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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgtaatttttctttattctgagctaccaaaatgatattgtgatgcaaatagcctaacaagtttctactgtgcag

Basic information

species Arabidopsis thaliana
transcript AT3G13470.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgtaatttttctttattctgagctaccaaaatgatattgtgatgcaaatagcctaacaagtttctactgtgcag-------------------
 || ||||||||||| |||||||| ||||| ||||||||||||||||| || ||||| || ||||| |||||||||||||  || ||||| || |||||||||  ||     |   |  |  ||||       |||  || |  ||   |  |  ||  ||  || ||  |                     
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcagcctgagcacacatacccctgctgtatgctgctttaatctgttt--cagtttcttattgcactatgtttccactatttttcag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 6
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgt---aatttttctttattctgagctaccaaaatgatattgtgatgcaaatagcctaacaagtttctactgtgcag-----------------------------
 || |||||||| || |||||||||||||| || || ||||| || || |||||||| || |||||||| |||||||| || |||||||| |||||||||||   |    ||||  | |  |   |||  |||   |    | |  || |||  || |   ||     || ||||                              
TCTCTATGTTGTTGAGGGAATGCAATTTGATCGCGGCTATATTTCTCCCTACTTTGTAACTGACAGTGAAAAAATGTCAGTGGAGTATGAGAATTGCAAGgtttgatgcattctagaattcggtgtacttaaactgtgcattaac-cagata--ctcatttgtgggctctatgcatttgatgctaatgttgattctatcacccag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgtaatttttctttattctgagctaccaaa--atgatattgtgatgcaaatagcctaacaagtttctactgtgcag-------------------------------------------------------------------------------------------------------------
 || ||||||||||| ||||||||||||||||||||||| ||||| || |||||||| |||||||||||||||||| |||  ||||| || || |||||||||| | |    |||   ||| || |||    |  | || || ||   || || |  |  ||||| |  |   |                                                                                                              
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatat---gagatatcaattcttttttttttgctgtttattgctttcct-gtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 6
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGg--taatttttctttattctgagctaccaaaatgatattgtgatgc-aaatagcctaacaagtttcta------ctgtgcag---------------------------
||| |||  ||| || |||||||| ||||||||||| ||||| || || ||||||||||| |||||||| |||||| | || |||||||| || |||||||  | ||  | |  |         ||| ||||  ||  |||  ||| |  |||    |  ||||| ||      |||| |                             
CCTCTATTCTGTTGAGGGAATGCAGTTTGACCGTGGCTATATTTCTCCCTACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAGgtttgatgctccccttcatcattgtactaaaa--attctgtagtgctatctagtaatagcagtttttatgacttctgtacgcttacggtgattttaattctattaccag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 5
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgtaatttttctttattctgagctaccaaaatgatattgtgatgcaaatagcctaacaagtttctactgtgcag--------------
 || |||||||| || || |||||||| |||||||||||||| || |||||||| || || ||||||||||||||| ||||||||||||| || || ||||| |    | | | |  |   |   | || |  |||| |    ||    |  ||   | ||    || |  |               
TCTGTATGTTGTTGAGGGGATGCAATTCGACCGTGGTTATATTTCTCCATACTTCGTTACTGACAGTGAGAAAATGGCTGTTGAGTATGAGAACTGTAAGgtgagacatttgtctgttttccctgcgaattattattttttaacatcctgtgtatttacttatagctttatatggtatgttatgcag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 5
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgta----atttttctttattctgagctaccaaaatgatattgtgatgcaaatagcctaacaagtttctactgtgcag--------------
 || |||||||| || || ||||||||||||||||||||||| || ||||||||||| || ||||||||||||||| | ||||| ||||| || || |||||     |||| ||| | |||   |  ||     |  |||| |    ||     | ||   | ||   ||| | ||               
TCTATATGTTGTCGAGGGGATGCAATTTGACCGTGGTTATATTTCTCCATACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGgtgtgacatttgtctgttttccctgtaacttgt-tattattttttaacatccttcatatttaattataactttacatggtatgttatgcag

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 6
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgta---atttttcttt--attctgagctaccaaaatgatattgtgatgcaaatag---cctaacaagtttctactgtgcag---------------
||| |||||||| |||||||||||||||||||||||||||||||| || |||||||| || || |||||||||||| | ||||| |  || || ||||||||    |||| ||||   |||  |     | || ||| || |    ||||| | |   | |      ||||||     ||                
CCTGTATGTTGTTGAAGGAATGCAATTTGACCGTGGTTATATCTCACCTTACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcatttctcttataatttaggagagctaatatggtacttc--tgcaagttggttctttctggctttctaactgacaaattttgttcatgtag

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|125193743|gb|EL208697.1|EL208697
EST:     TCTGTTGAGTATGACAATTGCAAG                         TTGGCTTCTTGTTGACAAGAAAGTAACCAATGCAAGGGATCTTGTTGGGGT
genomic: TCTGTTGAGTATGACAATTGCAAGgtaatttttc ... tactgtgcagTT-GCTTCTTGTTGACAAGAAAGTAACCAATGCAAGGGATCTTGTTGGGGT
EST: gi|124835757|gb|EH920196.1|EH920196
EST:     TGAGAAAATGTCTGTTGAGTATGACAATTGCAAG                         TTGCTTCTTGTTGACAAGAAAGTAACCAATGCAAGGGATCTTGTTGGGGTT
genomic: TGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgtaatttttc ... tactgtgcagTTGCTTCTTGTTGACAAGAAAGTAACCAATGCAAGGGATCTTGTTGGGGTT