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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagtattctcactctcactctcaccctatgtgtgttaaggtctgtgaattaatttgtatctgcattttttttttgtagCAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAGCTATTTTCAAACAAGCAAAAGAAGCGCAAGAGAAAGCAGATAGTGAGTTC

Basic information

species Arabidopsis thaliana
transcript AT3G09210.1
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|124861391|gb|EH945828.1|EH945828
EST:     ATGGAGTCGGAGGTTTCATAGGTTCAAAAGTTGGAAATAC                         CAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAGC
genomic: ATGGAGTCGGAGGTTTCATAGGTTCAAAAGTTGGAAATACgtgagtagta ... ttttttgtagCAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAGC
EST: gi|125006465|gb|EL078734.1|EL078734
EST:     AGAGACGTTGATGGAGTCGGAGGTTTCATAGGTTCAAAAGTTGGAAATAC                         CAAGAGACAGATTAATAAACCAAGACCAGTAG
genomic: AGAGACGTTGATGGAGTCGGAGGTTTCATAGGTTCAAAAGTTGGAAATACgtgagtagta ... ttttttgtagCAAGAGACAGATTAATAAACCAAGACCAGTAG
EST: gi|124953088|gb|EL028307.1|EL028307
EST:     GAGGTTTCATAGGTTCAAAAGTTGGAAATAC                         CAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAGC
genomic: GAGGTTTCATAGGTTCAAAAGTTGGAAATACgtgagtagta ... ttttttgtagCAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAGC
EST: gi|125238415|gb|EL252500.1|EL252500
EST:     GATGGAGTCGGAGGTTTCATAGGTTCAAAAGTTGGTAAATAC                         CAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAG
genomic: GATGGAGTCGGAGGTTTCATAGGTTCAAAAGTTGG-AAATACgtgagtagta ... ttttttgtagCAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctatgtgtgttaaggtctgtgaattaatttgtatctgcattttttttttgtagCAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAGCTATTTTCAAACAAGCAAAAGAAGCGCAAGAGAAAGCAGATAGTGAGTTC
                       aattaat  putative branch site (score: 3)
                                   tctgcatttttttttt  putative PPT
                       aattaatttgtatctg  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagtattctcactctcactctcaccctatgtgtgttaaggtctgtgaattaatttgtatctgcattttttttttgtagCAAGAGACAGATTAATAAACCAAGACCAGTAGATGACAGTGACTTGGAAGCTATTTTCAAACAAGCAAAAGAAGCGCAAGAGAAAGCAGATAGTGAGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT