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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag

Basic information

species Vitis vinifera
transcript Vv09s0002g03680.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
  |  || | |||||   |||| ||||||| ||||| |||||||| |||||||| || ||| | || |||||||| ||||||||  ||||||||||||||||| ||  | |     |||||||||   ||| | |     ||| |   | |    |||   || |   |||||   | |   |     ||||| |  | |||  |       |  |||  |   | || | |||  |     || |    |  || |||   |            
TTGCATAACATCTTGCTCAAATCTGTGGGCTCTAATCATGGATGCTGGCACTGGGTTCACTTCCCAGGTTTATGAACTTTCACCACATTTTCTTCACAAGgtgagtagcttgctccttgtttaactggtggaaaat---cttagc---aaactaatcacataact---tttcaa-ggcaaagtta---catataaggaagctctt-------gtatacattgtcaaatgtgattcca-----tggttttctggtcatttgaag------------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctc----atttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgag-gcatattacaaggctacttctttcagcttac--tgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
    || || ||||||  |||| |||||||  |||| |||||||| |||||||| |||||| | ||||| ||||||||||| |   ||||||||||||||||| ||       |||  | | ||   || | | |  | | |   |     ||    | |||| || |        |||| ||| |  |    ||   |  |      ||   |     ||||   |||  ||| |    | |  ||| || |    || |  |    | |  ||    |||
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtttcc-tgcatgctcctatccttctcatcca-tcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgata-tgctcgcctatgatgctcttag

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 12
--CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaag-gctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
  |||| |  | || |||  | || |||||||  ||||||||||||| |||||||||||||| || |||||  |||| || || |  || ||||||||||||||   |   ||| | | |  |    | || |  ||  ||||| | ||   || |||  |    |||    |||  || ||  || ||   |||   ||  || |                                                                        
TTCAGTTT--CATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaata--attgcgtgtcatcctactattgagtatgtattttttttcctatctgtggt-tggttactaatca--agcatactc-agctctatcctaattgccatc----------------------------------------------------------------------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
    || || ||  |   |||  |||||||  ||||||||||||| ||||||||||||||  | ||||| || || |||||    || ||||||||||||||  ||   ||   ||||||| |   ||  | ||   ||    |  || | | | |     |||  |||   ||     |   |      | ||| |     |                                                                        
TTCAGTTGCCTCCAGCTCAAACCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACATCTCAAGTATACGAACTTTCTAGTTACTTTCTTCACAAGgtaagtg--atcaattttgttgacttcaaag-atctgtaagggttctttcttttttttcttaatataatgatattcagctctcctgcttgttttagagaaaaa------------------------------------------------------------------------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
|   || || ||||||  |||| |||||||  | || |||||||| ||||| || |||||| | ||||| ||||| || || || |||||||||||||||||  |     | |    ||         ||| || | ||   ||||   || ||      || ||  ||||  |   | || ||    | | | | |      ||   ||  ||                                                             
CTCCGTTGCCTCTTGTTCAAATCTGTGGGCTTTGATAATGGATGCTGGCACCGGATTTACTTCTCAAGTGTATGAACTGTCTCCATATTTTCTTCACAAGgtaagc----tattaaatgccccctttttggtattc-tagcaatct---cacgt------cacttttatttatttgttgtgctccctccttttcaaattatagctcactttggc-------------------------------------------------------------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcat-acatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
|||||| || ||||||   ||| | ||||| || ||||||||||| ||||||||||| || |||||||||||||| || || ||| | || |||||||||||  |     |   || ||||| |    |||||| |   || |    ||     | ||||   || |  |||    | ||| ||||    ||  |  |  | || ||   | |  ||  | |||   | ||||  |   |   | |  || | |  ||| | | |  |        
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTGTCTCCCCACTTCCTTCACAAGgtttgc----tagtttatgttttagtggtggcattatgcatgtggtgttggtgatatcatattatcatctttgga-actattatcgttttat-ctgtactg-tattttactaattttgttttta---acttaacgtaggc---taacaaactcacgtttctgtttaatag------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA04G09070.2 (Glycine max), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcat-acatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
|||||| || ||||||   ||| | ||||| || ||||||||||| ||||||||||| || |||||||||||||| || || ||| | || |||||||||||  | ||  ||| |   |||| | |  |||||| |    | |    ||     | || |   || |  |||  | | ||| ||||    ||  |  |  | || ||   | |  ||  | |||   | ||||  |   |   | |  || | |  ||| | | |  |        
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTCTCTCCCCACTTCCTTCACAAGgt-tggctagtttat---gttttagcggtggcattatgcgtgtggtgttggtgatatcctattatcatcttt-gtaactattatcgttttat-ctgtactg-tattttactaattttgttttta---acttaacgtaggc---taacaaactcacgtttctgtttaatag------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcat-acatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
|||||| || ||||||   ||| | ||||| || ||||||||||| ||||||||||| || |||||||||||||| || || ||||  || |||||||||||  | ||  ||| |   |||| | |  |||||| |    | |    ||     | ||||   || |  |||  | | ||| |||     || |||   |  || |  |||     |  |||| |  | ||||| |   |   | |  || | || ||| ||| |  |        
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACAGCACAAGTTTATGAACTCTCTCCCTTCTTCCTTCACAAGgt-tggctagtttat---gttttagctgtggcattatgcgtgtgatgttggtgatatcatagtatcatgttt-gtaactattatc-----attttatctgtatagtattttactaattttgttttgaacttaatgtagtc---taacaaactcatgtttctttttaatag------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 12
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatg-atcgaggcatattacaaggctacttcttt-cagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
|||||| || ||||||  |||| ||||||| || ||||||||||| || || || |||||||| |||||||||||||| ||||     || || ||||||||| || |    | | | | | ||    |||     ||||  | |||  | |          |  |  | ||     ||||   |  | | |   |    |  |  | ||| |||                                                              
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACAGGATTTACTGCTCAAGTTTATGAGCTGTCACATGTATTCCTCCACAAGgtgggtgtgtggtgtctcgctcaagttttgggtagtatatgcagcttgtcgttcaatgatagaacagctatccctgttatgcgccatgccctcacattgagtcatatttttacag--------------------------------------------------------------

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|71885940|gb|DT034995.1|DT034995
EST:     CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAG                         GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA
genomic: CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctca ... ctgtctatagGAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA
EST: gi|156737302|gb|EV241423.1|EV241423
EST:     CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAG                         GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA
genomic: CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctca ... ctgtctatagGAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA
EST: gi|161714228|gb|FC064143.1|FC064143
EST:     CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAG                         GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA
genomic: CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctca ... ctgtctatagGAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA
EST: gi|71881724|gb|DT030779.1|DT030779
EST:     CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAG                         GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA
genomic: CTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctca ... ctgtctatagGAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaaggctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT