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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactgtatgtgtgtgcatattttacaactagtttggttgttttgctaacttctgccgtagtttggctgttttgctaacttctgccctcgcctgtttcagGCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATCATGACTCGG

Basic information

species Arabidopsis thaliana
transcript AT5G03650.1
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|116483369|gb|EG525961.1|EG525961
EST:     TGATGCCGGTATAACTTATAGAGAGTGGGCGCCTGGAGCTAAG                         GCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATC
genomic: TGATGCCGGTATAACTTATAGAGAGTGGGCGCCTGGAGCTAAGgtttgtttct ... cctgtttcagGCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATC
EST: gi|116412441|gb|EG455033.1|EG455033
EST:     TGATGCCGGTATAACTTATAGGGAGTGGGCGCCTGGAGCTAAG                         GCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATC
genomic: TGATGCCGGTATAACTTATAGAGAGTGGGCGCCTGGAGCTAAGgtttgtttct ... cctgtttcagGCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATC
EST: gi|116436516|gb|EG479108.1|EG479108
EST:     TGATGCCGGTATAACTTATAGAGAGTGGGCGCCTGGAGCTAAG                         GCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGACATC
genomic: TGATGCCGGTATAACTTATAGAGAGTGGGCGCCTGGAGCTAAGgtttgtttct ... cctgtttcagGCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacttctgccgtagtttggctgttttgctaacttctgccctcgcctgtttcagGCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATCATGACTCGG
                           tgctaac  putative branch site (score: 1)
                                 cttctgccctcgcct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactgtatgtgtgtgcatattttacaactagtttggttgttttgctaacttctgccgtagtttggctgttttgctaacttctgccctcgcctgtttcagGCTGCATCACTTATCGGAGATTTCAACAACTGGAATTCTAATGCAGATATCATGACTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - acaacta
- - - - - - - - - - - - - - - agtttgg
- - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - -cttctgc