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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAGgtactcacaatcttctagaatctgacatgcatggttgttttgtttcttcacgtgtattgagtgatgagagtctctgttaaaaaatggctag

Basic information

species Arabidopsis thaliana
transcript AT3G09560.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G09560.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os05g38710.1 (Oryza sativa), 5'ss of exon 9
CAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAGgtactcacaatcttctagaatctgacatgcatggttgttttgtttcttcacgtgtattgagtgatgagagtctctgttaaaaaatggctag
||| || || ||||| |||||||| || ||||| ||||||||||| ||||||| |||  | ||||| ||||| || || || || || |||||||||||||||    || |   ||||    | | |   |  | ||   || || |    |||  ||   | | |  |  || ||     |         
CAATCCATTTTATGCTGGATTTGGCAACAGAGATACAGATGAGCTTAGTTACAAAAAGATGGGAATTCCAAAAGGGAAAATCTTTATCATCAACCCAAAGgtatggccattacactag---ttaaaagttagtgatgccatgcttgtat-tgtgccttttttaaagtcatcctgtgcgtgcag--------

upper sequence: AT3G09560.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA10G05320.1 (Glycine max), 5'ss of exon 9
CAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAGgtactcacaatcttctagaatctgacatgcatggt-tgttttgtttcttcacgtgtattgagtga-----tgagagtctctgttaaaaaatggctag
 || || |||||||| |||||||| |||||||| |||||||| || |||||||||||  | |||||||| ||||| || ||||| || |||||||| |||||   ||   |   ||   || |   | |  | || | |||| ||| || |  | |  |  ||||     | |  | || ||  ||  ||  |    
TAATCCATTCTATGCTGGATTTGGCAATAGAGATACAGATGAACTTAGTTACAGAAAGATTGGAATCCCGAAGGGCAAAATATTTATTATCAACCCTAAGgtttgcatcctggactcatatttctgacgattagtatattttatttatttatttcttctttgtgaccaactaaatgcctatgcaaactaacag----

upper sequence: AT3G09560.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G35930.1 (Glycine max), 5'ss of exon 11
CAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAGgtactcacaatcttctagaatctgacatgcatggttgttttgtttcttcacgtgtattgagtgatgagagtctctgttaaaaaatggctag
 || ||||||||||| || ||||| ||||||||||| ||||| || |||||||| ||  | |||||||| ||||| |||||||| || || || || |||||    |   | || ||   | | |||   || ||  |||||||  ||| |      | | | |    |  | |||| ||  ||  |    
TAATCCGTTCTATGCGGGGTTTGGCAATAGAGACACGGATGAACTCAGTTACAGGAAGATAGGAATCCCGAAGGGCAAGATATTTATTATTAATCCTAAGgtgtggat--ttttttatttttttaca---atagtatttttgttagttctcacagggt-actaacagaatgccctgtaaactaacag----

upper sequence: AT3G09560.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA13G19730.1 (Glycine max), 5'ss of exon 9
CAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAGgtactcacaatcttctagaat--ctgacatgcatggttgttttgtttcttcacgtgtattgagtgatgagagtctctgttaaaaaatggctag
 || || ||||| || |||||||| |||||||| |||||||| || |||||||||||  | ||| |||| ||||| || ||||| || |||||||| |||||  |||   |   |    ||  ||||||   |   ||  ||| ||| ||      |  |||   |  | |  |   |   |||| |  |   
TAATCCATTCTACGCTGGATTTGGCAATAGAGATACAGATGAACTTAGTTACAGAAAGATTGGAGTCCCGAAGGGCAAAATATTTATTATCAACCCTAAGgtgttcatcctggacacatatttctgacaattagtatttatttatttattttttctttgtgaccaactaaatgcctag--gaaaactaacag-

upper sequence: AT3G09560.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv08s0040g02800.t01 (Vitis vinifera), 5'ss of exon 8
CAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAGgtactcacaatcttctagaatctgacatgcatggttgttttgtttcttcacgtgtattgagtgatgagagtctctgttaaaaaatggctag
||| || |||||||| || |||||||||||||||||||||||||| ||||| || ||  | || ||||||||||| || ||||| || |||||||| ||||||||         | |  || |  ||||        |  ||    | || | | |||   |  |   | | |   ||  ||  || |   
CAATCCATTCTATGCTGGTTTTGGAAATAGAGACACAGATGAGCTCAGTTATAGGAAGATTGGGATCCCAAAGGGCAAAATATTTATCATCAACCCTAAGgtactt------caccaatatttttcatggcctaccatcctgggattacaagggcattt--tacttgaaattttcatttgaacttgacag-

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|116396577|gb|EG439169.1|EG439169
EST:     ACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAG                         GGAGAAGTGGCAACAGGACATCGCATAGATGTCAAGAAATCTTACACTTCA
genomic: ACAGAAAACTCGGAATCCCAAAGGGAAAGATATTCATAATCAACCCAAAGgtactcacaa ... aaatggctagGGAGAAGTGGCAACAGGACATCGCATAGATGTCAAGAAATCTTACACTTCA