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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaattgtggtcacgatgttaacgaatttcgtatcagattcttccatttttctttaatatgtctagctttctcttgcttgttctgtatttacattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
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|47832017|gb|CK121701.1|CK121701
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|152033932|gb|BP820357.2|BP820357
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031310|gb|DR327063.1|DR327063
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031302|gb|DR327055.1|DR327055
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|116433606|gb|EG476198.1|EG476198
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         AGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|116433595|gb|EG476187.1|EG476187
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031298|gb|DR327051.1|DR327051
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031307|gb|DR327060.1|DR327060
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031303|gb|DR327056.1|DR327056
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031311|gb|DR327064.1|DR327064
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031308|gb|DR327061.1|DR327061
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031304|gb|DR327057.1|DR327057
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031313|gb|DR327066.1|DR327066
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031315|gb|DR327068.1|DR327068
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031316|gb|DR327069.1|DR327069
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGNTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031312|gb|DR327065.1|DR327065
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031300|gb|DR327053.1|DR327053
EST:     CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
EST: gi|86031317|gb|DR327070.1|DR327070
EST:     CCTTCCGTCTTCTCTACTCNNNNCGCAGAGCTTCAATTTCTCCCTCGCAG                         GGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG
genomic: CCTTCCGTCTTCTCTACTCACAACGCAGAGCTTCAATTTCTCCCTCGCAGgtatttttcg ... acattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttctttaatatgtctagctttctcttgcttgttctgtatttacattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG
      ctttaat  putative branch site (score: 4)
     tctttaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaattgtggtcacgatgttaacgaatttcgtatcagattcttccatttttctttaatatgtctagctttctcttgcttgttctgtatttacattcgtagGGATTCGGATCAGTTCAATTTCAAGTTTCTGAACCACTCATGGATCAGGCGGAGCTGAGTATAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - aacgaat