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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttattttaaaagatcttaataaaatatatgacggtctggtattgtccatatcctctgatcaaatattgattctgccatgtatctttttttagGACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAGGCATTTTTCGCAAATATGCCATTGTCTAAGACACTTACCATGAATCTTGACGTTCCAG

Basic information

species Arabidopsis thaliana
transcript AT1G71220.2
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 25
gtatgttattttaaaagatcttaataaaatatatgacggtctggtattgtccatatcctctgatcaaatattgattctgccatgtatctttttttagGACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAGGCATTTTTCGCAAATATGCCATTGTCTAAGACACTTACCATGAATCTTGACGTTCCAG
         | || |  |   |  ||   |  | ||   | |   ||      |    | ||   |    ||  || |    | |||  ||||  |||| ||||  |||||| | | || |    |  | || || |||||||||||||| || ||||||||||||||||| || |||||||||||||| ||||| |
--------gtatatattacacttttagcctgga-gataatttcagataagatttgaggtttgggta--ctttagtttt----tttattattttgcagGATGATTTTAGCAGTGCTGACTCTTCAATCAACGGCCCAAAGGCATTTTTCGCTAACATGCCATTGTCTAAGACTCTCACCATGAATCTTGATGTTCCCG

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 28
--gtatgttattttaaaagatcttaataaaatatatgacggtctggtattgtccatatcctctgatcaaatattgattctgccatgtatctttttttagGACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAGGCATTTTTCGCAAATATGCCATTGTCTAAGACACTTACCATGAATCTTGACGTTCCAG
   | | ||||| |   |  ||||||     ||    |    | |  |   |   |    |    |   | |  | ||||| |        | ||| |||| ||||  ||||  || | || ||   || |||| || || ||||| || ||||| ||||| ||||||||||| || |||||||||||||| ||||| |
gtatttcttattcttttaactcttaactctctaagataattccagacacgatatttgatgttaagtttcacagggtttctgac--------tctttcagGATGATTTTAGCAACACTGACTCTGCAATAAATGGTCCAAAAGCATTCTTTGCAAACATGCCGTTGTCTAAGACTCTCACCATGAATCTTGATGTTCCTG

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 26
--gtatgttattttaaaagatcttaataaaatatatgacggtctggtattgtccatatcctctgatcaaatattgattctgccatgtatctttttttagGACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAGGCATTTTTCGCAAATATGCCATTGTCTAAGACACTTACCATGAATCTTGACGTTCCAG
   ||| ||||||    |  |||||||    ||    |    | |  || ||   |    |  | ||  | |  | |||||         |||||  |||| ||||  ||||  || | || ||   || |||| ||  | ||| | || ||||| |||||| |||||||||| || |||||||||||||| ||||| |
gtatatcttatttatttaactcttaattctctaagataattccagacatggtatttgatgttaggtctcacagggtttctga--------tttttgcagGATGATTTTAGCAACACTGACTCTGCAATAAATGGCCCACAAGCACTCTTTGCAAACATGCCACTGTCTAAGACTCTCACCATGAATCTTGATGTTCCTG

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|164099043|gb|ES174361.1|ES174361
EST:     AGATATGTCTTACCTAATACG                         GACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAGGCATTTTTC
genomic: AGATATGTCTTACCTAATACGgtatgttatt ... ctttttttagGACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAGGCATTTTTC
EST: gi|163990259|gb|ES203097.1|ES203097
EST:     AGATATGTCTTACCTAATACG                         GACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAAGGCATTTTT
genomic: AGATATGTCTTACCTAATACGgtatgttatt ... ctttttttagGACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAA-GGCATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtattgtccatatcctctgatcaaatattgattctgccatgtatctttttttagGACGATTACAGCAGTACAGGCTTTGACGTAGATGGGCCTAAGGCATTTTTCGCAAATATGCCATTGTCTAAGACACTTACCATGAATCTTGACGTTCCAG
                          tattgat  putative branch site (score: 3)
                                          tatcttttttt  putative PPT
                                       atgtatcttttttta  TA-rich tract