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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattcatttgatcactgagtggattttatgtttttgattttaaaattcctctcttgattgagaaatttttgagatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAAGAATTGGAGAGGATTTCTGGTGTTGAGAGCAACGCTCTTACAGTTGATG

Basic information

species Arabidopsis thaliana
transcript AT1G12840.1
intron # 2
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|124713358|gb|EH804760.1|EH804760
EST:     ATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAA
genomic: ATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAA
EST: gi|124783142|gb|EH873024.1|EH873024
EST:     GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGAT
genomic: GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGAT
EST: gi|124889987|gb|EH968889.1|EH968889
EST:     TTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAA
genomic: TTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAA
EST: gi|124833474|gb|EH917913.1|EH917913
EST:     GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAA
genomic: GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAA
EST: gi|222358097|gb|GH718178.1|GH718178
EST:     GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAA
genomic: GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAA
EST: gi|124963007|gb|EL037371.1|EL037371
EST:     GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAAGGAG
genomic: GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAG
EST: gi|124891955|gb|EH970857.1|EH970857
EST:     TGTTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAAGGAGTTTCG
genomic: TG-TTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCG
EST: gi|125210854|gb|EL225808.1|EL225808
EST:     TGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAAG                         TCGAACAGCTTTGTGGAAGGAGTTTCGCAAAA
genomic: TGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAA-Ggtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAA
EST: gi|124882625|gb|EH961527.1|EH961527
EST:     GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAG                         TCGAACAGCTTTGTGGAAGGAGTTTCGCAAAA
genomic: GTGTTGGAACCTTAGATTCTCTACTCGCTCTCGGCGATGATCTGCTTAAGgtaaaattca ... agatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttttgattttaaaattcctctcttgattgagaaatttttgagatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAAGAATTGGAGAGGATTTCTGGTGTTGAGAGCAACGCTCTTACAGTTGATG
                         tcttgat  putative branch site (score: 4)
 ttttgattttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattcatttgatcactgagtggattttatgtttttgattttaaaattcctctcttgattgagaaatttttgagatttgtagTCGAACAGCTTTGTGGAAGGAGTTTCGCAAAAGATCAGGAGACAGATCGAAGAATTGGAGAGGATTTCTGGTGTTGAGAGCAACGCTCTTACAGTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA