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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttttccagtttgtgtttagtgtttgttcacctgtaaagacggatataaagtatgacacacgccagaaaacacgtaactgtatttatttctctatgccaggtaaattaatttctgtcgtgtctaacagGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCACCACCTAAAGTCAT

Basic information

species Arabidopsis thaliana
transcript AT2G31060.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 9
------------------------gtttgttcttttccagtt-tgtgtttagtgtttgttcacctgtaaagacggatat-aaagtatgacacacgccagaaa-acacgtaactgtatttatttctctatgccaggtaaattaatttctgtcgtgtctaac----agGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCACCACCTAAAGTCAT
                         |   ||||||| | | | | || |   |   || |    | |   ||   || | | || |   || ||| ||           ||    ||  |    |   |||||  || |  | ||  ||   ||  ||||    ||| |||||||||||||||||| | || ||||| |||||||| ||||| ||||| || ||||| ||
gtaagtatatgtaccactgatgaaatcccttctttttctgatatatgctatttaactgcttttttttcttgatttatttgagagcacttcatacgtcaacctcgtgtacaatataatgaaaagtttcctgccaactatagcatttgatgatctgcataacttccagGAATCTTGATTGAGAATATGCGCCGCGAAGGATTTGAGCTTTCAGTTTCACCCCCAAAAGTGAT

upper sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 9
gtttgttcttttccagtttgtgtttagtg-tttgttcacctgtaaagacggatataaagtatgacacacgccagaaaacacgtaactgtatttatttctctatgccaggtaaattaatttctgtcgtgtctaacagGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCACCACCTAAAGTCAT
|||||||| | |    ||    ||   || | || | | |   |    | | ||| |  |||| || |    | ||| | | | |     |||  |   || | |   |   ||||  |    || |   |||||||||| || |||||||||||||| || ||||| |||||| | || ||||||||||| ||||| ||
gtttgttcctgtttctttgaaattgcatgatctgatgatcctca----ctgttatta--tatg-catat---aaaaaccccatga-----tttgctgtgct-tacacagctgatta--tggcatctttattaacagGTATTTTAATTGAGAATATGAGACGTGAAGGGTTTGAGTTATCTGTCTCACCACCCAAAGTAAT

upper sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 9
gtttgttcttttccagtttgtgtttagtgtttgttcacctgtaaagacg-gatataaagtatgac-acacgccagaaaacacgtaactgtatttatttctctatgccaggtaaattaatttctgtcgtgtctaacagGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCACCACCTAAAGTCAT
                     |||| ||  |||||    || ||   |  |||    | | | |  | | ||    ||| ||   |   | ||   | ||   | |   |   ||||  |    || | | |||||||||| || |||||||||||||| || ||||| |||||| | || ||||| ||||||||||| ||
---------------------gttt-gttcttgtttctttgaaattgcatgatcctcactgttattatatgcatataaaaactccatgattttccgtgct---tacacagctgatta--tggcatcatat-taacagGTATTTTAATTGAGAATATGAGACGTGAAGGATTTGAGTTATCTGTCTCTCCACCTAAAGTAAT

upper sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 9
---------gtttgttcttt-tccagtttgtgtttagtgtttgttcacctgtaaagacggatataaag-----tatgacacacgccagaaaacacgtaactgtatttatttctctatgcca----ggtaaattaatttctg---------------tcgtgtctaacagGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCACCACCTAAAGTCAT
         |||  |  ||| ||||  || | | |  | |||   ||  |  ||  |   |   |||      ||| | ||  || |     | | |    || |  | || | |  ||||    | | ||||   |||||               | |||   |||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||
gtgagttccgttaatcatttatccatcttctatctcatattttaccaagttaaagcaaaaaaggaaaagttcttattatac-tgctacttttcccttttacgtctcaaattttgttcgccattaagttcaattgtcttctgaatgtggtttttatgttgtgcaaaacagGTATCTTAATTGAGAATATGAGGCGTGAAGGATTTGAGCTCTCCGTCTCACCACCTAAAGTCAT

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|47832144|gb|CK121828.1|CK121828
EST:     AGGCTTGTCAGAGTCATATGAAGTCCAAGGGAGAGGAGAACTTCAACTTG                         GTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCAC
genomic: AGGCTTGTCAGAGTCATATGAAGTCCAAGGGAGAGGAGAACTTCAACTTGgtttgttctt ... tgtctaacagGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCAC
EST: gi|125094792|gb|EL152167.1|EL152167
EST:     TATGAAGTCCAAGGGAGAGGAGAACTTCAACTTG                         GTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCT
genomic: TATGAAGTCCAAGGGAGAGGAGAACTTCAACTTGgtttgttctt ... tgtctaacagGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaactgtatttatttctctatgccaggtaaattaatttctgtcgtgtctaacagGTATCTTGATTGAGAATATGAGGCGGGAAGGTTTTGAGCTCTCAGTCTCACCACCTAAAGTCAT
                              aattaat  putative branch site (score: 3)
       tatttatttctctat  TA-rich tract