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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagaaacttttggtgctttttggttatattttcctccaaaattttaaatttggggtggataactagattgattatttgaattgcaattatatgcatcttatgttgtcattcttccttgatattatttctttgttatttccaactatttatcattggaagttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCACATGGACGAATCAGGACAAGAACTAATCGCTCTGGTGGGATACAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 9
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 9
lower sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 9
gtagagaaacttttggtgctttttggttatattttcctccaaa-attttaaatttggggtggataactagattgattatttgaattgcaattatatgcatcttatgttgtcattcttccttgatattatttctttgttat-ttccaactatttatcattggaagttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCACATGGACGAATCAGGACAAGAACTAATCGCTCTGGTGGGATACAG
                       |  | | | || | |    | || |   | |     ||  | |  | ||||      | ||  |  || |  || |    ||||| |  |||||  |   |  | | |||    | | ||| ||    |||      ||| ||  |  ||| || ||| ||||||||||||||||||||||||||||||  |  |||| |||||||   |  || |||||||| |||||||||||||||||||||
----------------------gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgatattggccgactaaacagggatcaattgaaca--atgttatt-ttcttgatcact--tgtgtctgaagtgtgttctaatggcttagt----gaaattattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 9
gtagagaaacttttggtgctttttggttatattttcctccaaaattttaaatttggggtggataactagattgattatttgaattgcaattatatgcatcttatgttgtcattcttccttgatattatttctttgttat-ttccaactatttatcattggaagttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCACATGGACGAATCAGGACAAGAACTAATCGCTCTGGTGGGATACAG
             |  |     ||| |||| | | | ||  |     |   | |       || | |   |||| |   | ||  |  || |  || |    ||||| |  |||||  |   |  ||| |||  | | | |||  |    |||      ||| |   |  ||| || ||| |||||||||||||||| |||||||||||||  |  |||| |||||||   |  || |||||||| |||||||||||||||||||||
------------gtactaaaacttgcttatttatacatctgagtgcctttgtct-------atgatt---ttgactgactaaacagggatcaattgaaca--atgttatt-ttcttgatcact--tatatctgaggtgtgttctgatggcttagt----gaaatcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
















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|110372418|gb|EC936581.1|EC936581
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACAGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|30326726|gb|CD009988.1|CD009988
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|156737328|gb|EV241442.1|EV241442
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCGC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|32249612|gb|CD715431.1|CD715431
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|30131232|gb|CB916571.1|CB916571
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|32247169|gb|CD712988.1|CD712988
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|110395213|gb|EC960849.1|EC960849
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|29783210|gb|CB349240.2|CB349240
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACAGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|352776660|gb|FQ465458.1|FQ465458
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|30325548|gb|CD008810.1|CD008810
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|110703011|gb|EE079483.1|EE079483
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACAGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|32248621|gb|CD714440.1|CD714440
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|110378991|gb|EC944156.1|EC944156
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|156737322|gb|EV241443.1|EV241443
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCGC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|29783264|gb|CB349323.2|CB349323
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACAGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
EST: gi|30324763|gb|CD008025.1|CD008025
EST:     TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAG                         GTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC
genomic: TTTGTCATTACCTGCAACAAAGGGCTTTGAATTTGGCAGTGGTTTTGCAGgtagagaaac ... gttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgatattatttctttgttatttccaactatttatcattggaagttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCACATGGACGAATCAGGACAAGAACTAATCGCTCTGGTGGGATACAG
 ccttgat  putative branch site (score: 5)
                                              ttcctgc  putative PPT
     atattatttctttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagaaacttttggtgctttttggttatattttcctccaaaattttaaatttggggtggataactagattgattatttgaattgcaattatatgcatcttatgttgtcattcttccttgatattatttctttgttatttccaactatttatcattggaagttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCACATGGACGAATCAGGACAAGAACTAATCGCTCTGGTGGGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG