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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttatctttcattgctatatattagtgttttagtgccaaatctccgttttctgatatcatttatttccttttttcaacattgattagGGGCGTCATGCTTTAGTGTATGATATTAACTCTGCGAATGAAACCTGGGAATGGGTAAATCTTAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT5G13020.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G39100.1 (Glycine max), 3'ss of exon 4
gtatcttatctttcattgctatatat-tagtgttttagtgccaaatctccgttttctgatatcatttatttccttttttca-acattgattagGGGCGTCATGCTTTAGTGTATGATATTAACTCTGCGAATGAAACCTGGGAATGGGTAAATCTTAAAGAG
                   | | | | |||| |  || |   || |      |   ||   || |||| |   | | || | | |||   ||||| |  |||||||| || |||||||| || || || |||||||| ||||| ||||| ||||||||||||
------------------gtgtgtttatagtatactattagaaactgaggaatacatggactcctttaatatttctatttacatattttgtagGGACTACATGCTTTGGTTTATGATATGAATTCAGCAAATGAAACATGGGAGTGGGTTAATCTTAAAGAG

upper sequence: AT5G13020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G02360.1 (Glycine max), 3'ss of exon 6
------gtatcttatctttcattgctatatattagtgttttagtgcca-aatctccg---ttttctgatatcatttatttccttttttcaacattgattagGGGCGTCATGCTTTAGTGTATGATATTAACTCTGCGAATGAAACCTGGGAATGGGTAAATCTTAAAGAG
       || |     |     ||   | | ||  |  | || |   | || ||  |   |     ||   | || || |   | |||  | |||   ||||| |  |||||||| || |||||||| || || || |||||||| ||||| ||||| ||||||||||||
gttcctctaacaacaatgctgctgaggtgtgtttatagtatactattagaaactgaggaatgcatggactcctttaatatttctatttacatattttgtagGGACTACATGCTTTGGTTTATGATATGAATTCAGCAAATGAAACATGGGAGTGGGTCAATCTTAAAGAG
















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|163979921|gb|ES137926.1|ES137926
EST:     TGACAACCAATACTACGAAGCTGTTATAACTGACTACAACCCCTGTTGAG                         GGGCGTCATGCTTTAGTGTATGATATTAACTC
genomic: TGACAACCAATACTACGAAGCTGTTATAACTGACTACAACCC-TGTTGAGgtatcttatc ... cattgattagGGGCGTCATGCTTTAGTGTATGATATTAACTC
EST: gi|124963557|gb|EL037885.1|EL037885
EST:     ATGACAACCAATACTACGAAGCTGTTATAACTGACTACAACCCTGTTGAG                         GGGCG-CATGCTTTAGTGTA
genomic: ATGACAACCAATACTACGAAGCTGTTATAACTGACTACAACCCTGTTGAGgtatcttatc ... cattgattagGGGCGTCATGCTTTAGTGTA
EST: gi|125222120|gb|EL236205.1|EL236205
EST:     ATGACAACCAATACTACGAAGCTGTTATAACTGACTACAACCCTGTTGAG                         GGGCGTCATGCTTTAGTGTATGATATTAACT
genomic: ATGACAACCAATACTACGAAGCTGTTATAACTGACTACAACCCTGTTGAGgtatcttatc ... cattgattagGGGCGTCATGCTTTAGTGTATGATATTAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgccaaatctccgttttctgatatcatttatttccttttttcaacattgattagGGGCGTCATGCTTTAGTGTATGATATTAACTCTGCGAATGAAACCTGGGAATGGGTAAATCTTAAAGAG
                ttctgat  putative branch site (score: 3)
                               tttccttttttcaac  putative PPT
                     atatcatttatttcct  TA-rich tract