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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattttctgtttacatttttccctgctggtgctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC

Basic information

species Vitis vinifera
transcript Vv16s0013g02020.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 2
---tgattt--tctgtttacatttttccctgctggtgctcta-tatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
   || |    | | |||||   |||   |  |     |  | ||||| ||| ||| |     ||||||    ||||     |||    |||| |  | |  ||||||||||||| | || ||||| ||||| || || ||||| |||||||||||||| || ||||||||||| || || |||||||   |||| ||| |||| |
gggtgctcccatttatttaccaatttatataatcacatttgaatattttgtc-ctgtaatcaaaatattgtgcttaactatttgt---cgttacc--tttcctcagGGTTATGTGGTTTACCGTGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTACGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
--tgattttctgtttacatttttccctgctggtgctctatatttagtcactgcagcgttaatattca--tattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
    |   | | || ||||  | |  | ||| | | ||   |||      |   ||  ||  || ||  ||||         ||  | || ||  |  |||||||| |||||| | || ||||| || || || || ||||| |||||||||||||| || ||||||||||| ||||| |||||||   |||| ||| | || |
agccaaaatgtattcacatgctgctgt-ctgattcact---tttgaatgttttggccctataatccaaatattgtgcataactattttttgaccttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 2
tgattttctgtttac-atttttccctgctggtgctctatatttagtcactgcagcgttaatattcatat--taatatcgtgta----catgtta--acaatc--ttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
         || | | || || || || |  ||||  || ||     | |||||  | | |||  || |  | || | || |       ||||     |||   | ||||||| |||||  |||| ||||| ||||| |  || ||||| ||||||||||| || || ||||||||||| ||||| |||||||   |||| ||| |||| |
-------tagtatgctatgttgccttgtt--tgcttcatctt--acaattgcagtttgagtatatatgtcctgattttgtctgacgttgtgttgtggtaattcatcttcagGGATATGTTGTCTACCGTGTCCGTGTGAAGCGTGGTGGCAGGAAGAGGCCTGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 2
tgattttctgtttacatttttccctgctggtgctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC-----------------------------
                 || | | ||   |||   |   || |   | | ||   |||| |||     | |     |             || | |||||||||||||  | || ||||| ||||| || || ||||| ||||||||||| || || || |||||||| ||||| ||||| |   |||| ||| |||| |                             
---------------gattgtacttgtcagtgtaatgctttgaactagttcactattaa-attgtctctgactctat-------------atttgttcagggttatgttgtttaccgtgtccgtgttagGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCCAGCTCAAGTTCCAGAGGAACAAGAGGTCT

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G084757_T02 (Zea mays), 3'ss of exon 1
-tgattttctgtttacatttt-tccctgctggtgctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
   |  || |  ||   | |  | | |     | || |   || |      |    | |  |           | |        |||||    | | ||||||| |||||  | || || || ||||| || || ||||| ||||||||||| || || ||||||||||| ||||| |||||||   |||| ||| |||| |
aacagcttgtacttgtctgtaatgcattgaattactttgctttgaaaattcgagtagctgctgggtgcccgggtctgaaccttgtgttatt--tttgttcagGGGTATGTTGTTTACCGCGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCTGTGCCGAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G034794_T01 (Zea mays), 3'ss of exon 2
-tgattttctgtttacatttttccctgctggtgctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
   | |||| ||||  | |        | | |  |   | |      | |||   |      ||||   | | || || |     |  | | | | |||||||||||||  | || ||||| ||||| || || ||||| ||||||||||| || || || |||||||| ||||| ||||| |   |||| ||| |||| |
gatagtttcagttttgagtagaatgaacagattgtacttgtcagtgtaatgctttgaactagttcactattaaattgtctctgactctata-tttgttcagGGTTATGTTGTTTACCGTGTCCGTGTTAGGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 2
tgattttctgtttacatttttccctgctgg--tgctctatatttagtcactgcagcg---ttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
    |  || | | ||||  |  |  ||||     ||    |  |||   |||| |    || || |  || || || | |  ||     |   || | || |||||||||||||| || ||||| |||||| || | |||||  ||||||| ||||| ||||| |||||||| |||||||||||||| ||||||||||| ||||
----tgcctttgtccattactatcaactgggccagtcctggtagagtatttgcaccttgcttcatttgaatcttgattttgattatgatcttgtaa-cattccagGGTTATGTGATTTACCGTGTTCGTGTACGAAGGGGTGGCCGGAAGAGACCAGTTCCAAAAGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G15230.1 (Glycine max), 3'ss of exon 2
-tgattttctgtttacatttttccctgctggtgctctata-tttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
      || || | | |     || ||   ||  |  ||| || |||  |  |    || |  |  || || ||   |  || ||  | | || | || |||||||| ||||| || ||||| || ||| || | |||||  | ||||| ||||| |||||||||||||| |||||||||||||| ||||||||||| ||||
tcagaattatgatgaaacaaa-ccttgtcagtaatgaataattgagttgcaccttgcttcacttgaatcttgattatgattatattcttataa-cattccagGGTTACGTGATTTACCGTGTTCGCGTACGAAGGGGTGGCCGTAAGAGACCAGTTCCAAAGGGTATTGTTTATGGTAAGCCCACCAACCAAGGTGTTACTC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 2
-----tgattttctgtttacatttttccctgctggtgctctatatttagtcactgcagcgttaa-tattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
     ||      | |  |    ||          ||    || |||| ||     ||  | || |  |  ||  ||| | ||  | ||||| |      | |||||| | |||  | || ||||||||||| ||||| |||||| | ||||||||||| || ||||||||||||||||||||||| |||||||| || || || |
gttagtggagaaatatggaagcgttgtttgatgattgaatcatttttaatc----tagtctcaaattctgttacaaatctagttgagatgttgatg--tatgtcagGGCTTTGTTGTGTACCGTGTACGTGTGAGACGTGGTGGACGCAAGAGGCCAGTGCCTAAGGGTATTGTGTATGGTAAGCCAACAAACCAGGGAGTGACAC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 3'ss of exon 2
tgat--tttctgtttacatttttccctgctggtgctctatatttagtcactgcagcgtt-aatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
||||   || | ||||     |             | ||  |||  |   ||     || | | |   | ||  |  | | |   | ||  |  | ||   |||| | |||  |||| ||||| || || ||||| |||||| | ||||||||||| || |||||||| ||||| ||||| ||||| ||||| || || || |
tgatacattttttttaagccctggatcaaaaaaattgtacttttgtttgatgagttattcactctctgtgttgctgacttctctttattctctgtatt---agGGGTTTGTTGTCTACCGTGTTCGAGTCAGACGTGGTGGACGCAAGAGGCCAGTGCCTAAGGGTATCGTGTACGGTAAACCCACCAACCAGGGAGTGACAC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
-------tgattttct--gtttacatttttccctgctggtgctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
           |  |   | ||| || ||| | |     || | | | || | ||  |||     ||||  | | || |  |||||     |||   |  |  ||| ||||||||||| | ||||| || || ||  | || || || ||||||||||||||  | ||||||||||||||||| ||||| |  ||||||||| | || |
tcaacatcagctcgccaaggttaaatatttacttaaca-tggtatttgttgattccatgcgattctaattctgacat-atcatcgt-----tgtggtc--ttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
tgattttctgtttacatttttccctgctggt-gctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
  |  |   ||| |   |  |   ||  | | | |  | |     |   ||     |     |  |   |  || | |    || |      |  ||| |||| |||||  | ||||| || || ||  | || || || ||||||||||||||  | ||||||||||||||||| |||||||  ||||||||| | || |
-cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagcttttaacattatgatttatggccttattttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC

upper sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S134_151V6.1 (Physcomitrella patens), 3'ss of exon 2
tgattttctgtttacatttttccctgctggtgc-tctatatttagtcactgcagcgttaatattcatattaatat-cgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
   | | || || |      |   || | | |   ||  |||   ||  |      |   ||    | |  || | ||  |     |  ||      | ||||| |||||| |||| ||||| |||||  | || || || ||||||||||||||  | ||||||||||||||||| |||||||  ||||| ||| | || |
--ttatacttttcagcacccttgttgttagggtgcctggattctatccatatgatatgtttagatgtctagattttcggatgataatggacctcaactgcagGGATATGTGGTCTACCGTGTCCGTGTCCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAGGGTATTACGC

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|77577251|gb|DV217329.1|DV217329
EST:     GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
EST: gi|110688477|gb|EE067077.1|EE067077
EST:     GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
EST: gi|161708611|gb|FC061307.1|FC061307
EST:     GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
EST: gi|77584870|gb|DV221515.1|DV221515
EST:     GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
EST: gi|77585149|gb|DV221663.1|DV221663
EST:     GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
EST: gi|71876495|gb|DT025550.1|DT025550
EST:     GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
EST: gi|77584906|gb|DV221536.1|DV221536
EST:     GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
EST: gi|351023690|gb|FQ448241.1|FQ448241
EST:     GCCCCACTCGACCAGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAG                         GGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA
genomic: GCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattg ... atcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC
                                     tgttaac  putative branch site (score: 2)
                                              tcttttc  putative PPT
          ttaatattcatattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattttctgtttacatttttccctgctggtgctctatatttagtcactgcagcgttaatattcatattaatatcgtgtacatgttaacaatcttttcagGGTTATGTGATCTATCGTGTACGTGTAAGACGCGGTGGAAGGAAGAGGCCAGTCCCAAAGGGTATTGTGTATGGTAAGCCCACAAACCAAGGTGTCACTC

- - - - - - - - - - -ccctgct
- - - - - - - - - - - - - - - - - - - - - - -cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatg