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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataattagcacacattattgtacttactaatatacttgcttctctatccttttgacaacctcagtgtgtgtgttatctccggtttcagGTGAGGGAGAGATGCAGAAACGAATGGACGATGTTCCAGAATCGCGTGGCAGAAGCTGATAAAGCATACATGGAACAACACAAGGTAAAAGAATAATTTG

Basic information

species Arabidopsis thaliana
transcript AT1G08040.1
intron # 14
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|86085178|gb|DR380937.1|DR380937
EST:     GGTGAGTCGGAGGAGGGGAAATCTCCATGGCAAGGG                         GTGAGGGAGAGATGCAGAAACGAATGGACGATGTTCCAGAATCGCGTGGCA
genomic: GGTGAGTCGGAGGAGGGGAAATCTCCATGGCAAGGGgtaataatta ... ccggtttcagGTGAGGGAGAGATGCAGAAACGAATGGACGATGTTCCAGAATCGCGTGGCA
EST: gi|163989013|gb|ES134040.1|ES134040
EST:     GGTGAGTCGGAGGAGGGGAAATCTCCATGGCAAGGG                         GTGAGGGAGAGATGCAGAAACGAATGGACGATGTTCCAGAATCGCGTGGC
genomic: GGTGAGTCGGAGGAGGGGAAATCTCCATGGCAAGGGgtaataatta ... ccggtttcagGTGAGGGAGAGATGCAGAAACGAATGGACGATGTTCCAGAATCGCGTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgcttctctatccttttgacaacctcagtgtgtgtgttatctccggtttcagGTGAGGGAGAGATGCAGAAACGAATGGACGATGTTCCAGAATCGCGTGGCAGAAGCTGATAAAGCATACATGGAACAACACAAGGTAAAAGAATAATTTG
                ttttgac  putative branch site (score: 3)
                                       ttatctcc  putative PPT
















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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataattagcacacattattgtacttactaatatacttgcttctctatccttttgacaacctcagtgtgtgtgttatctccggtttcagGTGAGGGAGAGATGCAGAAACGAATGGACGATGTTCCAGAATCGCGTGGCAGAAGCTGATAAAGCATACATGGAACAACACAAGGTAAAAGAATAATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA