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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAGgtacaaatggaatcaacaccaacaatatttagaaaagaaaagaaatccttctataaatgccatttcttcctctacagttttttttttctttctttttttt...

Basic information

species Vitis vinifera
transcript Vv14s0066g02540.t01
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 24
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAGgta--caaatggaatcaacaccaacaatatttagaaaagaaaagaaatccttctataaatgccatttcttcctctacagttttttttttctttctttttttt
|||||| ||| |||| |||||||||||||| || |||| | |||| |||||||||||||||||||| |||   ||    ||    |   |     ||||            ||||  ||  || ||||  | |  |     |   |  |          || | ||   
ATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAgtaaggaaccttaacgttctgtacttccatttgatctctcttttaaat--ttgcatgaatgttactgatggacttcttgagtagccacgaagtcatattgac

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA19G02260.1 (Glycine max), 5'ss of exon 22
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAGgtacaaatggaatcaacaccaacaatatt-tagaaaagaaaagaaatccttctataaatgccatttcttcctctacagttttttttttctttctttttttt
||||||||||||||||||||||||||||||||||||||  || |||||||||||||||||||||||||||   |          |   | |||  | |  ||   ||||   ||     |  ||  |  ||         |  | |     |    |||  |  | | 
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGGACTTGATGAGCTTTTCAAAGTTGCTCAGgtatgtagaagtgtgttagggaaaattctgtccaactcaaaaatgatttgatttgaagagagatgagagagaatgaaatcgagatcaagtttgatgatct-

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA13G05060.1 (Glycine max), 5'ss of exon 38
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAGgtacaaatggaatcaacaccaacaatatt-tagaaaagaaaagaaatccttctataaatgccatttcttcctctacagttttttttttctttctttttttt
||||||||||||||||||||||||||||||||||||||  ||  ||||||||||||||||||||||||||   |          |   | |||  | |  ||   ||||   ||     |  ||  |  ||         |  | |     |              | 
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGGACTTCATGAGCTTTTCAAAGTTGCTCAGgtatgtagaagcgtgttagggaaaattctgtccaactaaaaaatgatttgatttgaagagagatgagagagaatgaaatcgagatcaaagagagagagat-

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 22
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAGgtacaaatggaatcaacaccaacaatatttagaaaagaaaagaaatcctt----ctataaatgccatttcttcctctacagttttttttttctttctttttttt
||||||||||||||| ||||| ||||||||||||||||   |||||||||||||||| ||||||||||||    ||  |        |   | ||||       |  |||| | |||    || || | | ||      ||      | |||   |    ||  | |  ||
ATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAGgta----tgagagttctgttagggaaatttgtgctcaagtagaactacttgagcctgtataagacagactgaccaggcaggatttgaatccacttgatatactt

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 24
lower sequence: GLYMA18G49000.1 (Glycine max), 5'ss of exon 24
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAGgtacaaatgga--atcaacaccaacaatatttagaaaagaaaagaaatccttctataaatgccatttcttcctctacagttttttttttctttctttttttt
||||||||||||||| ||||| ||||||||||||||||   |||||||||||||||| ||||||||||||  |  |     | |     |    |  | | | |  |  |      | | |||||  ||    |   |    |   |||   |   |||  | |  || 
ATATGATCTCTTGCATAATGCCCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAGgtatgagagttctgttagggaaatttgtgctcaaatagaactacttgagcctgtataag-gcaggctgaccaggcaggatttgaatccacttgatatactt-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAGgtacaaatggaatcaacaccaacaatatttagaaaagaaaagaaatccttctataaatgccatttcttcctctacagttttttttttctttctttttttt

- - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc