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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgatatactgtgtctgtctctcagtgtttaaaactgtcctatttattaaacttatcttacttctgctccattttaatgggaattttttcatttattatgcttaatgccaggtctagttttgtttaacataatgtcaaattttgctcaaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACA

Basic information

species Vitis vinifera
transcript Vv05s0094g01550.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G13300.3 (Glycine max), 3'ss of exon 8
gtatgtgatatactgtgtctgtctctcagtgtttaaaactgtcctatttattaaacttatcttacttctgctccattttaatgggaattttttcatttattatgcttaatgccaggtctagttttgtttaacataatgtcaaattttgctcaaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACA
                                                        |  | | | | ||   | ||||| ||  |  ||||    ||||    || |  ||  |  |  | | ||  ||     | | | |  |||||||  |||  |||||||| ||||||||||||||||| | ||||||||| ||||| |||||||||||||| | |||||| |||||||| |||||||| || |||||||||  ||
--------------------------------------------------------tactataattgctatgcgattttgatttg--ttttgaagtttaaacagcatggtgata--tacattcttacttgtggaatttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTCACATCTGAAGGGGAAACTGCAAAGTGCAAAAAAGTTGTTTGTGATCCATCATATTTGCCCGGCA

upper sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G30140.3 (Glycine max), 3'ss of exon 8
gtatgtgatatactgtgtctgtctctcagtgtttaaaactgtcctatttattaaacttatcttacttctgctccattttaatgggaattttttcatttattatgcttaatgccaggtctagttttgtttaacataatgtcaaattttgctcaaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACA
                                                        || |  ||    |||  ||| | | |  || || |||      ||   |   ||||  | | ||   |  | |   ||  | | |  |||||||  |||  |||||||| ||||||||||||||||| | ||||||||||||||| |||||||||||||| | ||| || |||||||| |||||||| || ||||||||   ||
-------------------------------------------------------tttgtactataattgc--catgtgattttgatttgttttgaagtttgaacagcatgct-gatatacactcttgtggaat--ttttattttttgcttgaatgccagGTAGAATTTGATGAGGAAGGAAAGGTTGTTGGTGTTACATCTGAAGGGGAAACTGCAAAGTGTAAAAAAGTTGTTTGTGATCCATCATATTTGCCTGGCA
















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|110701800|gb|EE079788.1|EE079788
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|110700674|gb|EE077534.1|EE077534
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|110732501|gb|EE107845.1|EE107845
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAA                         GTAAAGTTTGATGAAGAAAGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|110371128|gb|EC934907.1|EC934907
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|110692608|gb|EE072046.1|EE072046
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|110731100|gb|EE108936.1|EE108936
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|110700715|gb|EE077610.1|EE077610
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|33406756|gb|CF212383.1|CF212383
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|37183843|gb|CF603197.1|CF603197
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
EST: gi|71888788|gb|DT037843.1|DT037843
EST:     TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAG                         GTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA
genomic: TCAGTGCTGTTTATGGTGGAACATACATGTTGAATAAACCTGAGTGCAAGgtatgtgata ... caaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatgccaggtctagttttgtttaacataatgtcaaattttgctcaaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACA
                    gtttaac  putative branch site (score: 3)
                                      ttttgctc  putative PPT
                     tttaacataatgtcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgatatactgtgtctgtctctcagtgtttaaaactgtcctatttattaaacttatcttacttctgctccattttaatgggaattttttcatttattatgcttaatgccaggtctagttttgtttaacataatgtcaaattttgctcaaatttcagGTAGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA