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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgttttatcccaaacaccaaattatttacacgttgttttgttaataatgagcaatgtactgttttgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAACCAGTCCTTTTCCGTTCCTCCCGGTTTGCTTAGACATCACTGAAGCCGC

Basic information

species Arabidopsis thaliana
transcript AT2G18230.1
intron # 8
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|116443156|gb|EG485748.1|EG485748
EST:     GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT                         GGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
genomic: GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCATgtaagtttgt ... tgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
EST: gi|163980162|gb|ES149479.1|ES149479
EST:     AAGCTTTCCTTCCCGCTCAAGCTGCCATAGAACGCTATCAAGGACTCCAT                         GGATCTTTACGCAGCTTACATCAAAGC
genomic: AAGCTTTCCTTCCCGCTCAAGCTGCCATAGA-CGCTATCAAGGACTCCATgtaagtttgt ... tgaaacgcagGGATCTTTACGCAGCTTACATCAAAGC
EST: gi|116443161|gb|EG485753.1|EG485753
EST:     GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT                         GGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
genomic: GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCATgtaagtttgt ... tgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
EST: gi|116451434|gb|EG494026.1|EG494026
EST:     GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT                         GGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
genomic: GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCATgtaagtttgt ... tgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
EST: gi|86075558|gb|DR371315.1|DR371315
EST:     GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT                         GGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
genomic: GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCATgtaagtttgt ... tgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
EST: gi|116451435|gb|EG494027.1|EG494027
EST:     GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT                         GGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
genomic: GAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCATgtaagtttgt ... tgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
EST: gi|125297047|gb|EL311132.1|EL311132
EST:     AGACGCTATCAAGGACTCCAT                         GGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA
genomic: AGACGCTATCAAGGACTCCATgtaagtttgt ... tgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatttacacgttgttttgttaataatgagcaatgtactgttttgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAACCAGTCCTTTTCCGTTCCTCCCGGTTTGCTTAGACATCACTGAAGCCGC
                   tgttaat  putative branch site (score: 3)
                                       ctgtttt  putative PPT
             ttgttttgttaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgttttatcccaaacaccaaattatttacacgttgttttgttaataatgagcaatgtactgttttgaaacgcagGGATCTTTACGCAGCTTACATCAAAGCTGGCCTGCAACGCTAATGAAGAAACCAGTCCTTTTCCGTTCCTCCCGGTTTGCTTAGACATCACTGAAGCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC