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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAACCTTAATCCAGTTTAGGAAAGCTTCATTGTTGGATGACTCCCAGGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatcatattactgcttgtgttacctatacagtcctggtgcacgatcctttcttttaccaatgtgggaataataggataagacaagatgatagac...

Basic information

species Vitis vinifera
transcript Vv10s0071g01010.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g01010.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA0048S00270.1 (Glycine max), 5'ss of exon 3
GTTGCAACCTTAATCCAGTTTAGGAAAGCTTCATTGTTGGATGACTCCCAGGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc----atatt--actgcttgtgttacctatacagtcctggtgcacgatcctttctttta-ccaatgt--gggaataataggataagacaagatgatagac
|| ||    ||||||||| | |||||||||||  ||||  |||| || || |||||||| ||||| |||||||| ||| |||| |||||||||||||||||||    ||     || ||  |||   ||  |||  |   || |||| ||||| | |  | |||| || |||| ||   |||| | ||    ||     ||        
GTAGCTGATTTAATCCAGCTAAGGAAAGCTTCTATGTTAAATGATTCACAAGTTGCTGAGATTCTGAATGAAATTTCACGACGAATTGTGCGAGACAAAGgtagtgtattttgaatgttggactagatgc-ttagttgatcactcctagtgcatggttgtatcttatagccaaggtctaggaaaagtaatccaaattctga--------

upper sequence: Vv10s0071g01010.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G00210.1 (Glycine max), 5'ss of exon 3
GTTGCAACCTTAATCCAGTTTAGGAAAGCTTCATTGTTGGATGACTCCCAGGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc----atatt--actgcttgtgttacctatacagtcctggtgcacgatcctttcttttaccaatgtgggaataataggataagacaagatgatagac
|| ||    ||||| ||  | |||||||||||  | ||  |||| || || |||||||| ||||| ||||| || ||| |||| ||||||||||||||||||||   ||     | |||  |||   ||  |||  |   || |||| ||||| | |  | |  | |   |  |      |  ||||| |||  |     ||    
GTAGCTGATTTAATTCATCTAAGGAAAGCTTCTATATTAAATGATTCACAAGTTGCTGAGATTCTGAATGATATTTCACGACGAATTGTGCGAGACAAAGgtaatgtattttgaacattggactagatgc-ttagttgatcactcctagtgcatggttgtattgtatcttatagccaaggtc-taggaaaagtaatccaaat----
















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|349820205|gb|FQ406881.1|FQ406881
EST:     GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAA
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAA
EST: gi|122691664|gb|EC981912.1|EC981912
EST:     GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA
EST: gi|351032891|gb|FQ461780.1|FQ461780
EST:     NGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGG
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGG
EST: gi|351054350|gb|FQ450433.1|FQ450433
EST:     GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA
EST: gi|351032201|gb|FQ460458.1|FQ460458
EST:     GGTTGCTGAAATTCTAAATGAAATCTCAAGACCTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATG
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATG
EST: gi|351016102|gb|FQ432057.1|FQ432057
EST:     GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAAGTTTCAAGAGAA
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA
EST: gi|351043992|gb|FQ431423.1|FQ431423
EST:     GTTGCTGAAATTCTAAATGAAATCTNCA-GACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCG
genomic: GTTGCTGAAATTCTAAATGAAATCT-CAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCG
EST: gi|351052517|gb|FQ456365.1|FQ456365
EST:     GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAGGAGAA
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA
EST: gi|352798379|gb|FQ480404.1|FQ480404
EST:     GGTTGCTGAAATTCTAAATGAAATCTCCAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGGTTTCA-GAGA
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGG-TTTCAAGAGA
EST: gi|351047688|gb|FQ455085.1|FQ455085
EST:     NGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAG                         GTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA
genomic: GGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatc ... tgcttttcagGTCCTGTTGTCATGGATATGTCGGGGTATTCTGAAAAAGGTTTCAAGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAACCTTAATCCAGTTTAGGAAAGCTTCATTGTTGGATGACTCCCAGGTTGCTGAAATTCTAAATGAAATCTCAAGACGTATTGTGCGAGACAAAGgtaactcatcatattactgcttgtgttacctatacagtcctggtgcacgatcctttcttttaccaatgtgggaataataggataagacaagatgatagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaga