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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatgagttgttccattgctttgaacttttagttgcattatttgggctgtttgttatggcgaggtggttattcttgc...

Basic information

species Vitis vinifera
transcript Vv05s0020g01890.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G02580.1 (Glycine max), 5'ss of exon 3
TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatgagttgttccattgctttgaacttttagttgcatt-atttgggctgtttgttatg-gcgaggtggttattcttgc----------------------------------------------------
||| ||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||||||||  |      || ||  ||||  | | ||  |   ||   |   |   | || || ||| | ||    |||   |  ||   ||  | |||  || ||                                                     
TGGAGCCACTGACTATGGTGTAGGAGTGGACCTCTGGAGTGCTGGCTGCATTCTTGCTGAATTGTTGGCTGGGAAGCCTATTATGCCTGGTCGAACCGAGgtaatctt-----taaatgattaatttcattttataatttctctaagagcataagatgtattcactttacttgtcaatggtgcaagattttgttgctcgtgttagaaggtttgtgcttctgatttggttgatatatatccactgtgcttcacag

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G28650.1 (Glycine max), 5'ss of exon 3
TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatgag---ttgttccattgctttgaacttttagttgcattatttgggct--gtttgttatggcgaggtggttattcttgc------------------------------------------------------------------------------------------
||||||||| |||||| ||||||| ||||||||||||||||||||||||||||| ||||| |||||||| || |||||||| ||||||||||| || |||||||  || |  ||  |||    | ||  |   |  |  |  |  ||  | ||||||   || | || ||   |  ||||  ||     |||||     | |||                                                                                           
TGGGGCCACTGAATATAGTGTAGGAGTGGACCTCTGGAGTGCTGGCTGCATTCTTGCTGAATTATTGGCTGGAAAGCCTATTATGCCTGGTCGAACAGAGgtaatctctatgatggatacactatatagggcttaatgtctatagttgcatcttttaagggcttaatgtgtattcagtttactagtctaaggtgcaaggttttgttgtcgatggcttctcaattttctgctacttgattgtgaaatttgtgcttcagattttactgctataattagcatcctttatgtgttatag

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G38140.1 (Glycine max), 5'ss of exon 3
TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatga--gttgttccattg----ctttgaacttttagttgcatta--tttgggctgtttgttatggcgaggtggttattcttgc-------------------------------------------------------------
||| ||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||| || ||||| || |||||||| ||||| ||||| ||||||||||  || | |  ||  |||| |  | |   ||  || |  |    |||| || ||| |   |||| |  | |   |  |||  |    || ||||     | |||                                                              
TGGAGCCACTGACTATGGTGTAGGAGTGGACCTCTGGAGTGCTGGCTGCATTCTTGCTGAATTGTTGGCTGGCAAGCCTATTATGCCCGGTCGAACCGAGgtaatctctaaatgattaatttcattttataatttctctacgggcatctttcaagtttcaagagcataaaatatatccactttacttgtccgtggtgcaagattttgttgctcgtgttaaaaggtttttgcttctgatttggttgatatatatccactgtgcttcatag

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA15G10470.1 (Glycine max), 5'ss of exon 3
TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatgagttgttccattgctttgaacttttagttgcattatttgggct--gtttgttatggcgaggtggttattcttgc-----------------------------------------------------------------------------------------
||||||||| |||||| ||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || |||||||| ||||||||||| || |||||||  |  |  ||  |||  | | ||  | | |    |||| |    ||||||   |||| || ||   |  ||||  ||     |||||     | |||                                                                                          
TGGGGCCACTGAATATAGTGTAGGAGTGGATCTCTGGAGTGCTGGCTGCATTCTTGCTGAATTGTTGGCTGGAAAGCCTATTATGCCTGGTCGAACAGAGgtaatct--atgatggatacattatatagggtctatagttgcat----cttttaagggcataatgtgtattcagtttactagtctaaggtgcaagattttgttgtccatggcctctcaattttctgctacttgattgtgaaatttgtgctttggattttacttctataattagcatccttatgtgttgtag

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ24328 (Selaginella moellendorffii), 5'ss of exon 4
TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatgagttgttccattgctttgaacttttagttgcattatttgggctgtttgttatggcgaggtggttattcttgc
                  ||| || ||||| ||||||||  ||||||| || |||||||| ||| |||| || ||||| ||||||||||| || || || |||   ||     | | |||||    |  | ||||   |  |      ||||       |||  | |  | |                            
------------------TGTTGGGGTGGATCTCTGGAGCACTGGCTGTATACTAGCTGAATTACTGGCTGGCAAGCCCATCATGCCTGGGCGAACGGAAgtatgctccttggtttttattt----tacgatgtttagtaacgcctgccttt----cttattgatcgaacag----------------------------

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ35595 (Selaginella moellendorffii), 5'ss of exon 2
TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatgagttgttccattgctttgaacttttagttgcattatttgggctgtttgttatggcgaggtggttattcttgc
 || || || |||||  |||| || ||||| ||||||||  ||||||| || |||||||| ||| |||| || ||||| ||||||||||| || || || |||   ||     | | | |||   | ||  | |   |  || |    | |||  |   |||  | |  | |                            
CGGTGCTACAGAATACAGTGTTGGGGTGGATCTCTGGAGCACTGGCTGTATACTAGCTGAATTACTGGCTGGCAAGCCCATCATGCCTGGGCGAACGGAAgtatgctcgttggtttttgtttt--acgatgtttagtaacgcct---gcctttcttcttattgatcgaacag----------------------------

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|30126701|gb|CB912040.1|CB912040
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|71873708|gb|DT022763.1|DT022763
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|110689805|gb|EE066351.1|EE066351
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|110726282|gb|EE101925.1|EE101925
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|34544526|gb|CF512758.1|CF512758
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|71871637|gb|DT020692.1|DT020692
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|77586479|gb|DV222360.1|DV222360
EST:     CATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: CATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGGCCACCGAATATGGTGTAGGTGTGGACCTCTGGAGTGCTGGCTGCATTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaacaatatatatttaaaatgagttgttccattgctttgaacttttagttgcattatttgggctgtttgttatggcgaggtggttattcttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatga