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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaagaacctctttctcagagatttatttgtcttgaaaagtttctatctggtgacgaaatgttctatctgtccag

Basic information

species Arabidopsis thaliana
transcript AT1G36160.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os10g21910.1 (Oryza sativa), 5'ss of exon 10
TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaagaacctctt--tctcagag-atttatttgtcttgaaa-agtttcta--tctggtgacgaaatgttctatctgtccag--------
 || || || |||||||||||| | || || || ||||||||||| || |||||||||||||| |||||||| || || ||||| || |||||||| |||||| |      ||    |||||  | | || ||     |   || |||||  || | || | | |    ||   | ||           
AAATAAGATCCACACTGGTTGGCTAGACAGCAGAATTGCTATGCGTGTTAGAGCTGAGAGGCCCCCATGGTACCTTTCAGTTGTTGGAGGAGCTCTATATgtatgctttgattaacttcagaacaatgatatggtagaaggtagcttctaaatcagatgtcaataccaacttgttttcttatgttgcag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 5'ss of exon 16
TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaagaacctctttctcagagatt--tatttgtcttgaa-aagtttctatctggtga-cgaaatgttctatctgtccag----------------------
 || || ||||| ||||||||| ||||||  ||||| || ||||| ||   |||||||||||||||||||||| | || || || || || ||| | |||||||||    || |  ||   |||   |||| | |  |  || |    |     ||| | | ||||  | |   |  |                       
AAATAAGATTCATACTGGTTGGCTGGATACCAGGATAGCCATGCGTGTTCAAGCTGAGAGGCCTCCATGGTATATTTCAGTCGTTGGAGGGGCTTTATATgtaagacaaactatgccactcattagcatttatgtgaagcaaatgcggaaaacatgatcaatatgtcgtcttatttaaatttatttatttttgtgctgcag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 14
TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaaga--acctctttctcagagatttatttgtcttgaaaagtttctatctggtgacgaaatgttctatctgtccag----------------
 ||||| || |||||||||||| ||||||  || || |||||||| ||   |||||||||||| ||||||||| |||| || || || || ||| | |||||||||  |     |  |   |   | |  | | |||  ||| | || |   |      ||  |   || |     |                
AAACAAGATCCACACTGGTTGGCTGGATACAAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATCTCAGTGGTTGGAGGTGCTTTATATgtaagataaagaaatcataccatgctaacatcttttgtcaagctactgtgaagatcattaagatctaatttaaatcgtcgttacatgctacag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA04G11550.1 (Glycine max), 5'ss of exon 12
TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaag--aacctctttctcagagatttatttgtcttgaaaagtttcta---tctggtgacgaaatgttctatctgtccag----------------
 |||||||||||||| |||||| |||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||| ||||| || || || || |||||||||||  ||| | ||| | | |   || | | | ||||    ||| ||   ||   ||  | |||     | |||| |                  
AAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCGTTGGAGGGGCACTCTATgtaagcaaacttgttttttatatccttttctct-ttgacttttttttagtttcatatggtggaattcatgacctgtgcttcttcctattaatgcag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA06G11120.1 (Glycine max), 5'ss of exon 12
TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaagaacctctttctcagagatttatttgtcttgaaaagtttcta---tctggtgacgaaatgttctatctgtccag----------------
 |||||||||||||| |||||| |||| ||||| ||||| |||||||| ||||| || |||||| | |||||||| || || || || || || ||||||||||| | ||  || |   | |||  ||| ||||| |   || |||   ||   ||  | |||     | |||  |                  
AAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAAAGGCCTGCCTGGTATCTTTCGGTCGTTGGAGGGGCACTCTATgtaagcaacttgtttttt-atattcttttctcttggacttttgctagtttcatatggtggaattcatgacctgcgcttcttccaattaatacag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 13
TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaagaacctctttctcagagatttatttgtcttgaaaagtttctatctggtg-acgaaatgttctatctgtccag----------------------------------------
 || ||||| ||||| ||||||||||| ||||| ||||||||| |||| ||||| || ||||| || |||||||| ||||| || || || ||||| || ||||| ||   | | | |    |   || |  ||  |||| || ||| |  || | |  || |||      |  |                                         
GAATAAAATCCACACCGGTTGGTTGGACAGTAGAATTGCTATGAGGGTTAGAGCAGAAAGGCCGCCTTGGTATCTTTCTGTGGTTGGAGGGGCTCTTTACgtaagcacacatgttttacctgtggtttgggtttctaaaggttttatgttatggaaggcattttcagatactataatttaaataattcacttctattttacactttatcacctcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATgtaagaacctctttctcagagatttatttgtcttgaaaagtttctatctggtgacgaaatgttctatctgtccag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT