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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggctatacatctcattgttactcacatagtggataatgactaattcgcaataagtcatatatttgtttcatttataataagttactgtaatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTCATTTACGACATCACATCAAAGTTGAAAACTAAACTTTTGGGTAACTCTG

Basic information

species Arabidopsis thaliana
transcript AT5G59420.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 5
--gtgcggctatacatctcattgttactcacatagtggataatgactaattcgcaataagtcatatatttgtttcatttataa-taagttactgtaatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTCATTTACGACATCACATCAAAGTTGAAAACTAAACTTTTGGGTAACTCTG
   |   | ||     ||      |   | || |    |  ||      || |  |    |  | | | ||| | || ||||| |||  || | ||| ||| ||||| || |||||||| |||||||||||||  ||||||||||| ||||| || |  || ||  | || |||||||||||||||||  ||||||| |||||||
ttattttgttaggtgacttgggacttagctcacaacaaagtatatgggttttgttac---ttttctctctgtgt-atatataaataaaatattttaaattt-cagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 5
gtgcggctatacatctcattgttactc---acatagtggataatgactaattcgcaataagtcatatatttgtttc-atttat---aataagttactgtaatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTCATTTACGACATCACATCAAAGTTGAAAACTAAACTTTTGGGTAACTCTG
         ||  |   |  || |||    || |||   | ||  |   ||  |   |  || |  | | | | ||  | |||   |||||  || | ||| ||| ||||| || |||||||| |||||||||||||  ||||||||||| ||||| || |  || ||  | || |||||||||||||||||  ||||||| || ||||
--------ttattttgtaaggtgacttgggacttagctcacaacaaagtatatgggttttgttacttttctctctctgtgtatataaataaaatattttaaattt-cagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAATTCTG

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 5
gtgcggctatacatctcattgt----tactcacatagtggataatgactaattcgcaataagtcatatatttgtttcatttataataagttactgtaatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTCATTTACGACATCACATCAAAGTTGAAAACTAAACTTTTGGGTAACTCTG
 |  || | | | |||||| |     | ||  | |  ||  || ||  |  |  |   |||     ||| | ||   || | |    | | | | | ||||  ||||| ||||||||||| || ||||||||||| ||||| || || ||||| |||| ||| ||  | |||||||| || ||||| ||| |||| || ||||   
atctggatgttc-tctcatggaaggatgctt-cctcatgattattgttttctctgttctaaagttcataatggta--atgtgtctgcattcattttgattt--cagGTCAGCCATCATCCTCCGATGAGTGCTGGGCATGCTGAAAATGAGCATTTCACTTATGAAGTTACATCAAAATTAAAAACCAAATTTTTAGGGAACTTCC

upper sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgcggctatacatctcattgttactcacatagtggataatgactaattcgcaataa-gtcatatatttgtttcatttataataagttactgtaatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTCATTTACGACATCACATCAAAGTTGAAAACTAAACTTTTGGGTAACTCTG
                                            | |  |  |||    |||  | ||||  | |   |    |  ||  ||||   |  ||||| ||||| ||||| ||||||||| ||| |||||| ||||| || || |||  |||||||||||||||||||||||  || ||  || | || |||||||
-------------------------------------------gtgaagcataatggcatcacgtttttggctgagc-aggtgagcttcgtgta---tgacagGTGAGCCACCATCCGCCAATGAGTTCTGCTCATGCAGAGAATGAACATTTCTCTTACGACATCACATCAAAGTTGAGGACAAAGTTTCTTGGCAACTCTG

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|47827935|gb|CK117619.1|CK117619
EST:     AGACATATGAGATGGTCAACCATGGTGGGATTTCTTTTATTTCTGAGCAG                         GTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTC
genomic: AGACATATGAGATGGTCAACCATGGTGGGATTTCTTTTATTTCTGAGCAGgtgcggctat ... aatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgcaataagtcatatatttgtttcatttataataagttactgtaatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTCATTTACGACATCACATCAAAGTTGAAAACTAAACTTTTGGGTAACTCTG
                                               tttttc  CT-rich tract
             atatatttgtttcatt  TA-rich tract