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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgtttttttattttttttccttctcactgttttattttaaattttatatgttgggtgatctcttattttctaggatcattatttgtttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGTTCTTTTATTAATGGATCCTTGGTGATATTCCGTTTAGCACCACAG

Basic information

species Vitis vinifera
transcript Vv12s0055g00710.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00710.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 14
-----attttgtttttttattttttttccttctcactgttttattttaaattttatatgttgggtgatctcttattttctaggatcattatttgtttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGTTCTTTTATTAATGGATCCTTGGTGATATTCCGTTTAGCACCACAG
     | | ||   | | || |  ||  |||||| || |  | |||| || ||||| | |  |   |         || | |||| |||  ||||| ||   |||||||| ||||||||  |||||||||||||||| |||||||| || || ||| ||||| || ||||| |  ||||||| |||||||| |||||||||
cctaaaatatgggatat-atctcattctcttctc-ctttaatcttttcaactttatgtat--gccaactgaagtgcttttgggattatttgttgttacttt-tagGGTCGAAAGTTTTCAGTTCAAGGTCTTTTGGGGAAAGAAATGTGTTCCAGTGCTTTTGTTGATGGACCAATGGTGATTTTCCGTTTGGCACCACAG
















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|32247401|gb|CD713220.1|CD713220
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAG                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
EST: gi|32269098|gb|CD718257.1|CD718257
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAG                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
EST: gi|32249664|gb|CD715483.1|CD715483
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAG                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
EST: gi|30327654|gb|CD010916.1|CD010916
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAG                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
EST: gi|110703791|gb|EE080956.1|EE080956
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAA                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
EST: gi|32249812|gb|CD715631.1|CD715631
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAG                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
EST: gi|32270392|gb|CD719551.1|CD719551
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAG                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
EST: gi|30325758|gb|CD009020.1|CD009020
EST:     GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAG                         GGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT
genomic: GTCTAACGGCATTTAAATCTGTTGAAGATTCTCTAAGATTTTGGATTAAGgtattatctg ... ttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatatgttgggtgatctcttattttctaggatcattatttgtttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGTTCTTTTATTAATGGATCCTTGGTGATATTCCGTTTAGCACCACAG
                                     ttatttgtttctcc  CT-rich tract
                                 atcattatttgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgtttttttattttttttccttctcactgttttattttaaattttatatgttgggtgatctcttattttctaggatcattatttgtttctccatagGGTCGGAAGTTTTCGATTCAAGGTCTTTTGGGAAAAGAAATATGCTCTAGTTCTTTTATTAATGGATCCTTGGTGATATTCCGTTTAGCACCACAG

- - - - - - - - - - - ccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgggtg