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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaaatgcgaattgggtgaagatcttgtagatttgtgcattacagtgtatgatcgttatatatgcattattctcgttaataagtgattccaaatgcagGGTCAAATGCAGGGTGTAGATCATGTAGTGATGAAATATACTGCTTCTGGGCTCAACAGAGAAGCTGTCAACATAGCTGTTGCAAACTATGGTGATAATC

Basic information

species Arabidopsis thaliana
transcript AT5G53330.1
intron # 3
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|124789245|gb|EH878924.1|EH878924
EST:     AGAATCCACCGGCTAAGTTTCATGAACCATCACCTTCTTCAGTG                         GGTCAAATGCAGGGTGTAGATCATGTAGTGATGAAATATACTGCTTCTG
genomic: AGAATCCACCGGCTAAGTTTCATGAACCATCACCTTCTTCAGTGgtatggctct ... ccaaatgcagGGTCAAATGCAGGGTGTAGATCATGTAGTGATGAAATATACTGCTTCTG
EST: gi|86083697|gb|DR379456.1|DR379456
EST:     GGAGTGAGAATCCACCGGCTAAGTTTCATGAACCATCACCTTCTTCAGTG                         GGTCAAATGCAGGGTGTAGATCATGTAGTGATGAAATATACTGCTTCTGGG
genomic: GGAGTGAGAATCCACCGGCTAAGTTTCATGAACCATCACCTTCTTCAGTGgtatggctct ... ccaaatgcagGGTCAAATGCAGGGTGTAGATCATGTAGTGATGAAATATACTGCTTCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtatgatcgttatatatgcattattctcgttaataagtgattccaaatgcagGGTCAAATGCAGGGTGTAGATCATGTAGTGATGAAATATACTGCTTCTGGGCTCAACAGAGAAGCTGTCAACATAGCTGTTGCAAACTATGGTGATAATC
                              cgttaat  putative branch site (score: 4)
            ttatatatgcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaaatgcgaattgggtgaagatcttgtagatttgtgcattacagtgtatgatcgttatatatgcattattctcgttaataagtgattccaaatgcagGGTCAAATGCAGGGTGTAGATCATGTAGTGATGAAATATACTGCTTCTGGGCTCAACAGAGAAGCTGTCAACATAGCTGTTGCAAACTATGGTGATAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
ttaaaaa
- - - - - - - - - - - - - - - -gatttgt