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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgttttttttccaatctgataagtggaacatcaattgagtttcttctgtctagttgattgtatatgtttgttatttgcatttatagtctgtctattattttttaatcatttgctatcttcccccaaagtgaaccatgaacatttaattgatttcctgtttttcttttggggtgggggtttgcag

Basic information

species Vitis vinifera
transcript Vv04s0008g05090.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g05090.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA04G07300.1 (Glycine max), 5'ss of exon 2
GTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgttttttttccaatctgataagtggaacatcaattgagtttcttctgtctagttgattgtatatgtttgttatttgcatttatagtctgtctattattttttaatcatttgctatcttcccccaaagtgaaccatgaacatttaattgatttcctgtttttcttttggggtgggggtttgcag
 |||||    ||  | ||||  ||||||||||||||||||||  |||| | | | |||||||| || ||||| |||||  ||||||| ||||||||||||||| | |||| ||     ||| ||  ||  |  ||  ||   |   ||| ||    ||| |    || |  |    |||| |  | | ||                                                                                                  
TTGATAAATTAAGGCAAAGACGATGACCAAGAAGAAGAATCCCCTGGTGTTTATGGATGTGTCCATCGATGGGGATCCTGTTGAAAGGATGGTTTTTGAGgtact-ttttgttcttgttcttat--gtttactatttatgccgcaacttttgcaatgttca----atctaatgaacatttcctctcacag--------------------------------------------------------------------------------------------------

upper sequence: Vv04s0008g05090.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA06G07380.1 (Glycine max), 5'ss of exon 1
GTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgttttttttccaatctgataagtggaacatcaattgagtttcttctgtctagttgattgtatatgtttgttatttgcatttatagtctgtctattattttttaatcatttgctatcttcccccaaagtgaaccatgaacatttaattgatttcctgtttttcttttggggtgggggtttgcag
                      ||||| ||||||||||||||  |||| | | | |||||||| || ||||| |||||  ||||||| ||||||||||||||| | |||| ||     ||||||  ||| |  ||  ||   |   ||| ||    ||| |    || |  |     ||| |  | | ||                                                                                                  
----------------------ATGACTAAGAAGAAGAATCCCCTGGTGTTTATGGATGTGTCGATCGATGGGGATCCTGTTGAAAGGATGGTTTTTGAGgtagt-ttttgttcttgttctgat--gtgtactatttatgctgcaacttttgcaatgttca----atctaatgaacgtttcccctcacag--------------------------------------------------------------------------------------------------

upper sequence: Vv04s0008g05090.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA06G07380.2 (Glycine max), 5'ss of exon 2
GTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgttttttttccaatctgataagtggaacatcaattgagtttcttctgtctagttgattgtatatgtttgttatttgcatttatagtctgtctattattttttaatcatttgctatcttcccccaaagtgaaccatgaacatttaattgatttcctgtttttcttttggggtgggggtttgcag
 |||||    ||  | ||||  ||||| ||||||||||||||  |||| | | | |||||||| || ||||| |||||  ||||||| ||||||||||||||| | |||| ||     ||||||  ||| |  ||  ||   |   ||| ||    ||| |    || |  |     ||| |  | | ||                                                                                                  
TTGATAAATTAAGGCAAAGACGATGACTAAGAAGAAGAATCCCCTGGTGTTTATGGATGTGTCGATCGATGGGGATCCTGTTGAAAGGATGGTTTTTGAGgtagt-ttttgttcttgttctgat--gtgtactatttatgctgcaacttttgcaatgttca----atctaatgaacgtttcccctcacag--------------------------------------------------------------------------------------------------

upper sequence: Vv04s0008g05090.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA14G14970.1 (Glycine max), 5'ss of exon 2
GTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgttttttttccaatctgataagtggaacatcaattgagtttcttctgtctagttgattgtatatgtttgttatttgcatttatagtctgtctattattttttaatcatttgctatcttcccccaaagtgaaccatgaacatttaattgatttcctgtttttcttttggggtgggggtttgcag
 | ||   | |    |      ||| | ||||||||||||||  |||| | | | |||||||| || ||||| |||||  ||||||| ||||||||||||||| | |||||| ||   | |   || ||     |  | ||| | | |   ||   |||    |||| || |  | || |  |||  | ||| || | ||   | | |                                                                                
ATAATTAAGCAGGTGTGGAGCGATGGCAAAGAAGAAGAATCCGCTGGTGTTTATGGATGTGTCCATAGATGGTGATCCTGTTGAAAGGATGGTTTTTGAGgtacttttttttatc---tttatgaattgtcggttttaatga-tgtatgaagtaatgtttgcagtatttgatc-tcatcta-attcttggtc-gttt-ttccctctcag-------------------------------------------------------------------------------

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|110687168|gb|EE064342.1|EE064342
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|34544006|gb|CF512238.1|CF512238
EST:     GTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: GTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|30295674|gb|CB972468.1|CB972468
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|352777331|gb|FQ473965.1|FQ473965
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|34543917|gb|CF512149.1|CF512149
EST:     TCTATTGATGGAGA--GATATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: TCTATTGATGGAGATCCA-ATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|34550009|gb|CF518241.1|CF518241
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|34550884|gb|CF519098.1|CF519098
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|352765311|gb|FQ466008.1|FQ466008
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|26262030|gb|CA813093.1|CA813093
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|352772302|gb|FQ469827.1|FQ469827
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
EST: gi|110723917|gb|EE099287.1|EE099287
EST:     ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAG                         CTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT
genomic: ATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgtttt ... gggtttgcagCTGTTCTCTGATGTTGCTCCCAAGACTGCAGAAAATTTTCGTGCACTCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAGATCCAATTGAAAGAATGGTTTTTGAGgtattgttttttttccaatctgataagtggaacatcaattgagtttcttctgtctagttgattgtatatgtttgttatttgcatttatagtctgtctattattttttaatcatttgctatcttcccccaaagtgaaccatgaacatttaattgatttcctgtttttcttttggggtgggggtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA