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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtattcatgacagatttcccatcactggacaagtgtgtctgagatgaaggtgtttctatgtcacatttcttattgagcttttgttgttccattttcagGCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAACGAGAAAGAAGCAGTCACCGCCACTGTTCTCCAG

Basic information

species Arabidopsis thaliana
transcript AT1G51980.2
intron # 5
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|47831013|gb|CK120697.1|CK120697
EST:     CAAAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAG                         GCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAACGAGAAA
genomic: CAAAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAGgtaggtattc ... ccattttcagGCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAACGAGAAA
EST: gi|164067627|gb|ES203852.1|ES203852
EST:     CAAAATCTCAGTATGTCGGTGGAGATTT-CGCCAACATACTGGTGGAGAG                         GCTACACACTTTGC
genomic: CAAAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAGgtaggtattc ... ccattttcagGCTACACACTTTGC
EST: gi|116431222|gb|EG473814.1|EG473814
EST:     CAAAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAG                         GCTACACACTTTGCGGTTGCT
genomic: CAAAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAGgtaggtattc ... ccattttcagGCTACACACTTTGCGGTTGCT
EST: gi|125227294|gb|EL241379.1|EL241379
EST:     AAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAG                         GCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAA
genomic: AAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAGgtaggtattc ... ccattttcagGCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAA
EST: gi|116431221|gb|EG473813.1|EG473813
EST:     CAAAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAG                         GCTACACACTTTGCGGTTGCT
genomic: CAAAATCTCAGTATGTCGGTGGAGATTTTCGCCAACATACTGGTGGAGAGgtaggtattc ... ccattttcagGCTACACACTTTGCGGTTGCT
EST: gi|164026725|gb|EL996322.1|EL996322
EST:     TTTTCGCCAACATACTGGTGGAGAG                         GCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAACGAGAAA
genomic: TTTTCGCCAACATACTGGTGGAGAGgtaggtattc ... ccattttcagGCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAACGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaggtgtttctatgtcacatttcttattgagcttttgttgttccattttcagGCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAACGAGAAAGAAGCAGTCACCGCCACTGTTCTCCAG
                                           ttccattttc  CT-rich tract
                     atttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtattcatgacagatttcccatcactggacaagtgtgtctgagatgaaggtgtttctatgtcacatttcttattgagcttttgttgttccattttcagGCTACACACTTTGCGGTTGCTTTCGAGGTGCCTGGCTGGAATAACGAGAAAGAAGCAGTCACCGCCACTGTTCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC