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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagactttgttttcttttcttgtcaagaagctaccctattttcttagatccgatctcttattttggatcttgttcttaattggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG

Basic information

species Arabidopsis thaliana
transcript AT5G53120.1
intron # 2
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|86043712|gb|DR339467.1|DR339467
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86043709|gb|DR339464.1|DR339464
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86043707|gb|DR339462.1|DR339462
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATNTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86043711|gb|DR339466.1|DR339466
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86043704|gb|DR339459.1|DR339459
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86043708|gb|DR339463.1|DR339463
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86073008|gb|DR368765.1|DR368765
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86043705|gb|DR339460.1|DR339460
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|86043706|gb|DR339461.1|DR339461
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|47831735|gb|CK121419.1|CK121419
EST:     TTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
genomic: TTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
EST: gi|125233004|gb|EL247089.1|EL247089
EST:     TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTG                         GGAAAAAAGGCGGCAAAG
genomic: TCACTCCACTGTTGTTTCTGGGTGGTTTTCGGAACCTCACCCTCGCTCTGgttagacttt ... ttggatgcagGGAAAAAAGGCGGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctattttcttagatccgatctcttattttggatcttgttcttaattggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG
                                       tcttaat  putative branch site (score: 3)
                     tcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagactttgttttcttttcttgtcaagaagctaccctattttcttagatccgatctcttattttggatcttgttcttaattggatgcagGGAAAAAAGGCGGCAAAGCAGTCTATTTCAACAACCCTATGTGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG