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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttattcccttcccaatttactttcctagtgtcccataccatccttcgatgctggtgatgctattttccactgattccaattatgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGGTAATATGAGAGTTGGATTTGCAGAAGCGGCATAAGAGAAACCCACCTGG

Basic information

species Vitis vinifera
transcript Vv10s0116g01210.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 12
gtattttattcccttcccaatttactttcctagtgtcccataccatccttcgatgctggtgatgctattttccactgattccaattatgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGGTAATATGAGAGTTGGATTTGCAGAAGCGGCATAAGAGAAACCCACCTGG
|||   ||| |  |||| ||              ||   |||   ||  |   ||    |  ||  || ||  |||||| |    ||     |||||||||||||| ||||| |||||||||  |||||| ||||||||||| || || || ||||| ||||| || ||  |  |||| |||  |            
gtaaactatgcatttccaaacccttgaattagcagtgaaataatttcacttcttgtcatttttg--atctttgactgatgcaccctacaatttgcagGATCCTGGGTGACGTTTTCATGGGTGCCTACCATACCGTGTTCGACTACGGCAAGATGAGGGTTGGCTTCGCGAAGTCGGCCTAAACGTGTTGTTGTCAC

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G11670.1 (Glycine max), 3'ss of exon 12
--gtattttattcccttcccaatttactttcctagtgtcccataccat--------ccttc-------gatgctggtgatgctattttccactgattccaattatgt----actgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGGTAATATGAGAGTTGGATTTGCAGAAGCGGCATAAGAGAAACCCACCTGG
    |   |||  | ||   |||||| ||| || | | | ||||| ||        ||||        |||||   ||||   ||| ||   | ||  ||  |   |    | ||||||||||| ||||| ||||||||||| ||||| |||||| | || |||||||||||  ||||||| |||||||| || || |||||    |    | | || 
gtacaaactatgacattaa-aatttaatttgcttgaggcacatactatggcatttaccttttaattgtgatgcatttgatatgattctcacttaatggcacatgcatcataaatgcagGATCCTTGGAGATGTCTTCATGGGGCGCTATCACACCATCTTTGATTATGGTAAGTTGAGAGTCGGATTTGCTGAGGCAGCATAGAGAATGTTCTCATGT

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA09G00810.1 (Glycine max), 3'ss of exon 12
gtattttattcccttcccaatttactttcctagtgtcccataccatccttcgatgctggtgatgctattttccactgattccaattatgt----actgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGGTAATATGAGAGTTGGATTTGCAGAAGCGGCATAAGAGAAACCCACCTGG
|||  |||  |  ||    |  | ||     |   |  | |        | |||||   ||||   ||  ||   | ||  ||  |   |    | ||||||||||| ||||| ||||||||||| || || |||||  | || |||||||||||  ||||||| |||||||| ||||| |||||    |    |    | 
gtacattaaactttttgagacatgctcaatgaaatttaccttttgattgt-gatgcatttgatatgatgctcacttaatggcacatgcatgataattgcagGATCCTTGGAGATGTCTTCATGGGGCGTTATCACACAATCTTTGATTATGGTAAGCTGAGAGTCGGATTTGCTGAAGCAGCATAGAGAATGTTCTTGAGT

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|77577410|gb|DV217422.1|DV217422
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|30300182|gb|CB976976.1|CB976976
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCC-TGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATG
EST: gi|32247021|gb|CD712840.1|CD712840
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|30127472|gb|CB912811.1|CB912811
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|26266741|gb|CA817804.1|CA817804
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|34549550|gb|CF517782.1|CF517782
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|110395600|gb|EC961267.1|EC961267
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|110718432|gb|EE095257.1|EE095257
EST:     TTAGTGGCTTTATTGCCATGGACGTCCCTCCNTC-ACGAGGACCCCTCTG                         GATCCTGGGAGA
genomic: TTAGTGGCTTTATTGCCATGGACGTCCCTCC-TCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGA
EST: gi|33402264|gb|CF207891.1|CF207891
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|30326639|gb|CD009901.1|CD009901
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|110692890|gb|EE068644.1|EE068644
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|26264648|gb|CA815711.1|CA815711
EST:     ATTAATGGCTTTATTGCCATGGACGGCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCCTTCATGGGTCACTACCACACCGTGTTCGATTATG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTC-TTCATGGGTCGCTACCACACCGTGTTCGATTATG
EST: gi|71890243|gb|DT039298.1|DT039298
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTAT
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTAT
EST: gi|34550114|gb|CF518332.1|CF518332
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|32269157|gb|CD718316.1|CD718316
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|34542385|gb|CF510617.1|CF510617
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|110387693|gb|EC952381.1|EC952381
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|71889630|gb|DT038685.1|DT038685
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|110394613|gb|EC959800.1|EC959800
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|26265277|gb|CA816340.1|CA816340
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATG
EST: gi|110716609|gb|EE091739.1|EE091739
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|34549014|gb|CF517246.1|CF517246
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|87584007|gb|DY473330.1|DY473330
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|110394775|gb|EC960081.1|EC960081
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|34549024|gb|CF517256.1|CF517256
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACCCCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|110396003|gb|EC961677.1|EC961677
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|77589411|gb|DV223973.1|DV223973
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
EST: gi|30126510|gb|CB911849.1|CB911849
EST:     ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTG                         GATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG
genomic: ATTAGTGGCTTTATTGCCATGGACGTCCCTCCTCCACGAGGACCCCTCTGgtattttatt ... tgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatccttcgatgctggtgatgctattttccactgattccaattatgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGGTAATATGAGAGTTGGATTTGCAGAAGCGGCATAAGAGAAACCCACCTGG
                              cactgat  putative branch site (score: 3)
                                        aattatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttattcccttcccaatttactttcctagtgtcccataccatccttcgatgctggtgatgctattttccactgattccaattatgtactgcagGATCCTGGGAGACGTCTTCATGGGTCGCTACCACACCGTGTTCGATTATGGTAATATGAGAGTTGGATTTGCAGAAGCGGCATAAGAGAAACCCACCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA