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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatttgcttaatcaaaaatagaaacttgacttggggtttacattcttgcgtctttctaatgttatcatgatgtatcacactgttatttgtattttccagGTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAGCAAATTGGAAAAGGATCTTTTGGGTCAGCTCTTTTAGTGAGACATAAGC

Basic information

species Arabidopsis thaliana
transcript AT1G54510.1
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|86063725|gb|DR359482.1|DR359482
EST:     CCTTAAACTCTTAAACTCTCGCCATCAGATCTTTTTCTCTGATTTCTTGG                         GTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAG
genomic: CCTTAAACTCTTAAACTCTCGCCATCAGATCTTTTTCTCTGATTTCTTGGgtcagtattc ... tattttccagGTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAG
EST: gi|86063724|gb|DR359481.1|DR359481
EST:     CCTTAAACTCTTAAACTCTCGCCATCAGATCTTTTTCTCTGATTTCTTGG                         GTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAG
genomic: CCTTAAACTCTTAAACTCTCGCCATCAGATCTTTTTCTCTGATTTCTTGGgtcagtattc ... tattttccagGTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAG
EST: gi|86063722|gb|DR359479.1|DR359479
EST:     CCTTAAACTCTTAAACTCTCGCCNTCAGATCTTTTTCTCTGATTTCTTGG                         GTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAG
genomic: CCTTAAACTCTTAAACTCTCGCCATCAGATCTTTTTCTCTGATTTCTTGGgtcagtattc ... tattttccagGTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcgtctttctaatgttatcatgatgtatcacactgttatttgtattttccagGTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAGCAAATTGGAAAAGGATCTTTTGGGTCAGCTCTTTTAGTGAGACATAAGC
         ttctaat  putative branch site (score: 2)
                                             tattttcc  putative PPT
                                    tgttatttgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatttgcttaatcaaaaatagaaacttgacttggggtttacattcttgcgtctttctaatgttatcatgatgtatcacactgttatttgtattttccagGTGAGAAAATAACAAAGCTAGCTAGAAATGGAACAGTATGAGTTTCTTGAGCAAATTGGAAAAGGATCTTTTGGGTCAGCTCTTTTAGTGAGACATAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC