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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaccattgatagtgaaaatatacattgcttgttggaccatcttggtccaactgacatgcttgaggcacatatatatcatagattttctctttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGGAATCTGTTACAGCAGAGCAGAAGTATTTGAAAGCTCGAGATACTCGTCA

Basic information

species Vitis vinifera
transcript Vv05s0020g04150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G22845.1 (Arabidopsis thaliana), 3'ss of exon 2
----------acaccattgata-gtgaaaatatacat---tgcttgttggaccatcttggtccaact-gacatgcttgaggcacatatatatcatagattttctc-tttg--ttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGGAATCTGTTACAGCAGAGCAGAAGTATTTGAAAGCTCGAGATACTCGTCA
          |  ||  | ||   |||  || | |||   |||    || |   | |   |  | || ||  || ||   |    ||| |    |   |||| |  ||||  |   |||||||||||||||  |||||||||| || |||||||||||||||||  |||||||||||   || ||||||||||||||||||||||| || ||||||||
gttcgtttccattccccttatgtatgatcatcttcattgatgcaatctgtattttgtgcattgagcttgagctgttttgtgatgttatgttctttctgttttgttgtttggttcttagAACATTTGGACCCGGTAAATGTTAAGATAGCTGAGTTGAGAGAGGCTTTGGAATCTGTTGTTGCTGAGCAGAAGTATTTGAAAGCTCGTGACACTCGTCA
















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|51051985|gb|CO819332.1|CO819332
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|32244957|gb|CD710776.1|CD710776
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|30304834|gb|CB981628.1|CB981628
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|351041440|gb|FQ447567.1|FQ447567
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|22009989|gb|BQ795023.1|BQ795023
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|18458532|gb|BM436810.1|BM436810
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110391808|gb|EC956810.1|EC956810
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110689594|gb|EE065965.1|EE065965
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|30329489|gb|CD012751.1|CD012751
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|351045647|gb|FQ440832.1|FQ440832
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110715167|gb|EE092904.1|EE092904
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|71879666|gb|DT028721.1|DT028721
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|87585357|gb|DY474109.1|DY474109
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110707896|gb|EE084817.1|EE084817
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110386948|gb|EC951583.1|EC951583
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|51051053|gb|CO818862.1|CO818862
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|71878189|gb|DT027244.1|DT027244
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|32245175|gb|CD710994.1|CD710994
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|27582549|gb|CB005244.1|CB005244
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110373933|gb|EC938946.1|EC938946
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110367618|gb|EC931562.1|EC931562
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|46917814|gb|CN547143.1|CN547143
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110715764|gb|EE094189.1|EE094189
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|71877713|gb|DT026768.1|DT026768
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|71878721|gb|DT027776.1|DT027776
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110427983|gb|EC994440.1|EC994440
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
EST: gi|110701935|gb|EE080075.1|EE080075
EST:     CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATG                         AACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG
genomic: CTATATACATGTTGGCCATATTCCCAATGAGCACAACCTCGCCAAAGATGgtatgttcaa ... tttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccaactgacatgcttgaggcacatatatatcatagattttctctttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGGAATCTGTTACAGCAGAGCAGAAGTATTTGAAAGCTCGAGATACTCGTCA
    aactgac  putative branch site (score: 2)
                                      ttttctctttgttac  putative PPT
                        atatatatcatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaccattgatagtgaaaatatacattgcttgttggaccatcttggtccaactgacatgcttgaggcacatatatatcatagattttctctttgttacagAACATTTGGACCCCATAAATGTTAAAATTGCTGAGTTGAGAGAGGCACTGGAATCTGTTACAGCAGAGCAGAAGTATTTGAAAGCTCGAGATACTCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
-caccatt
- - - - - - - gaaaata
- - - - - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - - - -ccatctt
- - - - - - - - - - - - - - - - - - - - - - - tccaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacata