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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgcgttggggaatggtttatattcctctcgttatgtagtcttcattgttaattacatatcagtttatctcaagtttctccttcctcatgctttcagGCAAAGGCAGGACGACAAATGGGAGCATGATCTTTTCAGTAGTGACAAACCTCAACTTTCAA

Basic information

species Arabidopsis thaliana
transcript AT3G07170.1
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|163989379|gb|EL971501.1|EL971501
EST:     GACATCTCTACTCGCGTGCGACAAGTGACTGGGAAGAG                         GCAAAGGCAGGACGACAAATGGGAGCATGATCTTTTCAGTAGTGACAAACC
genomic: GACATCTCTACTCGCGTGCGACAAGTGACTGGGAAGAGgttcttatct ... atgctttcagGCAAAGGCAGGACGACAAATGGGAGCATGATCTTTTCAGTAGTGACAAACC
EST: gi|152034944|gb|BP840658.2|BP840658
EST:     GGCGGTTCTGGAGACATCTCTACTCGCGTGCGACAAGTGACTGGGAAGAG                         GCAAAGGCAGGACGACAAATGGGAGCATGATCTTTTCAGTAGTGACAAACC
genomic: GGCGGTTCTGGAGACATCTCTACTCGCGTGCGACAAGTGACTGGGAAGAGgttcttatct ... atgctttcagGCAAAGGCAGGACGACAAATGGGAGCATGATCTTTTCAGTAGTGACAAACC
EST: gi|152038244|gb|BP811889.2|BP811889
EST:     GGCGGTTCTGGAGACATCTCTACTCGCGTGCGAAAAGTGACTGGGAAGAG                         GCAAAGGCAGGACGA
genomic: GGCGGTTCTGGAGACATCTCTACTCGCGTGCGACAAGTGACTGGGAAGAGgttcttatct ... atgctttcagGCAAAGGCAGGACGA
EST: gi|152034950|gb|BP840772.2|BP840772
EST:     GGCGGTTCTGGAGACATCTCTACTCGCGTGCGACAAGTGACTGGGAAGAG                         GCAAAGGCAGGACGACA
genomic: GGCGGTTCTGGAGACATCTCTACTCGCGTGCGACAAGTGACTGGGAAGAGgttcttatct ... atgctttcagGCAAAGGCAGGACGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattgttaattacatatcagtttatctcaagtttctccttcctcatgctttcagGCAAAGGCAGGACGACAAATGGGAGCATGATCTTTTCAGTAGTGACAAACCTCAACTTTCAA
    tgttaat  putative branch site (score: 3)
                                tttctccttcctcatg  putative PPT
      ttaattacatatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgcgttggggaatggtttatattcctctcgttatgtagtcttcattgttaattacatatcagtttatctcaagtttctccttcctcatgctttcagGCAAAGGCAGGACGACAAATGGGAGCATGATCTTTTCAGTAGTGACAAACCTCAACTTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - -ggtttat
- - - - - - - - - - - - - -cctctcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atctcaa