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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacgactttgacactgatttaagctttgagaacctagtagttcctgtaagaggttaaaattactataagaagcggaattatcgatatatactta...

Basic information

species Arabidopsis thaliana
transcript AT1G54100.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G130440_T02 (Zea mays), 5'ss of exon 7
GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacgactttgacactgatttaagctttgagaacctagtagttcctgta-agaggttaaaattactataagaagcggaattatcgatatatactta----
||||||||||||| |||||| | ||||||||||| ||||| |||||||||  |  |  |      |||||  ||  ||  ||  | |  || | | |||| |||  ||      | | | | |    || || | | |   |  |||    
GTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTGgtaagaatggtttacttttctgat--aaaattccagtgc-tgata-tacatgtatagaaattgttgccattctgaaatattgagtt-tggctccctgattattca
















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|116486592|gb|EG529184.1|EG529184
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACGCCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
EST: gi|116420799|gb|EG463391.1|EG463391
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
EST: gi|116420807|gb|EG463399.1|EG463399
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
EST: gi|116420806|gb|EG463398.1|EG463398
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
EST: gi|116486590|gb|EG529182.1|EG529182
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACGCCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
EST: gi|116486594|gb|EG529186.1|EG529186
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACGCCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
EST: gi|301501173|gb|HO206713.1|HO206713
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT
EST: gi|301502366|gb|HO207906.1|HO207906
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACACCG
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCG
EST: gi|116486591|gb|EG529183.1|EG529183
EST:     GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG                         GAAAGGTGCTCCAACTACGCCGTTAATAACTATCGCAATGACCAAGCTAGT
genomic: GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacg ... gattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGgtaaataacgactttgacactgatttaagctttgagaacctagtagttcctgtaagaggttaaaattactataagaagcggaattatcgatatatactta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataagaag