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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtacctctctttctatgctttgctgcataatcaagaaccacttaaaaagtttaatcttttcaactgacacttaaaaccaatcttgcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTTGTGGAGCCTACGATAATCGAGATATCAGCAGATGCTGCTGTCGTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G54100.1
intron # 11
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|116420809|gb|EG463401.1|EG463401
EST:     CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
EST: gi|116420799|gb|EG463391.1|EG463391
EST:     CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
EST: gi|164149050|gb|ES050404.1|ES050404
EST:     CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
EST: gi|116420807|gb|EG463399.1|EG463399
EST:     CTGAATCAAAAAAGAACGTTGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
EST: gi|86080345|gb|DR376102.1|DR376102
EST:     CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
EST: gi|86080922|gb|DR376679.1|DR376679
EST:     TGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: TGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
EST: gi|116414405|gb|EG456997.1|EG456997
EST:     CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
EST: gi|116420795|gb|EG463387.1|EG463387
EST:     CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAG                         GGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT
genomic: CTGAATCAAAAAAGAACTTTGAGAAAGGAATTGAAGTCATCAAATCCCAGgcaagtacct ... gcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttaaaaagtttaatcttttcaactgacacttaaaaccaatcttgcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTTGTGGAGCCTACGATAATCGAGATATCAGCAGATGCTGCTGTCGTCAAAG
                      aactgac  putative branch site (score: 2)
     aaaagtttaatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtacctctctttctatgctttgctgcataatcaagaaccacttaaaaagtttaatcttttcaactgacacttaaaaccaatcttgcatttgcagGGTGGTAAAATACTAACGGGAGGTAAAGCAGTCGAAGGTGAAGGAAACTTTGTGGAGCCTACGATAATCGAGATATCAGCAGATGCTGCTGTCGTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT