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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgcttatgctgtactgatgttattatagcacaaataagtatctgcataggtcagtattcaggatattcacttagacattcaatgtttgccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC

Basic information

species Vitis vinifera
transcript Vv00s0282g00040.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 11
agttgcttatgctgtactgat--gttattatagcacaaataagtatctgcataggtca--gtattcaggatattcacttaga--cattcaatgtttgcca-tcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC
       ||  | || ||| |   |    |  |    | ||  |||     |   |||   |  |  | ||||  | |||    | ||  ||  |||  | | | |||  || || || ||||||||||| |||||||| |||||||||||||| ||  |||||||||||||||| ||||||||||| || || ||||||||||| |
-------taaacagtgctggtcaatgggaacggagggagtatatattgatttttctcatcctgatatgcatatctaattaatttcttttgattgttgtaacttgtagGCCCCAGTAAACTATGTATGCCTTCATTGTGTAAAACCAAGTTTGCGGCCATTATCAATGGCTATGTCAACTGTTGCAATCCATATATTTGGTGATGTGC

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G06880.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------------agttgctta--tgctgtactgatgttattatagcacaaataagtatct------gcataggtca-gtattca--ggatattcac---ttagacattcaatgtttgccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC
                                                                     |||   | |  | ||||  |   ||  |  |     || | |||||||       | || || |  |  | |  | ||  | |    | ||  ||   ||  ||  | |   |||| ||||| ||||||||||| ||||||||||| |||||||||||| | ||||| || |||||||||||||||||||| ||||| || ||||| ||||| |
gtaattcacttcctcatgtttacctttttatagtaagacatgctagactatataggtgcttatcatgttagtatttcaactactgtgtttgagtattcctttattaactgagtatcttgaagttcctaagttatattcttaatgaattattatatttcagtgatcttataattttctttttagGGTCCTGTGAATTATGTATGTCTCCATTGTGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTGC

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA07G30370.1 (Glycine max), 3'ss of exon 13
-----------------------------------------------------------------------------------------------agttgcttatg-ctgtactgatgttattatagcacaaataagtatctg-cataggtcagtattcaggatattcacttagacattca-atgtttgccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC
                                                                                                  ||  | || || | |   |||||    || |     || |  ||  | ||  |   || | |     |    ||    ||||  ||  ||  | |   |||| ||||| ||||||||||| ||||||||||| |||||||||||| | ||||| || |||||||||||||||||||| ||||| || ||||| ||||| |
gtaattcacttctctgtgaagaagatttcctcatgtttgccttattatagtaagacatgctaaactatatgtacttataatgttagtatttcaactactgtgtttgactattcctctgttagctgagtatcttgaaatccctaacttatattcttaatgaactattatgtttcagtattcttataattttctttttagGGTCCTGTGAATTATGTATGTCTCCATTGTGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTAC

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G32670.1 (Glycine max), 3'ss of exon 13
agttgcttatgctgtactgatgttattatagcacaaataagtatctgcataggtcagtattcaggatatt--cacttagacattcaat---gtttgccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC
     || || ||  | || ||||  | | | |  |||   | | |     | |||| | |  | |  ||  |||| | |  ||   |     ||  | |  ||||| ||||| ||||||||||| || | |||||| |||||||||||| | || ||||| |||||||||||||||||||  ||||| || ||||| ||||| |
-agaactaat-ctaaattgttgttcct-tggaaagaatt--tctgtaacctgatcagaagttggaagttttgcactcaaagttttgcttggaattttcttttcagGGTCCTGTGAATTATGTATGTCTACGTTGTGTTAAACCAAGTTTGAGGCCTCTATCTATGGCTATGTCTACTGTTGTTATTCATATCTTTGGCGATGTAC

upper sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G06660.1 (Glycine max), 3'ss of exon 13
agttgcttatgctgtactgatgttattatagcacaaataagtatctgcataggtcagtattcaggatattcacttagacattcaatgtttgccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC-----------------------------
                            || | |  ||  | |  || | || |  | | | |  || ||  |||       |||| ||     |    ||| ||||| |||||||||||  | | |||||| | |||||||||| | || ||||| |||||||||||| ||||||| ||||| || ||||  ||||| |                             
---------------------------gtaac-ctgatcggaagttgaa-agttttgcactaa--atgtttgcttg------caattttc----ttttcgggtcctgtgaattatgtatgtttacgttgtgttataccaagTTTGAGGCCTCTATCTATGGCTATGTCTGCTGTTGCTATTCATATATTTGTAGATGTACCTTCCTCGCCTCTTGTTGGAGTTCTCCAG

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|22011957|gb|BQ796991.1|BQ796991
EST:     GTTTCCTAGCTCTTTTCTCAATTGGTGAATTACTCGTTTTTGCTACTCAG                         GGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCG
genomic: GTTTCCTAGCTCTTTTCTCAATTGGTGAATTACTCGTTTTTGCTACTCAGgtaatttcat ... gccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCG
EST: gi|110376483|gb|EC941548.1|EC941548
EST:     GTTTCCTAGCTCTTTTCTCAATTGGTGAATTACTTGTTTTTGCTACTCAG                         GGTCCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCG
genomic: GTTTCCTAGCTCTTTTCTCAATTGGTGAATTACTCGTTTTTGCTACTCAGgtaatttcat ... gccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCG
EST: gi|71871367|gb|DT020422.1|DT020422
EST:     GTTTCCTAGCTCTTTTCTCAATTGGTGAATTACTTGTTTTTGCTACTCAG                         GGTCCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCG
genomic: GTTTCCTAGCTCTTTTCTCAATTGGTGAATTACTCGTTTTTGCTACTCAGgtaatttcat ... gccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcataggtcagtattcaggatattcacttagacattcaatgtttgccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC
                    atattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgcttatgctgtactgatgttattatagcacaaataagtatctgcataggtcagtattcaggatattcacttagacattcaatgtttgccatcgcagGGACCTGTCAATTATGTATGCCTCCATTGTGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTC

- - -cttatgc
- - - - - - - - ctgatgt
- - - - - - - - - - - - - - - -cacaaat
- - - - - - - - - - - - - - - - - - - - - - -tgcatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcaa