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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcag

Basic information

species Arabidopsis thaliana
transcript AT5G18620.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcag
||||||  | || ||||| |  || || ||| | ||  |||| || || ||||| ||||||||||||||| | || ||||| || ||||||||||| ||||||||       | ||||| ||  | |      | ||  |    |   || | ||| ||  ||| ||    |  || |  |      | ||||
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgc------tctatcataccatctc-----actttctgcacacatttgttttcaaacgtgacat--gtctaattagttgtcacatttcag

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA07G38050.1 (Glycine max), 5'ss of exon 22
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctattt------atcaaactctttgttgagatttcattgttattgttt-tattc-----------taatatgatattgacccgatgaa---cttgtgattatcag-------------------
||||||  |||| |||||||  || || ||||| ||| ||||||| |||||||| || |||||||||||| | ||||||||||| || ||||| |||||||| ||| || |||||       |     | ||||   | ||||  || || | |||  | |||           || | || | ||  ||  |   |   |||||| ||                        
GAAGAAGTTGGACCGCTACAAGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGGAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaaatttatttccttttgtttttatttttgcccaaatttatttcttttcgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttttctgacttcacttaaaacttgcag

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 22
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctattt------atcaaactctttgttgagatttcattgttattgttt-tattc-----------taatatgatattgacccgat-gaacttgtg-attatcag--------------------
||||||  |||| |||||||| || || ||||| ||| ||||||| |||||||| || |||||||| ||| | ||||||||||| || ||||| |||||||| |||  | |||||       |     | ||||   | |||   || || |||||  | |||           || | || | ||  ||  |  ||| |  ||  || || |                    
GAAGAAGTTGGACCGCTACAGGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGAAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcag

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 22
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctat-ttatcaaactctttgttgagatttcattgttattgttttattctaatat-gatattgacccgatgaacttgtgattatcag
 |||||  |||| |||||||  || |||||||| ||  ||||||| || ||||| || |||||||||||| ||||||||||||| || ||| | |||||||||  |  | ||| |  |  || | ||| ||    | |   | |   |   | || ||  ||| | | |  |    |    ||    |||  |||
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAATGAAGAATGTGACAGATTCATGgtacaaattttatgtctttcaattttttttttctttctaggtctagctccatcatccttctatcggtttctaaaaaaattgctataaatttacag

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcag
 |||||  |||| |||||||  || |||||||| ||  ||||||| || ||||| || |||||||||||| ||||||| ||||| || ||| | |||||||||  |  | | ||| || |  |||          | |||  |  || | |   | |   |  | ||||   | || || ||           
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaa--tttttttttctaggtct-------agctccatcatccttctatgggtttctaaaaaaattg---ctataaatttacag-------

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 22
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgat--attgacccgatgaacttgtgattatcag----------
||||||  ||||||||||||  || || ||||||||||| ||||| || ||||| || |||||||||||| ||||||||||||| ||||| ||||| |||||  ||  |  | | |||   ||  ||  |  |||   | ||||  ||| || || |   | |||  ||   ||   || | |  ||  |               
GAAGAAGTTGGATCGCTACAAGAATCCATGGCTGGAACTAAAGATCCAGTATGGGCAAAACAAAGGGAAGTTGTACAATGAAGAATGCGATCGTTTTATGgtgagaattgcaatcatctctctagtttgtttgatacaaatgttggtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctccatacttcatgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA