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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggcttctaagactttgcataacatgttttagacagacaaaaaagaaaaagactttgcataacatgtatgaatttttattttattttgtttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCTGACACAACCCTCCAATATTTAGGCTCAATTCATCTCAAAAGCGGCGTTA

Basic information

species Arabidopsis thaliana
transcript AT3G10520.1
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|125021983|gb|EL094252.1|EL094252
EST:     CTCACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATG                         ACATGTGAAACAGCTATACAG
genomic: CTCACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATGgtaattactt ... ttgtgtgtagACATGTGAAACAGCTATACAG
EST: gi|164141315|gb|ES076528.1|ES076528
EST:     TGCTGTTAAAGTCTTCAAGATG                         ACATGTGAAACAGCTATACAGCTGAGGGAGGGAAGGAAAGGTGGTAGTGGC
genomic: TGCTGTTAAAGTCTTCAAGATGgtaattactt ... ttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGG-AAGGAAAGGTGGTAGTGGC
EST: gi|301501455|gb|HO206995.1|HO206995
EST:     CTCACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATG                         ACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT
genomic: CTCACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATGgtaattactt ... ttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT
EST: gi|86080209|gb|DR375966.1|DR375966
EST:     CTCACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATG                         ACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT
genomic: CTCACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATGgtaattactt ... ttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT
EST: gi|164074144|gb|ES133230.1|ES133230
EST:     CACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATG                         ACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT
genomic: CACAACAATCCTAAACTCAAAGCTCATGCTGTTAAAGTCTTCAAGATGgtaattactt ... ttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT
EST: gi|125055645|gb|EL125750.1|EL125750
EST:     TGCTGTTAAAGTCTTCAAGATG                         ACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT
genomic: TGCTGTTAAAGTCTTCAAGATGgtaattactt ... ttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaagactttgcataacatgtatgaatttttattttattttgtttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCTGACACAACCCTCCAATATTTAGGCTCAATTCATCTCAAAAGCGGCGTTA
            gcataac  putative branch site (score: 3)
                                       ttttgttt  putative PPT
              ataacatgtatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggcttctaagactttgcataacatgttttagacagacaaaaaagaaaaagactttgcataacatgtatgaatttttattttattttgtttgtgtgtagACATGTGAAACAGCTATACAGCTGAGGGAGGAAGGAAAGGTGGTAGTGGCTGACACAACCCTCCAATATTTAGGCTCAATTCATCTCAAAAGCGGCGTTA

- - - - - - - - - cataaca
- - - - - - - - - - - - - - - -agacaga
- - - - - - - - - - - - - - - - - - - caaaaaa
- - - - - - - - - - - - - - - - - - - - aaaaaga