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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCTTGTTTACCTACCTAGGCTTATATCTGATGAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactcaagtgacaagtgacaacaaatagcatgaattacgtcttttattttgctgatggcatgaatttgtattattatcattttgatctttttttcctgttccaattctgttattcag

Basic information

species Vitis vinifera
transcript Vv05s0062g01250.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 13
GTCTCTTGTTTACCTACCTAGGCTTATATCTGATGAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactcaagtgacaagtgacaacaaatag-catgaattacgtcttttattttgctgatggcatgaat-ttgtattattatcattttgatctttttttcctgttccaattctgttattcag
| || ||  ||||||| || |   | |  |||||| | ||||||||||||||||| || || || ||||||||||||||  |||||||  |      |      |   | || | |  |||| |||   | | || |||| ||      |||| | ||   | |||   | |     ||    |   | |  |  | | |        
GCCTTTTCCTTACCTATCTTGCGCTCTTCCTGATGGACGGGCATGGTCAACCTGCGCTGCTGTACCTTGTTCCATGTACATTAGgtaagtatatgcatcgttcctt-tagcacacaatcatggattgtttttattctttt-ctttccatatgactcttaagtcattgcaagtgacgactcccatgtatttctcgttccag--------

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA08G47600.1 (Glycine max), 5'ss of exon 12
GTCTCTTGTTTACCTACCTAGGCTTATATCTGATGAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactcaagtgacaagtgacaacaaatagcatgaattacgtcttttattttgctgatggcatgaatttgtattattatcattttgatctttttttcctgttccaattctgttattcag
| ||| | || || ||  | ||  ||||||||||||||||  |||| ||||||||||| ||||| ||||||||||| || ||||||||| | |    ||   |      |    ||  |||  |  |||| || | ||          ||  || | | | ||   || ||  |||                              
GCCTCGTTTTGACATATATGGGACTATATCTGATGAATGGAAATGGACAACCTGCACTTCTCTACCTTGTTCCATGCACACTAGgtaactagttttttgctgaaattagatgcgta--atggttctcgtcgttaagttaa--------atctatctatctcatgcccaatt-aatcaacag-------------------------

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA10G44490.1 (Glycine max), 5'ss of exon 13
GTCTCTTGTTTACCTACCTAGGCTTATATCTGATGAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactcaagtgacaagtgacaacaaatagcatgaattacgtcttttattttgctgatggcatgaatttgtattattatcattttgatctttttttcctgttccaattctgttattcag
| ||||| || || || || ||  ||||| ||||||| || ||||| ||||||||||| ||||| || ||||||||||| ||||||||| |   |  |      |    |  |   |    | |||  |   ||   |     |    |||||                                                     
GCCTCTTCTTCACATATCTGGGGCTATATATGATGAACGGTCATGGACAACCTGCACTGCTCTACCTGGTTCCATGTACACTAGgtaactaactagttttgtgcttttgatcaggtgtgc-atttatatagcttgcctgatcca-attatgaacag--------------------------------------------------

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA18G53880.1 (Glycine max), 5'ss of exon 12
-GTCTCTTGTTTACCTACCTAGGCTTATATCTGATGAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactcaagtgacaagtgacaac-aaatagcatgaattacgtcttttattttgctgatggcatgaatttgtattattatcattttgatctttttttcctgttccaattctgttattcag
 | ||| | || || ||  | ||  |||| |||||||| ||  |||| ||||||||||| ||||| |||||||||||||| ||||||||  | |    |      |       ||||   |||  | | |  | |  |  |     |    | ||| | | | ||   || ||  |||                              
GGCCTCGTTTTGACATATTTGGGACTATACCTGATGAACGGAAATGGACAACCTGCACTTCTCTACCTTGTTCCATGTACACTAGgtaattagttttttttttttttttgctgaaattagatgcgtaatggttctcgtcgtttaagt----taaatctatctcatgcccaatt-aatcaacag-------------------------

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA20G39260.1 (Glycine max), 5'ss of exon 12
GTCTCTTGTTTACCTACCTAGGCTTATATCTGATGAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactcaagtgacaagtgacaacaaatagcatgaattacgtcttttattttgctgatggcatgaatttgtattattatcattttgatctttttttcctgttccaattctgttattcag
| ||||| || || || || ||  ||||| ||||||| || ||||| ||||||||||| || || || ||||||||||| ||||||||        || || |||         ||| || |  |  || |    || |   | | |  |||  |   |||||   ||                                      
GCCTCTTCTTCACATATCTGGGGCTATATATGATGAACGGTCATGGACAACCTGCACTGCTGTACCTGGTTCCATGTACACTAGgtaa-------ggtaactagttttgtgctttag-ataaggtgggtgtgcatttatatagcttgtctgatatccaattatggacag-------------------------------------

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|110367857|gb|EC931810.1|EC931810
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|30128129|gb|CB913468.1|CB913468
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|30137132|gb|CB922470.1|CB922470
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|71889453|gb|DT038508.1|DT038508
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGATAAGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|71882115|gb|DT031170.1|DT031170
EST:     GCATGGTCAACCTGCACTCCTCTATCTTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GCATGGTCAACCTGCACTCCTCTATC-TTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|110688633|gb|EE067409.1|EE067409
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|110696700|gb|EE073044.1|EE073044
EST:     CAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: CAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|110420095|gb|EC986356.1|EC986356
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|110731688|gb|EE106318.1|EE106318
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTANGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|110415004|gb|EC980872.1|EC980872
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|110395316|gb|EC960974.1|EC960974
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
EST: gi|110697095|gb|EE073781.1|EE073781
EST:     GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAG                         GTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG
genomic: GAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactc ... tgttattcagGTGTCACTATTATTTTGGGTCTGATGAGGGGTGAGCTAGGTCATCTATGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTCTTGTTTACCTACCTAGGCTTATATCTGATGAATGGGCATGGTCAACCTGCACTCCTCTATCTTGTTCCATGTACTCTAGgtaacaactcaagtgacaagtgacaacaaatagcatgaattacgtcttttattttgctgatggcatgaatttgtattattatcattttgatctttttttcctgttccaattctgttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC