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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGATGTCAAAAAGAAGGTTAACTCTGATTCTGATTCAGACGACGACGAGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatagctcaaaccttattattacctctcaatttgttttattgcattctttagattctgaatattctgaatttctgtttcctcag

Basic information

species Arabidopsis thaliana
transcript AT4G21660.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G31350.1 (Glycine max), 5'ss of exon 1
AGAAGATGTCAAAAAGAAGGTTAACTCTGATTCTGATTCAGACGACGACGAGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatagc----tcaaaccttattattacctc--tcaatttgttttattg--catt-ctttagattctg--aatattctgaa---tttctgtttcctcag
 ||  |||  |  |  ||    ||  | || || ||||| || || || ||  | | |||| || | ||||||||||||||||| || ||||||||||||||||||     |  ||  || |||||   |   |   |||| |  |||    ||  | ||   ||||     ||| || ||   ||| | | | |||||
CGAGAATGCAACTACCAATAAGAAAGCAGACTCGGATTCTGAAGAGGAAGAAAACGTTAATGAGCAAAAAGAGAAAGGCATCTCAAACAAGAAGAAAAAGgtatagtgatttgtaatgtttttatttatttattttgtttgctcaattaactatcacattcccttctactgttatgctaaaagttttatttgttctcag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G25110.2 (Glycine max), 5'ss of exon 3
AGAAGATGTCAAAAAGAAGGTTAACTCTGATTCTGATTCAGACGACGACGAGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatagc----tcaaaccttattattacctc--tcaatttgttt-----------tattgcattctttagattctgaatattctgaatttctgtttcctcag
 ||  |||  |  |  ||    ||  | || || ||||| || || || ||  | |||||| || | ||||||||||||||||| || ||||||||||||||| ||     |  ||  |  |||||   ||  | | |||||||           |||| ||||  ||         ||  |   | |||   | |  ||||
TGAGAATGCAACTACCAATAAGAAAGCAGACTCGGATTCTGAAGAGGAAGAAAATGATAATGAGCAAAAAGAGAAAGGCATCTCAAACAAGAAGAAAAAGgtacagtggtttgtaatgtatttatttattcatttattttgtttgctcaattaactattacatttctttctacagttatgctaaaagttttattgtgttcag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G07760.1 (Glycine max), 5'ss of exon 3
AGAAGATGTCAAAAAGAAGGTTAACTCTGATTCTGATTCAGACGACGACGAGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatagc---tcaaaccttattattacctctca-------atttgttttattgcattctttagattctg---aatattctgaatt---tctgtttcctcag----
|||| |||     |  ||    ||  ||||||||||||| || || || ||  | |||||| || | ||||||||||||||||| || |||||||||||||| |||    |   | ||| || ||   | ||        |||  |||| |    || | |   || ||   | |||||| || |   | | |||  |       
AGAAAATGCAGCTACTAATAAGAAGGCTGATTCTGATTCTGAAGAGGAAGAAAACGATAATGAGCAAAAAGAGAAAGGCATCTCAAACAAGAAGAAAAAGgtgtagtaatttgtaacttgtttttttttttcttctgtttattcattttttactgttgtcttccttttgataattattctaaaataactttatttttttgttcag

upper sequence: AT4G21660.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G31550.2 (Glycine max), 5'ss of exon 3
AGAAGATGTCAAAAAGAAGGTTAACTCTGATTCTGATTCAGACGACGACGAGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatag----ctcaaaccttattat-tacctctcaatttgttttattgcattct--ttagattc-------tgaatattctgaa-----tttctgtttcctcag-----
|||| |||    ||  ||    ||  || |||||||||| || || || ||  | |||||| || | ||||||||||||||||| || |||||||||||||| |||     |  ||| | |||||  || | |   | |||||  |    || |  ||   |||       | | |||||| ||     ||| | |||  |  |     
AGAAAATGCAGCAACTAATAAGAAGGCTAATTCTGATTCTGAAGAGGAAGAAAACGATAATGAGCAAAAAGAGAAAGGCATCTCAAACAAGAAGAAAAAGgtgtagtaatttgtaacatgattatacacattttcttctgtttattcattttttacttgtcttccctttgataattattctaaaaaaagtttattttttttttgttcag

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|301501195|gb|HO206735.1|HO206735
EST:     AGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAG                         CTTCAACGGAGAATGAAGATTGCTGAGCTGAAGCAGGTTTCCGCTAGGCCT
genomic: AGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatagctca ... gtttcctcagCTTCAACGGAGAATGAAGATTGCTGAGCTGAAGCAGGTTTCCGCTAGGCCT
EST: gi|86070989|gb|DR366746.1|DR366746
EST:     AGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAG                         CTTCAACGGAGAATGAAGATTGCTGAGCTGAAGCAGGTTTCCGCTA
genomic: AGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatagctca ... gtttcctcagCTTCAACGGAGAATGAAGATTGCTGAGCTGAAGCAGGTTTCCGCTA
EST: gi|125242052|gb|EL256137.1|EL256137
EST:     AAGAAGAAAAAG                         CTTCAACGGAGAATGAAGATTGCTGAGCTGAAGCAGGTTTCCGCTAGGCCT
genomic: AAGAAGAAAAAGgtatagctca ... gtttcctcagCTTCAACGGAGAATGAAGATTGCTGAGCTGAAGCAGGTTTCCGCTAGGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGATGTCAAAAAGAAGGTTAACTCTGATTCTGATTCAGACGACGACGAGCAGGATAATCAGAACAAAGAGAAAGGCATCTCTAATAAGAAGAAAAAGgtatagctcaaaccttattattacctctcaatttgttttattgcattctttagattctgaatattctgaatttctgtttcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA