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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTACAAGCGAAGGAAATGCTAGAGCATTTAGAGAGTGTTCTAGCTAATGAGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagttacctctcttctgctcaatttgagcattaaggttgtcgaagatatctaattatagacgtttgtgcttgttcttgtgtgagaatag

Basic information

species Arabidopsis thaliana
transcript AT1G06410.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06410.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv12s0028g01670.t01 (Vitis vinifera), 5'ss of exon 2
TTTACAAGCGAAGGAAATGCTAGAGCATTTAGAGAGTGTTCTAGCTAATGAGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagt------tacctctcttctgctca--atttgagcattaaggttgtcgaagatatctaattatagacgtttgtgcttgttcttgtgtgagaatag--
 |  || || ||||||||| | || ||| ||||||||||  |||| ||||| || || || |||||||| ||||| |  || |||||||| ||||||||||||  |       |  ||  ||     ||  ||| ||   | ||        |  | |  ||||| | ||  |   ||    ||  |   |  | |||   
CTCTCAGGCAAAGGAAATGTTGGATCATCTAGAGAGTGTATTAGCAAATGAACCTGTTGCTGTCAAAAGTGGTCATTTTATTGTAGAAGTTAAGCCTCAGgtacatatcgtgcatttcaatttcatccataattcgactctgaaaaagaaaaagtagaaataattct-gatctaaatgaagtttgatacatttgcataaat
















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|125169341|gb|EL193430.1|EL193430
EST:     AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAG                         GGAGTGAGCAAAGGATCCGTGTCAGAAA
genomic: AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagttacc ... gtgagaatagGGAGTGAGCAAAGGATCCGTGTCAGAAA
EST: gi|124955101|gb|EL030140.1|EL030140
EST:     CGGTCACTACATAGTAGAAGTCAAGCCTCAG                         GGAGTGAGCAAAGGATCCGTGTCAGAAAAGATATTTTCA
genomic: CGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagttacc ... gtgagaatagGGAGTGAGCAAAGGATCCGTGTCAGAAAAGATATTTTCA
EST: gi|164237310|gb|ES172409.1|ES172409
EST:     AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAG                         GGAGTGAGCAAAGG
genomic: AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagttacc ... gtgagaatagGGAGTGAGCAAAGG
EST: gi|125017877|gb|EL090146.1|EL090146
EST:     AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTAAAGCCTCAG                         GGAGTGAGCAAA
genomic: AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagttacc ... gtgagaatagGGAGTGAGCAAA
EST: gi|125004389|gb|EL076658.1|EL076658
EST:     AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAG                         GGAGTGAGCAAAGGATCCGTGTCAGAAAAG
genomic: AGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagttacc ... gtgagaatagGGAGTGAGCAAAGGATCCGTGTCAGAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTACAAGCGAAGGAAATGCTAGAGCATTTAGAGAGTGTTCTAGCTAATGAGCCAGTGGCAGTCAAAAGCGGTCACTACATAGTAGAAGTCAAGCCTCAGgtaagttacctctcttctgctcaatttgagcattaaggttgtcgaagatatctaattatagacgtttgtgcttgttcttgtgtgagaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT