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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagaattggaaactgataggcatccatgccgtgcttgtgcttgtgcttatgctacatataggttgattataacttctggtagtttattcttcatgtagGAAAGACGCAATGCATTAATCATTTCCGGATCAACGACAAGTGGTACTTGGTAGATTTGCCTGGTTACGG

Basic information

species Arabidopsis thaliana
transcript AT5G11480.1
intron # 1
splice site 3'
intron type U2

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|164204602|gb|ES044227.1|ES044227
EST:     CAATTCGTTGGTGAGGAGGAAACGCCTTGCCTTGACTTCTAAGAAACCTG                         GAAAGACGCAATGCATTAATCATTTCCGGAT
genomic: CAATTCGTTGGTGAGGAGGAAACGCCTTGCCTTGACTTCTAAGAAACCTGgtaagctgag ... cttcatgtagGAAAGACGCAATGCATTAATCATTTCCGGAT
EST: gi|116474051|gb|EG516643.1|EG516643
EST:     CAATTCGTTGGTGAGGAGGAAACGCCTTGCCTTGACTTCTAAGAAACCTG                         GAAAGACGCAATGCATTAATCATTTCCGGATCAACGACAAGTGGTACTTGG
genomic: CAATTCGTTGGTGAGGAGGAAACGCCTTGCCTTGACTTCTAAGAAACCTGgtaagctgag ... cttcatgtagGAAAGACGCAATGCATTAATCATTTCCGGATCAACGACAAGTGGTACTTGG
EST: gi|124935034|gb|EL012053.1|EL012053
EST:     TTCGTTGGTGAGGAGGAAACGCCTTGCCTTGACTTCTAAGAAACCTG                         GAAAGACGCAATGCATTAATCATTTCCGGATCAACGACAAGTGGTACTTGG
genomic: TTCGTTGGTGAGGAGGAAACGCCTTGCCTTGACTTCTAAGAAACCTGgtaagctgag ... cttcatgtagGAAAGACGCAATGCATTAATCATTTCCGGATCAACGACAAGTGGTACTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttatgctacatataggttgattataacttctggtagtttattcttcatgtagGAAAGACGCAATGCATTAATCATTTCCGGATCAACGACAAGTGGTACTTGGTAGATTTGCCTGGTTACGG
                       ttataac  putative branch site (score: 2)
                                       tttattcttc  putative PPT
                   ttgattataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagaattggaaactgataggcatccatgccgtgcttgtgcttgtgcttatgctacatataggttgattataacttctggtagtttattcttcatgtagGAAAGACGCAATGCATTAATCATTTCCGGATCAACGACAAGTGGTACTTGGTAGATTTGCCTGGTTACGG

- - - - - -aaactga
- - - - - - - - - - - - -ccatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acatata