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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGCACACAAGTGCTTCTCTGACTATAAATGAAAATTACGACTCGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaatttttcccttctgtgcttgctttggcagagtagtttatttgaaaagtgatttttatatggtgtttgattttataatttcag

Basic information

species Vitis vinifera
transcript Vv18s0122g00190.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA15G17340.1 (Glycine max), 5'ss of exon 3
TTCAGCACACAAGTGCTTCTCTGACTATAAATGAAAATTACGACTCGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaatttttcccttctgtgcttgctttggca------gagtagttta---tttgaaaagtgattttta---tatggtgtttgattttataatttcag--
| || ||||||||||||||||| || || ||||| ||||| ||||  || ||||| ||||| || || || |||||||     ||||||||||||||||||||||   ||  || ||| | ||   |      ||   |||||    ||  || || | |  ||   ||| |  ||  ||| |  |  |  |   
TGCATCACACAAGTGCTTCTCTTACCATCAATGAGAATTATGACTATGATGTTCGGGATGATACAGAAACCTTCCTCAATGGGATAGTTCCAGAGgttaatttttttatttagttcttacattaatatttatggaaaggtttaaatattttaaggttactgataaattattgaattctattctggatctctaata
















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|30329651|gb|CD012913.1|CD012913
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|26262702|gb|CA813765.1|CA813765
EST:     CAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110387568|gb|EC952248.1|EC952248
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110398891|gb|EC965370.1|EC965370
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|351014365|gb|FQ437367.1|FQ437367
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110386869|gb|EC951501.1|EC951501
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|71857030|gb|DT006085.1|DT006085
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110732164|gb|EE107221.1|EE107221
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|26257553|gb|CA808616.1|CA808616
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|28959343|gb|CB339672.1|CB339672
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|26258319|gb|CA809382.1|CA809382
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|254916144|gb|GR904002.1|GR904002
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|28959153|gb|CB339578.1|CB339578
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCCCCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|30301103|gb|CB977897.1|CB977897
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|26257283|gb|CA808346.1|CA808346
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|71856841|gb|DT005896.1|DT005896
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110426779|gb|EC993200.1|EC993200
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110711159|gb|EE087374.1|EE087374
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110425239|gb|EC991621.1|EC991621
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|110379372|gb|EC944560.1|EC944560
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|30301035|gb|CB977829.1|CB977829
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|28960863|gb|CB340439.1|CB340439
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GAAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|28959155|gb|CB339579.1|CB339579
EST:     GGACGTTCGAGATGACACTGAGACTATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCCCCTTGGAAGCATACACTGGAAG
genomic: GGACGTTCGAGATGACACTGAGAC-ATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|30137614|gb|CB922952.1|CB922952
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|28959315|gb|CB339658.1|CB339658
EST:     GGACGTTCGAGATGACACTGAGACTATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: GGACGTTCGAGATGACACTGAGAC-ATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG
EST: gi|27584720|gb|CB007415.1|CB007415
EST:     CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAG                         GGAAGATCTGCACCTTGGAAGCATACACTGGAAG
genomic: CGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaattttt ... ataatttcagGGAAGATCTGCACCTTGGAAGCATACACTGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGCACACAAGTGCTTCTCTGACTATAAATGAAAATTACGACTCGGACGTTCGAGATGACACTGAGACATTCCTCAGCAAAATAGTTCCAGAGgttaatttttcccttctgtgcttgctttggcagagtagtttatttgaaaagtgatttttatatggtgtttgattttataatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG