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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttggaagatgtactattgatgttactgttttaaattttttccaaagtaacagagccgtctgactagaattatgttgcattgtttctgcag

Basic information

species Vitis vinifera
transcript Vv19s0090g00690.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G43140.1 (Glycine max), 5'ss of exon 10
GTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttggaagatgtactattgatgttactgttttaaattttttccaaagtaacagagccgtctgactagaat--tatgttgcattgtttctgcag
||||||||||| ||||| ||||| | ||| | |||||| | |||||||||||||| ||||| |||| ||||||||||||||| |||| |||   || |   || |||  ||| |     |   |||||  ||        | |||| |||  || ||||   || || |||| | | |||||
GTAATTTGTGGCGTGAATTGTGGGAAACATCTAAACCAGTTCCAGCTGTTAAACAGGCACCTCTCTATGATGAGGATTTGGCAGTgtaagtgtaaata---accatttttgtgaac---tgggattttaccct------taaagccatctctcttgaatggcattttacatt-tatttgcag

upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA02G46190.1 (Glycine max), 5'ss of exon 11
GTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttggaagatgtactattgatgttactgttttaaattttttccaaagtaacagagccgtctgactagaattatgttgcattgtttctgcag
||||||||||| ||||| ||||| | ||| |||||||| | || |||||||| || ||||| || |||||||||||||||||  ||| ||||||  |||| |   ||  ||  | |  |||| || |||     |     | | || |||    |     ||||| |||   || |  ||
GTAATTTGTGGCGTGAATTGTGGGAAACATCCAAACCAGTACCTGCTGTTAAGCAGGCACCTCTGTTTGATGAGGATTTGGCATTgtaagttggt-gatgaagattttttgc-attaatttatatatttc----aaccctaaatccatctcttgaatcccatgttacatccatt-tatag

upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA14G02550.1 (Glycine max), 5'ss of exon 11
GTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttggaagatgtactattgatgttactgttttaaattttttccaaagtaacagagccgtctgactagaattatgttgcattgtttctgcag
||||||| ||| ||||| ||||| | ||| |||||||| | || |||||||| || || || || ||||||||||||||||| |||| ||||||  |||| |   ||  ||  | |  |||| || |||     |     | |||| |||    |     ||||||||||  || |  ||
GTAATTTATGGCGTGAATTGTGGGAAACATCCAAACCAGTACCTGCTGTTAAGCAGGCGCCTCTGTTTGATGAGGATTTGGCAGTgtaagttggt-gatgaagattttttgc-attaatttatatatttc----aaccctaaagccatctcttgaatcccatgttgcattcatt-tatag

upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA18G10700.1 (Glycine max), 5'ss of exon 5
GTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttggaagatgtactattgatgttactgttttaaattttttccaaagtaacagagccgtctgactagaat--tatgttgcattgtttctgcag
||||||||||| ||||| ||||| | ||| | ||| || | ||||||||||||||  |||| |||| |||||||||||| || |||| |||   ||  |  |  |   || |||     ||  |||||  ||        | |||| ||| ||| ||||   || || ||||  || || ||
GTAATTTGTGGCGTGAATTGTGGGAAACATCTAAATCAGTTCCAGCTGTTAAACAGACACCTCTCTATGATGAGGATTTAGCAGTgtaagtctaaa--taaaggacctattttatgagcttggattttaccct------taaagccatctcacttgaatggcattttacattcatt-tgtag

upper sequence: Vv19s0090g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT5G55060.1 (Arabidopsis thaliana), 5'ss of exon 11
GTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttggaa---gatgtactattgatgttactgt--tttaaattttttccaaagtaacagagccgtctgactagaattatgttgcattgtttctgcag
||||||| ||| |||| |||||| | ||||| |||||| | || ||||||||||||||||| ||||||||||| ||||| || |||| ||||  ||    |||| || || |   || ||   | |  ||||  ||   | | |  |||   | || | |    | | |    |   || | |||
GTAATTTATGGCGTGAGCTGTGGGAAACAGCTAAACCACTCCCTGCTGTTAAACAAGCACCTCTCTTTGATGAAGATTTAGCTGTgtaagtttcaatagcatgtcctcttaaacgtagtgaaatctgtatttgatc---actcatggagatct-tgtcca----tttctcatttaacttatacag

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|110732247|gb|EE107367.1|EE107367
EST:     CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGT                         GGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA
genomic: CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttgga ... gtttctgcagGGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA
EST: gi|110362938|gb|EC926500.1|EC926500
EST:     CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGT                         GGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA
genomic: CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttgga ... gtttctgcagGGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA
EST: gi|110693434|gb|EE069664.1|EE069664
EST:     CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGT                         GGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA
genomic: CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttgga ... gtttctgcagGGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA
EST: gi|110362337|gb|EC925865.1|EC925865
EST:     CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGT                         GGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA
genomic: CCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttgga ... gtttctgcagGGAAGGTATTCTACATTTCCTAGACGACATCCCACCTTCTGAGCTTTTTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAATTTGTGGTGTGAACTGTGGAAGACAGCCAAACCATTGCCAGCTGTTAAACAAGCACCCCTCTTTGATGAGGATTTGGCCGTgtgagttggaagatgtactattgatgttactgttttaaattttttccaaagtaacagagccgtctgactagaattatgttgcattgtttctgcag

- - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT