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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcagcctataatttcatgttttgcggtgcccagactaattctgtcagctgctgatctggctggatcactcataatatggtttgagtgtgattattcagGTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACACAAAGTTTGTTCCAAGAAAACGGTGGGGTGAAAGCCGATGTGATGCTGAT

Basic information

species Arabidopsis thaliana
transcript AT1G04140.1
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|164235510|gb|ES002519.1|ES002519
EST:     GCAAAACCNGTGGCTAATGTCCATCGCCAGAG                         GTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATT-CACCAAACAC
genomic: GCAAAACCAGTGGCTAATGTCCATCGCCAGAGgtcaggacta ... gattattcagGTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACAC
EST: gi|116443186|gb|EG485778.1|EG485778
EST:     CGGTCGATGATACCTTCAGCAAAACCAGTGGCTAATGTCCATCGCCAGAG                         GTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACAC
genomic: CGGTCGATGATACCTTCAGCAAAACCAGTGGCTAATGTCCATCGCCAGAGgtcaggacta ... gattattcagGTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACAC
EST: gi|86085412|gb|DR381171.1|DR381171
EST:     AACCAGTGGCTAATGTCCATCGCCAGAG                         GTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACAC
genomic: AACCAGTGGCTAATGTCCATCGCCAGAGgtcaggacta ... gattattcagGTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagctgctgatctggctggatcactcataatatggtttgagtgtgattattcagGTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACACAAAGTTTGTTCCAAGAAAACGGTGGGGTGAAAGCCGATGTGATGCTGAT
     tgctgat  putative branch site (score: 3)
                         tcataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcagcctataatttcatgttttgcggtgcccagactaattctgtcagctgctgatctggctggatcactcataatatggtttgagtgtgattattcagGTGTAGGAGTGTCTTCAAGTTACTAGTCCAGAGGGAAATTTCACCAAACACAAAGTTTGTTCCAAGAAAACGGTGGGGTGAAAGCCGATGTGATGCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT