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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaagagatggagatgtattttcctgtgctatgaaatttagttgatacatatgctcaaattacttagtgcatttggttttcaatcttttctacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAATACCA

Basic information

species Vitis vinifera
transcript Vv12s0059g00660.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g00660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G10510.1 (Glycine max), 3'ss of exon 2
-------gcaagagatggagatgtattttcctgtgctatgaaatttagttgatacatatgctcaaattacttagtgcatttggttttcaatcttttctacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAATACCA
         |     ||   ||  | || | | || | ||    || | ||||  |  | | | |  |  ||  |  || ||   |  || | ||||   |||||||| ||||||||||| |||||  |||| || |||||||||||||| |||||||| |||
aacatcattagtgagtgtgtataaacttgcatttgttttgcccgtttggtgatttaggtccaccatatgttttcta-atctg---tggaaacatttc---atgccagAGAGGAGGCAGGCTGAAGCATCTCGAATAAGAGAGAAGTATCCTGACAGAATTCCA
















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|34550263|gb|CF518481.1|CF518481
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCGAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCAGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110376041|gb|EC941080.1|EC941080
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCAGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110727718|gb|EE104797.1|EE104797
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|29785432|gb|CB342415.2|CB342415
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110715799|gb|EE094264.1|EE094264
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110702636|gb|EE078779.1|EE078779
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|22007625|gb|BQ792659.1|BQ792659
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110415048|gb|EC980917.1|EC980917
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCAGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|30297965|gb|CB974759.1|CB974759
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110411241|gb|EC976948.1|EC976948
EST:     AGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: AGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110691284|gb|EE069210.1|EE069210
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCAGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|28963447|gb|CB342480.1|CB342480
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|110402467|gb|EC968868.1|EC968868
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCAGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|34550348|gb|CF518566.1|CF518566
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCGAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCAGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
EST: gi|351017545|gb|FQ435898.1|FQ435898
EST:     TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCG                         AAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA
genomic: TACAGGTGTTGCCATGGCCAAAATCTCATTCAAGATGGAGCACCCTCTCGgtctgtaata ... tacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatatgctcaaattacttagtgcatttggttttcaatcttttctacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAATACCA
                               ttttcaatcttttct  CT-rich tract
           aaattactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagagatggagatgtattttcctgtgctatgaaatttagttgatacatatgctcaaattacttagtgcatttggttttcaatcttttctacatgccagAAAGGAGGCAGGCAGAAGCTGCTCGCATCAGAGAGAAGTATCCGGACAGAATACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
-caagaga
- - - - - - - - - - ttcctgt
- - - - - - - - - - - - - - ctatgaa
- - - - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caaatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg