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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtccattttttcatcttctgtagcataccttaaaccttggttcttagtcttaaagcacatcattatagactgaaaatttcctcaacctctctttttcattgaaaatgaccataattgatttttctttccaatgttgatatgttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG

Basic information

species Vitis vinifera
transcript Vv07s0005g03680.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 5
gtgtccattttttcatcttctgtagcataccttaaaccttggttcttagtcttaaagcacatcattatagactgaaaatttcctcaacctctctttttcattgaaaatgaccataattgatttttctttccaatgttgatatgttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG
                                          |   |   |||||||||    || || ||    | | | ||| ||    | | ||   || ||||  || ||| ||   ||||||||    | |  | || ||  |  ||| ||| ||||| ||| || |||||||| ||||||||||||||  ||||||||||||||||  || |||||||  | ||||| || ||  | || |     |
-----------------------------------------atatgtctacttaaagca----atcatggaaaatataatgccttaat---tatattgggttcaaaa--acaatactta--ttttctttatgttttcta-atttttttcgcagAGAGAAGCTATAATCGTATATGCAACTCATATTTTTGATGGACTGGAGACATGGGCAACTCATTTGGCATACATACAAGATGGTGAACTGAGAAGAGCAG

upper sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G44110.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgtccattttttcatcttctgtagcataccttaaaccttggttcttagtcttaaagcacatcattatagactgaaaatttcctcaacctctctttttcattgaaaatgaccataattgatttttctttccaatgttgatatgttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG--
                                                                   ||  |     | |  | |  ||||   || |  ||  ||||  | |    |||||||  | |      || |||| | | |   || |||||||||||||||| |||||||| |||||||| || ||| | ||||||||||| |   || |||| ||  |  | | ||| ||  | |        |  
------------------------------------------------------------------gtaagccattcactaaccccccctcatcttatgtttagaaatatcaaatgctgattttcatgt------tttatatttgagt---agagAGGAGCTACAATTGTATATGCAACTCATATTTTCGACGGGCTCGAGACATGGGCTAGTCATTTGGCTTACATTAATGGAGGAGAGCTGAAACTCTCGGCC

upper sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G44110.3 (Arabidopsis thaliana), 3'ss of exon 5
gtgtccattttttcatcttctgtagcataccttaaaccttggttcttagtcttaaagcacatcattatagactgaaaatttcctcaacctctctttttcattgaaaatgaccataattgatttttctttccaatgttgatatgttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG
                                                                   ||  |     | |  | |  ||||   || |  ||  ||||  | |    |||||||  | |      || |||| | | |   || |||||||||||||||| |||||||| |||||||| || ||| | ||||||||||| |   || |||| ||  |  | | ||| ||  | |        |
------------------------------------------------------------------gtaagccattcactaaccccccctcatcttatgtttagaaatatcaaatgctgattttcatgt------tttatatttgagt---agAGAGGAGCTACAATTGTATATGCAACTCATATTTTCGACGGGCTCGAGACATGGGCTAGTCATTTGGCTTACATTAATGGAGGAGAGCTGAAACTCTCGG

upper sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ37690 (Selaginella moellendorffii), 3'ss of exon 5
gtgtccattttttcatcttctgtagcataccttaaaccttggttcttagtcttaaagcacatcattatagactgaaaatttcctcaacctctctttttcattgaaaatgaccataattgatttttctttccaatgttgatatgttaat--tacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG
                                                                                             | |   |   |||||    || ||   |||||     |   |  | |   |  ||     || ||||    || ||||| |||||||| || ||||||||||| |||||| | ||||||||| | ||||| |||||    || ||  |  |   |  | || 
--------------------------------------------------------------------------------------------gtatgcaacacaaaatcttgatgatatttttttggaggctgagaggctgcttggatgccgtagAGAGGGTGCACCATTGTTTATGCAACACACATTTTTGATGGATTGGAGGCCTGGGCAACACACCTGGCCTATGTGGTTGATGGAAAACTTGAGCGGTTTA

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|33406635|gb|CF212262.1|CF212262
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|71890478|gb|DT039533.1|DT039533
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|349812583|gb|FQ407202.1|FQ407202
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGGTGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|351045986|gb|FQ441369.1|FQ441369
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|110403165|gb|EC964426.1|EC964426
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|351027875|gb|FQ448445.1|FQ448445
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|110383570|gb|EC947949.1|EC947949
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|71867051|gb|DT016106.1|DT016106
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|33401651|gb|CF207278.1|CF207278
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGTAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|351045639|gb|FQ440824.1|FQ440824
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|71867344|gb|DT016399.1|DT016399
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
EST: gi|71869053|gb|DT018108.1|DT018108
EST:     TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAG                         CGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA
genomic: TTGTGGCAAGGATGGATTTACTTGAATTCTTCAAGGAAGAATGTGATCAGgtgtccattt ... ttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgaaaatgaccataattgatttttctttccaatgttgatatgttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG
                                           tgttaat  putative branch site (score: 3)
              ataattgatttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtccattttttcatcttctgtagcataccttaaaccttggttcttagtcttaaagcacatcattatagactgaaaatttcctcaacctctctttttcattgaaaatgaccataattgatttttctttccaatgttgatatgttaattacagCGAGGAGCTACAATTGTGTATGCAACCCATATTTTTGATGGGTTGGAGACATGGGCAACAGATCTGGCATATGTCCAAGAAGGCGATTTAAGGAAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA