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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttctctctttgactctctctatattgagttgttatttatttattttttaaaaaataccggaagaaatttataaaaattaattttaattttgttttatttaatagAGCATATGATAGAGCTGCTATTAAATTCCGTGGAGTAGAAGCGGATATCAATTTCAACATCGACGATTATGATGATGACTTGAAACAG

Basic information

species Arabidopsis thaliana
transcript AT4G36920.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36920.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G18170.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------gtatttttctctctttgactctctctatattgagttgttatttatt-tattttttaaaaaataccggaagaa------atttataaaaattaattttaattttgttttatttaatagAGCATATGATAGAGCTGCTATTAAATTCCGTGGAGTAGAAGCGGATATCAATTTCAACATCGACGATTATGATGATGACTTGAAACAG
                                                  | ||| | | ||||  | |    ||| ||  | || | |  |||| ||  |   |     |   ||  |||        | | | ||| |  | |   ||   | |   ||   || |||||||||||||| |||||||||||||| ||||| || ||||| || || |||||||| || |||||||| ||||||||||| |||
gtgagcccttgcccccctcctctagtattataccaagcttgtaatataactttttctatgtcttgaattgaaccta-atctaattatcaaatattataaatcacatttcgttgtgggggaatgtgaggctcaaagaaaattgtgtattttccatctctctttgcagTGCATATGATAGAGCGGCTATTAAATTCCGAGGAGTGGAGGCGGACATTAACTTCAACATTGAAGATTATGAAGATGACTTGAAGCAG

upper sequence: AT4G36920.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G39520.2 (Glycine max), 3'ss of exon 3
---------------------------------------------gtatttttctctctttgactctctctatattgagttgttatttatttattttttaaaaaataccggaagaaatttataaaaattaattttaattttgttttatttaatagAGCATATGATAGAGCTGCTATTAAATTCCGTGGAGTAGAAGCGGATATCAATTTCAACATCGACGATTATGATGATGACTTGAAACAG
                                                ||| |   ||||  || |  || | ||  | ||    |   ||| ||   || ||| |   ||     ||| |||||| |  ||||  ||||| | |   |    || || |||||||||||||||||||||||||| ||||| || || || ||||| ||||||||||| || ||||| || |||||||| |||
gtgagcacttgctccctctcttcctattgttcagcttgtaatataagttttctacatcttgaacccaatccacataaaatt----tcgttttcttgcatataaatttaaggttcggattaataaaagt--attt--attttatctgtatgctcagTGCGTATGATAGAGCTGCTATTAAATTCCGGGGAGTGGAGGCAGACATCAACTTCAACATCGAAGACTATGAGGAAGACTTGAAGCAG

upper sequence: AT4G36920.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G05720.1 (Glycine max), 3'ss of exon 2
---------------------------------------------gtatttttctctctttgactctctctatattgagttgttatttatttattt-----tttaaaaaataccggaa---gaaatttataaaa--attaattttaattttgttttatttaatagAGCATATGATAGAGCTGCTATTAAATTCCGTGGAGTAGAAGCGGATATCAATTTCAACATCGACGATTATGATGATGACTTGAAACAG
                                                ||| |   ||||  |  |  ||   ||  | || |  ||| |||   |     |||||       || ||     |||||||||||  ||| ||||||  | | || |  | | |   || ||||||||||| |||||||||||||| ||||| || || || ||||| ||||||||||| || ||||| || |||||||| |||
gtgagcacttgctccctctctacctattgttcagcttgtaatataagttttctacttcttgaaaccaatccccataaaatt-tcgtttttttgcatagagatttaaggtggttcgaaacttcgaatttataaaagtatttattttatctgtcttctgctcagT---GCGTATGATAGAGCAGCTATTAAATTCCGGGGAGTGGAGGCAGACATCAACTTCAACATCGAAGACTATGAGGAAGACTTGAAGCAG

upper sequence: AT4G36920.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G18640.2 (Glycine max), 3'ss of exon 3
------------------------------------------gtatttttctctctttgactctctctatat-tgagttgttatt--tatttattttttaaaaaataccggaa------gaaatttataaaaattaattttaattttgttttatttaatagAGCATATGATAGAGCTGCTATTAAATTCCGTGGAGTAGAAGCGGATATCAATTTCAACATCGACGATTATGATGATGACTTGAAACAG
                                           ||||  | | ||  || ||    | | || | |  | |||||   | | |  |||         ||||        ||   | | | ||| |  | |   ||  || |   ||   || || ||||||||||| |||||||||||||| ||||| || || || || || ||||| || || || ||||| ||||||||||| |||
gtgagcccttgccccctcctttagtattataccaagcttgtaatattactttttccatgtcttgaaccaaatatcaaatattattgtaaatcacatttcgttgtgggccggggaattgtgagtctcaaagaaaattgtgtattttccgtctctcttttcagTGCTTATGATAGAGCGGCTATTAAATTCCGAGGAGTGGAGGCTGACATTAACTTCAATATTGAAGACTATGAAGATGACTTGAAGCAG

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|164177294|gb|ES051846.1|ES051846
EST:     GTGGATTTGACACTGCTCATGCAGCAGCTCG                         AGCATATGATAGAGCTGCTATTAAA
genomic: GTGGATTTGACACTGCTCATGCAGCAGCTCGgtatttttct ... tatttaatagAGCATATGATAGAGCTGCTATTAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaataccggaagaaatttataaaaattaattttaattttgttttatttaatagAGCATATGATAGAGCTGCTATTAAATTCCGTGGAGTAGAAGCGGATATCAATTTCAACATCGACGATTATGATGATGACTTGAAACAG
                               ttttaat  putative branch site (score: 3)
                                     ttttgtttt  CT-rich tract
              aaatttataaaaatta  TA-rich tract