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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctatcttaaatttgccgctttagtctgccagttcttacctatgcctatgtttgaaccgaggcatgttttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAATTATCAGCCAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G39770.1
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|301502516|gb|HO208056.1|HO208056
EST:     TCCCAAAGCCCCTTGTCGATTTTGCTAATAAACCCATGATCCTTCATCAG                         ATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
genomic: TCCCAAAGCCCCTTGTTGATTTTGCTAATAAACCCATGATCCTTCATCAGgtaatctatc ... tttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
EST: gi|116433537|gb|EG476129.1|EG476129
EST:     TCCCAAAGCCCCTTGTTGATTTTGCTAATAAACCCATGATCCTTCATCAG                         ATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
genomic: TCCCAAAGCCCCTTGTTGATTTTGCTAATAAACCCATGATCCTTCATCAGgtaatctatc ... tttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
EST: gi|116433540|gb|EG476132.1|EG476132
EST:     TCCCAAAGCCCCTTGTTGATTTTGCTAATAAACCCATGATCCTTCATCAG                         ATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
genomic: TCCCAAAGCCCCTTGTTGATTTTGCTAATAAACCCATGATCCTTCATCAGgtaatctatc ... tttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
EST: gi|125159603|gb|EL187609.1|EL187609
EST:     TGTTGATTTTGCTAATAAACCCATGATCCTTCATCAG                         ATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
genomic: TGTTGATTTTGCTAATAAACCCATGATCCTTCATCAGgtaatctatc ... tttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
EST: gi|124803219|gb|EH891648.1|EH891648
EST:     ACCCATGATCCTTCATCAG                         ATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT
genomic: ACCCATGATCCTTCATCAGgtaatctatc ... tttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctgccagttcttacctatgcctatgtttgaaccgaggcatgttttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAATTATCAGCCAGAG
          ttcttac  putative branch site (score: 2)
                                          tgttttctt  putative PPT
                        tatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctatcttaaatttgccgctttagtctgccagttcttacctatgcctatgtttgaaccgaggcatgttttcttgtagATAGAGGCTCTTAAGGCAGTTGGAGTTGATGAAGTGGTTTTGGCCATCAATTATCAGCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG