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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcccacttgttgtctttataattcttcttcgataaattttgttccgacatacctccctatgttgcaaacaactgacgtattgaacaaatatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCACAAAACGTGGTTGTTTTGACACCTGACAATTTCGATGAGATTGTTCTGGATCAAAACAAAGATGTCCTAGT

Basic information

species Arabidopsis thaliana
transcript AT2G47470.2
intron # 4
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|125301792|gb|EL315877.1|EL315877
EST:     GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAG                         GCACCAACGTAAAATTAGCTGCAGTTCCA
genomic: GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAGgtatgatagt ... tatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCA
EST: gi|164228010|gb|ES057155.1|ES057155
EST:     CAAGGAAGGAG                         GCACCAACGTAAAATTAGCTGCAGTTCCACAAAACGTGGTTGTTTTGACAC
genomic: CAAGGAAGGAGgtatgatagt ... tatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCACAAAACGTGGTTGTTTTGACAC
EST: gi|125248627|gb|EL262712.1|EL262712
EST:     AATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAG                         GCACCAACGTAAAATTAGCTGCAGTTCCA
genomic: AATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAGgtatgatagt ... tatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCA
EST: gi|116441306|gb|EG483898.1|EG483898
EST:     GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAG                         GCACCAACGTAAAATTAGCTGCAGTTCCACAAA-CGTGGTTGTTTTGACAC
genomic: GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAGgtatgatagt ... tatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCACAAAACGTGGTTGTTTTGACAC
EST: gi|301501187|gb|HO206727.1|HO206727
EST:     GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAG                         GCACCAACGTAAAATTAGCTGCAGTTCCACAAAAACGTGGTTGTTTTGACA
genomic: GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAGgtatgatagt ... tatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCACAAAA-CGTGGTTGTTTTGACA
EST: gi|164083473|gb|ES106372.1|ES106372
EST:     GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAG                         GCACCAACGTAAAATTAGCTAGCAGTTCCACAAAACGTGGTTGTTTTG
genomic: GGGTCCACGCAATGCTGAAGCTTTGGCTGAATACGTGAACAAGGAAGGAGgtatgatagt ... tatgtttcagGCACCAACGTAAAATTAGCT-GCAGTTCCACAAAACGTGGTTGTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgacatacctccctatgttgcaaacaactgacgtattgaacaaatatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCACAAAACGTGGTTGTTTTGACACCTGACAATTTCGATGAGATTGTTCTGGATCAAAACAAAGATGTCCTAGT
                          aactgac  putative branch site (score: 2)
                                  tattgaacaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcccacttgttgtctttataattcttcttcgataaattttgttccgacatacctccctatgttgcaaacaactgacgtattgaacaaatatgtttcagGCACCAACGTAAAATTAGCTGCAGTTCCACAAAACGTGGTTGTTTTGACACCTGACAATTTCGATGAGATTGTTCTGGATCAAAACAAAGATGTCCTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG