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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacatttttacttcttatattattctgcctactcttctcatcatatccaaaaataatgcctaatcatctcttctcattaatattggggcttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGTTAGTGGCAATCTACCGTGAGAAG

Basic information

species Vitis vinifera
transcript Vv14s0006g01660.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G04360.1 (Glycine max), 3'ss of exon 5
gaacatttttacttcttatattattctgcctactcttctcatcatatccaaaaataatgcctaatcatctcttctcattaatattggggcttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGTTAGTGGCAATCTACCGTGAGAAG-
  ||| ||  || ||     |  || |  ||  | ||||  | | |    |||   ||   |    || |    | | | | |||| |  |  |    ||| |||||||| |||||||||||||| |||||||| ||||| ||   |||| ||||  || |||| ||||||||| 
-gacacttgaacctcaagcttgtttttttctttttttctttttagaaaataaatccatatatgtatatttacatttaatcaaattgtgcttccttgtcagtATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAGG

upper sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G33970.1 (Glycine max), 3'ss of exon 5
-gaacatttttacttcttatattattctgcctactcttctcatcatatccaaaaataatgcctaatcatctcttctcattaatattggggcttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGTTAGTGGCAATCTACCGTGAGAAG
      | ||     |||      |   || |  | ||||  | | |    |||   || | |    || | |  | | ||| |||  |  |  |    ||| |||||||| |||||||||||||| |||||||| ||||| ||   |||| ||||  || |||| |||||||||
tttgggtgttgggcacttgagcc-taaagcttttttttctttttagagaataaatctatacatgtatatttgtatttaataaaattatgcttccttgtcagTATGTGATCCAGTGATGGGTGATGAAGGAAAGCTTTATGTTCCTCAAGAGCTAGTATCAGTCTATCGTGAGAAG
















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|110380611|gb|EC945891.1|EC945891
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
EST: gi|110715098|gb|EE092763.1|EE092763
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
EST: gi|71859315|gb|DT008370.1|DT008370
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
EST: gi|294966903|gb|GW839778.1|GW839778
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCCTATGTCC-AACAGAG
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTC-TATGTCCCAACAGAG
EST: gi|37186505|gb|CF605858.1|CF605858
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
EST: gi|71863971|gb|DT013026.1|DT013026
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
EST: gi|18458843|gb|BM437121.1|BM437121
EST:     TAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: TAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
EST: gi|71859789|gb|DT008844.1|DT008844
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
EST: gi|161712131|gb|FC061503.1|FC061503
EST:     ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG                         TTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT
genomic: ATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATGgtgagtagat ... ttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccaaaaataatgcctaatcatctcttctcattaatattggggcttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGTTAGTGGCAATCTACCGTGAGAAG
                              cattaat  putative branch site (score: 3)
                                            cttttatc  putative PPT
                          ttctcattaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacatttttacttcttatattattctgcctactcttctcatcatatccaaaaataatgcctaatcatctcttctcattaatattggggcttttatcaagTTTGTGATCCTGTGATGGGTGATGACGGAAAGCTCTATGTCCCAACAGAGTTAGTGGCAATCTACCGTGAGAAG

- - - - - - - - - - - - tctgcct
- - - - - - - - - - - - - - - - - - -ctcatca
- - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctaa