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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGAATGCATCAAGTAACCTTCACGTCAGTGCTAACCTAGCAATACTTGTTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtttacaaccttttcaagatttcacttcgctgatgtgctttgttcagttacttctccattaatttgtcactatttctgtcagaacacataggataa...

Basic information

species Arabidopsis thaliana
transcript AT1G02080.2
intron # 34
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02080.1 (Arabidopsis thaliana), 5'ss of exon 35
lower sequence: GLYMA03G27270.1 (Glycine max), 5'ss of exon 36
CGAGAATGCATCAAGTAACCTTCACGTCAGTGCTAACCTAGCAATACTTGTTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtttacaaccttttcaagatttcacttcgctgatgtgctttgttcagttacttctccattaatttgtcactatttctgtcagaacacataggataa
 || ||||||||||  ||| |||| |||| |||| | || || || ||   ||| || |||||||||||||||| || ||| || ||||| |||||||||||||||||     |  |   |  |  ||  |   | ||       | |   ||| |        |  ||   |  |    | |     | |||    |||
TGATAATGCATCAAACAACATTCATGTCACTGCTCATCTTGCTATCCTAACTGCCATTCGTGATGTTTGCAAGCTTGCTGTCAAGGAGCTTACTAGTTGGgtatgttttgtttcactgacaagtcacatattctttatacttgaagcttttttaataaaattgcatatttggaaaaaaattattgattctcattccttaa

upper sequence: AT1G02080.1 (Arabidopsis thaliana), 5'ss of exon 35
lower sequence: GLYMA07G14770.1 (Glycine max), 5'ss of exon 36
CGAGAATGCATCAAGTAACCTTCACGTCAGTGCTAACCTAGCAATACTTGTTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtttacaaccttttcaagatttcacttcgctgatgtgctttgttcagttacttctccattaatttgtcactatttctgtcagaacacataggataa-----
 || ||||||||||  ||  |||| |||  |||| | || || || ||   ||| || |||||||||||||||| || ||| || ||||| |||||||||||||||||        |   | |  |||| |      | | |||     ||||  || |  || || ||| ||   |       | |  |   |   | |     
TGATAATGCATCAAACAATATTCATGTCTCTGCTCATCTTGCTATCCTGACTGCCATTCGTGATGTTTGCAAGCTTGCTGTCAAGGAGCTTACTAGTTGGgtatgtttcgtttaactgacaaaagtcacatattctgtatacttga---agtt-ttttttaataaaattg-catattcggaaaaaaattattcattctcattcct

upper sequence: AT1G02080.1 (Arabidopsis thaliana), 5'ss of exon 35
lower sequence: Vv00s0144g00010.t01 (Vitis vinifera), 5'ss of exon 7
CGAGAATGCATCAAGTAACCTTCACGTCAGTGCTAACCTAGCAATACTTGTTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtt--tacaacct---tttcaagatttcacttcgctgat-gtgctttgttcagt-tacttctccattaatttgtcactatttctgtcagaacacataggataa
 |||||||||||||  |   | || ||||||||| | || ||||| |||| |||||| || ||||||||||||| ||||||||| ||||||||||||||||||||||  ||  | ||    |   | ||   |  |     || |   ||||||     ||||  |  |  | | ||||| | ||  | | | |      |      
TGAGAATGCATCAAACAGTTTACATGTCAGTGCTCATCTTGCAATCCTTGCTGCTATTCGAGATGTTTGCAAGCTTGTTGTTAAGGAGCTCACTAGTTGGgtatgttgctatgaactggactcttatatcctatgttagaaattgaagtttgttttccatactatttaaggattctgtcatttttaat-taatattttgca------

upper sequence: AT1G02080.1 (Arabidopsis thaliana), 5'ss of exon 35
lower sequence: Vv15s0021g02610.t01 (Vitis vinifera), 5'ss of exon 3
CGAGAATGCATCAAGTAACCTTCACGTCAGTGCTAACCTAGCAATACTTGTTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtt----tacaaccttttcaagatttcacttcgctgatgtgctttgttcag--ttacttctccattaatttgtcactatttctgtcagaacacataggataa
 |   |||||||||  |    | | ||   |||| | || ||||| || ||||| || |||||| ||||||||| ||||||||| |||||||||||||||||||| |    |  |  |||       | |    | | || |||  ||||    |  |||  |      ||   ||  |    |  ||     |||||| |     
TGCCGATGCATCAAACAGTTCTAATGTTGCTGCTTATCTTGCAATTCTGGTTGCCATTCGTGATCTTTGCAAGCTTGTTGTTAAGGAGCTCACTAGTTGGgtatgctctgttgtactcttcctgttctctagaataggtgttgtagtttggaaggccttatgttctttgtagcatgaaatgggtaatgctg--acacattga----

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|124866873|gb|EH951310.1|EH951310
EST:     TTGTTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGG                         GTGATTTATTCAGAGGAGGATC
genomic: TTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtttac ... tttgacacagGTGATTTATTCAGAGGAGGATC
EST: gi|19875482|gb|AU236313.1|AU236313
EST:     GCGTGTTGTTAAAGAGCTCACTAGTTGG                         GTGATTTATTCAGAGGAGGATCCGGAAGCTCAACAAAGATATTACTATTGG
genomic: GCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtttac ... tttgacacagGTGATTTATTCAGAGGAGGAT-CGGAAGCTCAACAAAGATATTACTATTGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGAATGCATCAAGTAACCTTCACGTCAGTGCTAACCTAGCAATACTTGTTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGgtatgtttacaaccttttcaagatttcacttcgctgatgtgctttgttcagttacttctccattaatttgtcactatttctgtcagaacacataggataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA