||||| |||||||||||||| || ||||||||||| |||||  ||   ||||||||
cttcttaagaatttttttccaatctcatccaatccatgt--gtattgggaataaccgaacaaagcctggtgtgaacactattctttgcccatgttttctcagGTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 16
ttctgcaacatgcctactagaattctgtaaaataaactttggcttca-gtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgt------agGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
       |||  |||| |  |  || ||| |      ||  |||  |   || |       | | ||    | || |       |||     | | |||      |||| || ||||||||||||||||| || |||||||||||  ||||||||||||| |||||  ||   ||| ||||
-------acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaacaccattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
    | ||  ||  ||| ||| |  |     | ||  |||  || |  || |  | |   |  |     |||       |              |   |||| || ||||| ||||| ||||| |||||||||||||| || ||||||||||| |||||  ||   ||||||||
----gtaatgtgg-taccagattgatc----acaatttttcactcctttggtttcagccta-ctggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
--ttctgcaacatgcctactag-aattctgtaaaataaactttggct-tcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
   |   ||  |  ||   ||  |  | |    | |   || | ||| | |||  ||  | |     | | |  || ||   ||| | |||        ||||||||||||| |||||||| ||||| |||||||||||||| ||  | |||||| ||| |||| ||   || | |  
tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatt-tattcctgata-cgactgaacttgagttttaaatgg--tgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
-----ttctgcaacatgcctactagaattctgtaaaataaactttggct-tcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
       |   || | |  ||  |||  | |    | |   || | | | | ||| |||  | |     | | |  || ||   ||| | |||        ||||||||||||| |||||||| ||||| ||||| |||||||| ||  | |||||| | | |||| ||   || | |  
tgatacacattaaaacggataacaga--tgtactcattgctctctagatattagtcataatt-tattcctgata-cgactgaacttgagttttcaacgg--tgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 17
--------------------------------ttctgcaacatgcctactagaattctgtaaaat---------aaactttggcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacac------ttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
                                | || ||| || ||  | | || ||   || |          |  ||  ||  | |   ||  ||   || | ||   |   | |  ||| || |  |   |       ||  |||| || ||||| ||||| ||||| ||||||||||||||||||||||||||||| | |||| ||  ||||||| |
gtagtatctctatccttcgtttaccatggtgatccttcaatattccaccaacaactccacaacaccttacctacatgctaggggcttatgaatctcttgcgaatcaattttttatttacttgcgaatccgatgatggcttgttacagGTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAG

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 15
-------------------------------------------------------------ttctgcaacatgcctactagaattctgtaaaataaactttg--gcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
                                                                 | || | ||   |    | || | | |||     | |   |||||   |    |||   | |       | |  ||   |    |       |   |||| |||||||||||||| ||||| |||||||| ||||| || |||||  | || | |||| |  | |||     
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaaaaagcacccagctactcggaataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagt-cttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA

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|110391493|gb|EC956472.1|EC956472
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|110418511|gb|EC984670.1|EC984670
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|110361418|gb|EC924886.1|EC924886
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|110429398|gb|EC995889.1|EC995889
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|34320089|gb|CF372843.1|CF372843
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTACTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|34363396|gb|CF404981.1|CF404981
EST:     AGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: AGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|34415969|gb|CF414723.1|CF414723
EST:     AGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTT-AAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: AGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|29785895|gb|CB343236.2|CB343236
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|71866113|gb|DT015168.1|DT015168
EST:     TACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|110372355|gb|EC936513.1|EC936513
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|71866222|gb|DT015277.1|DT015277
EST:     TACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|110362967|gb|EC926531.1|EC926531
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
EST: gi|77577886|gb|DV217693.1|DV217693
EST:     TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAG                         GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC
genomic: TTTCAAAGCTTTATGAAGTGGTGCCTCCTATTCTTACTGAGCTTGGCAAGgtattatcat ... acacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG
               agttaac  putative branch site (score: 3)
                          attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG

ttctgca
- - - - catgcct
- - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - -tggcttc
- - - - - - - - - - - - - - - - - - - - - - - - - -tacctgt