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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagctgctattactttttagaaacaatgcatccagaaaagtgctggtggatcttatttgtgtgtttctgtctttgccttaattttataacatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTGGTTGACCACGAAACTCTGGCACTCGATCAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 6
--agtagctgctattactttttagaaacaatgcatccagaaaagtgctggtggatctt--atttgtgtgtttctgtctttgccttaattttataacatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTGGTTGACCACGAAACTCTGGCACTCGATCAG
  | || || |  | ||    |   ||  || ||  ||      |   | | | |  |  | |||  | | | ||||| ||   |  |||| |    ||| ||| ||||||| |||||||| ||||| ||| | ||||||||||| || || ||||| |||||||| | | |  ||||||| |||
ttattaact-cagtgacccaattctaatgattcacgcaactctttaaagtttgcttctggacttgcttatgtttgtctctgttgtttttttgtg---tctccagATTCTTGCCTATGTCTCGCAAGTTCACCATGTTGTACTTCCAGAAGAATTGGTAGACCACGAGAATTTAACACTCGAACAG
















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|30326726|gb|CD009988.1|CD009988
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTTAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|32249612|gb|CD715431.1|CD715431
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTTAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|71877721|gb|DT026776.1|DT026776
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGCAACTGAG                         GTTCTTGCTTATGTCTCTC
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTC
EST: gi|352778035|gb|FQ467088.1|FQ467088
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAATGCACAAGGTTGTACTTCCTGAAGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|32247169|gb|CD712988.1|CD712988
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTTAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|71879200|gb|DT028255.1|DT028255
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGCAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|30325548|gb|CD008810.1|CD008810
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTTAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|71880874|gb|DT029929.1|DT029929
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGCAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGC
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGC
EST: gi|352776661|gb|FQ465459.1|FQ465459
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|32248621|gb|CD714440.1|CD714440
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTTAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|352777956|gb|FQ467009.1|FQ467009
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGGAAATGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAAGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|351024445|gb|FQ426254.1|FQ426254
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGCAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|352778092|gb|FQ467145.1|FQ467145
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCTTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|352763986|gb|FQ467556.1|FQ467556
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTCAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAATGCACAAGGTTGTACTTCCTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTG
EST: gi|156737322|gb|EV241443.1|EV241443
EST:     TACTCAAAATTTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: TACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
EST: gi|30324763|gb|CD008025.1|CD008025
EST:     CAGCTGGAGCTGTTGCTNNNNNNNTACTTAAAAATTTTTCTGGAACTGAG                         GTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG
genomic: CAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtccat ... acatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtggatcttatttgtgtgtttctgtctttgccttaattttataacatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTGGTTGACCACGAAACTCTGGCACTCGATCAG
                                        ttataac  putative branch site (score: 2)
                                  ttaattttataacatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtagctgctattactttttagaaacaatgcatccagaaaagtgctggtggatcttatttgtgtgtttctgtctttgccttaattttataacatctgcagGTTCTTGCTTATGTCTCTCAAGTGCACAAGGTTGTACTTCCTGAGGATTTGGTTGACCACGAAACTCTGGCACTCGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - -ctgctat
- - - - - - - - - - - aaacaat
- - - - - - - - - - - - - - -gcatcca
- - - - - - - - - - - - - - - - - - - - -gtgctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgtg