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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctccttttccatatttcccgatctgggtcatgtaaagatgtctcttttatatactattatatcgtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCTTATAGTTGATTCTGGTAGTACTGTTACTTATGTTCCTTGTTCTGATTGT

Basic information

species Arabidopsis thaliana
transcript AT3G50050.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G21800.1 (Glycine max), 3'ss of exon 1
----------------------------------------gtaatctccttttccatatttcccgat--ctgggtcatgtaaagatgtctct---tttatatactattatatcgtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCTTATAGTTGATTCTGGTAGTACTGTTACTTATGTTCCTTGTTCTGATTGT
                                         |  ||| ||| | | | ||   || |   |   |||      | |   ||    ||| | |   |||  || || ||| |||||||||||| ||| |||||||||| ||||| || || || ||||||||||| || |||||| | || || |||||||| |||||||| || ||   ||| 
gtaaaaacctattacgtcgtcgtttaacgcgctttctttcttcttcttcttcttcttcttcttcgcttcttaaatcaaaattcggtaattcgagatttgtgtga-attgaatggtttttttagGTATTACACGACGCGGCTTTGGATCGGTACTCCTCCGCAGATGTTTGCTCTCATTGTTGATACGGGGAGCACTGTTACGTATGTTCCGTGCTCCACTTGC

upper sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G05490.1 (Glycine max), 3'ss of exon 1
----------------------------------gtaatctccttttccatatttcccgatctgggtcat----gtaaagatgtctcttttatatactat--tatatcgtattt-gtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCTTATAGTTGATTCTGGTAGTACTGTTACTTATGTTCCTTGTTCTGATTGT
                                      ||  |||||   | |||  | |  |   |  |     |   | |||   || | | |  | |   | || | ||   |||||||||| || |||||||||||||| ||||| || || || | |||||||||||| |||||| | || || ||||| || |||||||| || |||  ||| 
gttagtctctttcactccctcgcttcctctacgtcccttcctcttttttttctttttcaaattaatttttcacttttttgttgttaattatgtgtgttttgggaaattggatggagtagGTATTATACGACGAGGCTTTGGATCGGTACTCCTCCGCAGAGGTTTGCTCTTATTGTTGATACGGGGAGCACTGTCACCTATGTTCCGTGCTCTACTTGC

upper sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G17990.1 (Glycine max), 3'ss of exon 1
-----------------------------gtaatctccttttccatatttcccgatctgggtcatgtaaagatgtctcttttatatacta-ttatatcgtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCTTATAGTTGATTCTGGTAGTACTGTTACTTATGTTCCTTGTTCTGATTGT
                              |  ||     || | | ||  ||  |     |||  |   ||  |      | | |   | ||  || || ||| |||||||||||| ||| |||||||||| || || || || || |||||||| || || |||||| | || || |||||||| |||||||| || ||    || 
gtaaaaacctcttacgtcgtcgtttcacgctcttccttcatttcttcttcgccttttcaaatcaaattcggaaattcaagatttgtgtgaattgaatggtttttttagGTATTACACGACGCGGCTTTGGATCGGGACTCCTCCGCAGATGTTTGCGCTCATTGTTGATACGGGGAGCACTGTTACGTATGTTCCGTGCTCCACATGC

upper sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G39800.1 (Glycine max), 3'ss of exon 4
----------------------------gtaatctccttttcca---tatttcccgatctgggtcatgtaaagatgtctct-tttatatactattatatcgtattt-gtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCTTATAGTTGATTCTGGTAGTACTGTTACTTATGTTCCTTGTTCTGATTGT
                             |  | |  |||||||   || ||  || | |   |  |||    |  | | | | | | |  |   | || | ||   |||| || || ||  || |||||||||| || || || || || | |||||||||||| |||||| | || ||||||||||| |||||||| || |||  ||||
gttagtctctttcactccctcgcttcctcttttttttttttccaaaatagttttcgctttttttgttgttgttaattatgtgtgtgtgttttgggaaattggatggagtagCTACTATACGGCGCGGCTTTGGATCGGCACTCCTCCGCAGAGGTTTGCTCTTATTGTTGATACGGGGAGTACTGTTACCTATGTTCCGTGCTCTACTTGT

upper sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0129g00600.t01 (Vitis vinifera), 3'ss of exon 1
-------gtaatc-tccttttccatatttcccgatctgggtcatgtaaagatgtctcttttatatactattatatcgtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCTTATAGTTGATTCTGGTAGTACTGTTACTTATGTTCCTTGTTCTGATTGT
       ||  || |||  |    | |||| ||||     |||| | |       |||| | |  | | | |  |  |  || ||||||||||||||||||| ||||||| || ||||| || || |  ||||| || || |||||| | || |||||| |||| |||||||| || |||   || 
gtacccggtgttcctcccctcttttttttctcgattgcattcattttatttctgttcttgtgttgaat-tgaggtgcttcttttagGTATTACACTACGAGGATTTGGATCGGAACACCGCCTCAGACATTTGCGCTCATTGTTGATACGGGGAGTACTCTTACGTATGTTCCATGCTCTACGTGC

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|164129416|gb|ES010409.1|ES010409
EST:     TCACTTCCTCACTCTCGCATGAGACTCTACGACGATCTTCTTATTAATGG                         GTATTACACTACGAGGCTTTGGATTGGTACACC
genomic: TCACTTCCTCACTCTCGCATGAGACTCTACGACGATCTTCTTATTAATGGgtaatctcct ... gtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACC
EST: gi|19876974|gb|AU237805.1|AU237805
EST:     TCACTTCCTCACTCTCGCATGAGACTCTACGACGATCTTCTTATTAATGG                         GTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCT
genomic: TCACTTCCTCACTCTCGCATGAGACTCTACGACGATCTTCTTATTAATGGgtaatctcct ... gtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCT
EST: gi|164065323|gb|ES066335.1|ES066335
EST:     CACTTCCTCACTCTCGCATGAGACTCTACGACGATCTTCTTATTAAATGG                         GTATTACACTACGAGGCTTTGGATTGGTACACC
genomic: CACTTCCTCACTCTCGCATGAGACTCTACGACGATCTTCTTATTAA-TGGgtaatctcct ... gtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatctgggtcatgtaaagatgtctcttttatatactattatatcgtatttgtagGTATTACACTACGAGGCTTTGGATTGGTACACCACCACAAATGTTTGCTCTTATAGTTGATTCTGGTAGTACTGTTACTTATGTTCCTTGTTCTGATTGT
                          ttttatatactattat  TA-rich tract