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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacagttttgaatcatcacgattatatctgggattcactggttccattggtaaaagctgcaagtatttgttagtgttttgatataagattaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAAATCGATATATTGGTTGCGGGGATTGGAACTGGTGGAACTATCACTGGTG

Basic information

species Arabidopsis thaliana
transcript AT2G43750.2
intron # 5
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|125237812|gb|EL251897.1|EL251897
EST:     CCAATTCCTACATGCTCCAACAGTTTGACAACCCTGCCAATCCCAAG                         ATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA
genomic: CCAATTCCTACATGCTCCAACAGTTTGACAACCCTGCCAATCCCAAGgtctgtaatt ... ttaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA
EST: gi|125241272|gb|EL255357.1|EL255357
EST:     CCCTGCCAATCCCAAG                         ATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA
genomic: CCCTGCCAATCCCAAGgtctgtaatt ... ttaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA
EST: gi|124832063|gb|EH916502.1|EH916502
EST:     TTTGACAACCCTGCCAATCCCAAG                         ATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA
genomic: TTTGACAACCCTGCCAATCCCAAGgtctgtaatt ... ttaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA
EST: gi|124903928|gb|EH978008.1|EH978008
EST:     CCTACATGCTCCAACAGTTTGACAACCCTGCCAATCCCAAG                         ATTCATTATGAGACGACTGGTCCTGAGATTTAGGGAAGATACAAGAGGCAA
genomic: CCTACATGCTCCAACAGTTTGACAACCCTGCCAATCCCAAGgtctgtaatt ... ttaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTT-GGGAAGATACAAGAGGCAA
EST: gi|124897766|gb|EH973980.1|EH973980
EST:     CAACCCTGCCAATCCCAAG                         ATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA
genomic: CAACCCTGCCAATCCCAAGgtctgtaatt ... ttaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattggtaaaagctgcaagtatttgttagtgttttgatataagattaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAAATCGATATATTGGTTGCGGGGATTGGAACTGGTGGAACTATCACTGGTG
                                ttttgat  putative branch site (score: 4)
                              tgttttgatataagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatacagttttgaatcatcacgattatatctgggattcactggttccattggtaaaagctgcaagtatttgttagtgttttgatataagattaaatgcagATTCATTATGAGACGACTGGTCCTGAGATTTGGGAAGATACAAGAGGCAAAATCGATATATTGGTTGCGGGGATTGGAACTGGTGGAACTATCACTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA