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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGGCATGACTTTCCTATAGTTTTTTACCTTGCTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcctatctttttaacattttagtcaagccattctaatttcttgactgttggataataaaagctaatttatcactgatcaagttctgaatattattgcag

Basic information

species Vitis vinifera
transcript Vv08s0105g00590.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G19340.1 (Glycine max), 5'ss of exon 5
GCAGGGCATGACTTTCCTATAGTTTTTTACCTTGCTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcctatctttttaacattttagtcaagccattctaatttct-tgactgttggataataaaagctaatttatcact-gatcaagttctgaatattattgcag
||||||||||| || |||||||| |||||||||||  |||||||| |  | ||||| || ||||| ||||| || ||||||||||||| ||    | |||| |   |  |  |     | || || ||||| |  || |||  || |         || |||| | || ||||||||  || |  ||  ||
GCAGGGCATGATTTCCCTATAGTATTTTACCTTGCAGTGGGTGGAGCCATACTGTCTTATATATATTCTGCGCCTCCTTTAAAGgtagttt----ttttttaattgtcctgattttttctttatattttctatttctcttgcttatt---------ttgatcatttgaccaagttctacatttctttctag

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA18G43310.1 (Glycine max), 5'ss of exon 8
-GCAGGGCATGACTTTCCTATAGTTTTTTACCTTGCTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcctatctttttaacattttagtcaagccattctaatttcttgactgttggataataaaagctaatttatcactgatcaagttctgaatattattgcag
 ||||||||||| || |||||||| |||||||||||  |||| ||| |  | ||||| || ||||| ||||| || ||||||||||||| ||    |  ||  ||  |  |  |       ||   ||||  ||  |||          | | | ||||      ||  |||||||  || |   |  | 
GGCAGGGCATGATTTCCCTATAGTATTTTACCTTGCGGTGGGCGGAGCCCTACTGTCTTATATATATTCTGCACCTCCTTTAAAggtagttt----ttcttaaaatctcctgatttttttctttatattttctgtttgtcttgcctatgatgatcattt------gactaagttctacatttctgtcta-

upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 8
GCAGGGCATGACTTTCCTATAGTTTTTTACCTTGCTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcctatctttttaa-cattttagtcaagccattctaatttct-tgactgttggataataaaagctaatttatcact-gatcaagttctgaatattattgcag
||||||||||| || |||||||| |||||||||||  |||||||| |  | ||||| || ||||| || || || ||||||||||||| ||  | | |||||||   |  |  |     | || || ||||| |  || |||  || |         || |||| | || ||||||||  || |  ||  ||
GCAGGGCATGATTTCCCTATAGTATTTTACCTTGCAGTGGGTGGAGCCCTACTGTCTTATATATATTCCGCGCCTCCTTTAAAGgtagttttttttttttttaaatgtcctgattttttctttatattttctatttctcttgcttatt---------ttgatcatttgaccaagttctacatttctttctag

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|34547700|gb|CF515932.1|CF515932
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTAT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTAT
EST: gi|30252103|gb|CB968742.1|CB968742
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|349830671|gb|FQ416969.1|FQ416969
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|161716004|gb|FC065529.1|FC065529
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAA-TTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351033623|gb|FQ447782.1|FQ447782
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351041270|gb|FQ447397.1|FQ447397
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGTTCCGCCTTTAAAG                         CTCAGACAGAATGGGTGGA----AA-TTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351034199|gb|FQ463133.1|FQ463133
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351025946|gb|FQ427958.1|FQ427958
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351031189|gb|FQ445016.1|FQ445016
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|352791138|gb|FQ477465.1|FQ477465
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTC
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTC
EST: gi|351028530|gb|FQ444811.1|FQ444811
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|349833147|gb|FQ416525.1|FQ416525
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCATTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351014975|gb|FQ444264.1|FQ444264
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351017844|gb|FQ436197.1|FQ436197
EST:     TCTGGGTGGATCTTTGCTGTCCTACATAATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGAAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: TCTGGGTGGATCTTTGCTGTCCTACATA-TACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|110712697|gb|EE087971.1|EE087971
EST:     CTCTGGGTGGATCTTTGCTGTCCTAC-TATACTCTGCTCCGCCTTTAATG                         CTCAAACAGAATGGGGTGGTTTGGAAATTTTGCTCTAAGAACTACCTAAAT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGG-TGGATTGGAAATTTTGCTCTAGGAGCTAGCTATAT
EST: gi|110698374|gb|EE075807.1|EE075807
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|161709250|gb|FC060129.1|FC060129
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|351018561|gb|FQ424668.1|FQ424668
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
EST: gi|349829107|gb|FQ419639.1|FQ419639
EST:     CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAG                         CTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT
genomic: CTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcct ... attattgcagCTCAAACAGAATGGGTGGATTGGAAATTTTGCTCTAGGAGCTAGCTATATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGGCATGACTTTCCTATAGTTTTTTACCTTGCTCTGGGTGGATCTTTGCTGTCCTACATATACTCTGCTCCGCCTTTAAAGgtagcttcctatctttttaacattttagtcaagccattctaatttcttgactgttggataataaaagctaatttatcactgatcaagttctgaatattattgcag

- - - - - - - - - - - - - - - - - - -  GGTGGA