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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcag

Basic information

species Arabidopsis thaliana
transcript AT1G52360.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 20
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaat-tcattagtagtcacttgagagtttggaaaatcaa-----attta-----tgcacctttggttaactgtgtgacaatattttttcctcag-----
|  || |  | |||||||||||||||||||||||||| || || |||||  | |||||||| || ||||||||||| ||| | || || ||  | || ||||| |  |||| |     |||      |||   |   |||     ||| |     || |  |||  ||   || ||||  |  || | | |||       
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTTGGAAAACTGGAAGAATGTCTTCAATTGTTAATCGAAAGgtattgccatttgccaagactatcctatttaatagtacaatgcttattcagaaaatgtattttttattttatg-gtgatcacgttatattctctatacag

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 11
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaat-tcattagtagtcacttgagagtttggaaaatcaa-atttatgca----------cctttggttaactgtg-tgacaatattttttcctcag--
|  || |  | |||||||||||||||||||||||||| || || |||||  | |||||||| || ||||| ||||| ||  | ||||| ||  | || ||||| |  |||| |     |||      |||   |   |||   |||| ||            |||  || |  ||| | ||  ||| || ||   |   
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAACTTGAAGAATGCCTTCAGTTGTTAATCGAAAGgtattgccatttgccaagactatcctatttaatagtacaatgcttattcagaaaatatattttttattttatggtgatcacgttatattctctatacag

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 20
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgta----------------attcattagtagtcacttgagagtttggaaaatcaaa-------tttatgcacctttggttaactgt-gtgacaatattttttcctcag
||||||| ||||||||||| ||||||||||| ||||| || || |||||| |||||||| |||||||||| || || ||  | ||  | ||||| || |||||                ||   ||| || | || | |  ||   || |   |||       || ||     |   |||   ||| |      |||  |||   |||
TTGCAACTCTTGCTAAAGAGCAAGGGAAGAATAATGTTGCATTCCTTTGCTTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcag

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 9
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcag-----------------------------------
||||||| ||||||||||| ||||||||||| ||||| || || |||||| |||||||| |||||||||| || || ||  | ||  | ||||| || ||||| |   |||     |  |      |||    ||| | |||  || ||     |  |   | | |         |      |                                    
TTGCAACTCTTGCTAAAGAGCAAGGGAAGAATAATGTTGCATTCCTTTGCTTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattatttta----ccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagttatgcttttggcag

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaatt-----cattagtagtcacttgagagtttggaaaatca---aatttatgcacctttggttaactgtgtgacaatattttttcctcag
||||| | |||||||||||||| ||||||||||| || ||||| |||||  | |||||| |||||||| ||||||| ||| ||||| | |||||||| ||||||||       ||| |    || || ||     || | |     |  |  | ||| |||||   |   |     |  ||| | |   |||
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgg--gatgatactgaagcattctctttgcag

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 20
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcag---------------------------------------------------------------------------------
|||   |||| |||||| | || |||||||| |||||||| || |||||  |||||| |||||||||| ||||||| ||  | ||| | |||||||||||||||| ||||     |  | |   |   | ||||||||| |      ||   |  || | |        |  | |||   | |                                                                                  
TTGTTTCACTGGCTAAAAAGCAGGGGAAGAATAATGTCGCATTCCTTTGTTTATTCACGCTGGGTAAATTGGAAGAGTGCCTTCAGCTGTTGGTGGAGAGgtaat-cattttccttaccatataaccatagaaaatcaactgctgatac---taatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAACACTTGCTAAAGAACAAGGGAAGAACAATGTCGCCTTTCTTTGCCTATTCATGCTGGGTAAACTGGAAGATTGTTTGCAGTTATTGGTGGAGAGgtaattcattagtagtcacttgagagtttggaaaatcaaatttatgcacctttggttaactgtgtgacaatattttttcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA