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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacattttcgtcttttcttgtatggaattttcatagatctggagagatctgatttttatggtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGAGAGGATGGAGGCGGCGGAGCTGAAAGAGCTTGAGGAGAAAGCGGAGACT

Basic information

species Arabidopsis thaliana
transcript AT1G60870.1
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|86054639|gb|DR350396.1|DR350396
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGACGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
EST: gi|86054637|gb|DR350394.1|DR350394
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGACGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
EST: gi|86054650|gb|DR350407.1|DR350407
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGACGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
EST: gi|124878389|gb|EH957826.1|EH957826
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGAGGAGTATAGGCGG
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGG
EST: gi|86054638|gb|DR350395.1|DR350395
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGACGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
EST: gi|86054646|gb|DR350403.1|DR350403
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGRTATGGAGTGGGGGATGGACGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
EST: gi|164027864|gb|ES175228.1|ES175228
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGAT
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGAT
EST: gi|86054627|gb|DR350384.1|DR350384
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
EST: gi|125030398|gb|EL102667.1|EL102667
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGGTGGGGGATGGAGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAG-TGGGGGATGGAGGA
EST: gi|86054626|gb|DR350383.1|DR350383
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGG
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGG
EST: gi|86054645|gb|DR350402.1|DR350402
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGACGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA
EST: gi|86054659|gb|DR350416.1|DR350416
EST:     CTCGNAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGAT
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGAT
EST: gi|86054630|gb|DR350387.1|DR350387
EST:     CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCG                         GGATATGGAGTGGGGGATGGACGAGTATAGGCGGACGTTGGAGGAGATGGA
genomic: CTCGAAGAAGCTGAAGAATCTCTCCGTGAAGCTGAACTTGAACTTGATCGgtaacatttt ... gtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtatggaattttcatagatctggagagatctgatttttatggtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGAGAGGATGGAGGCGGCGGAGCTGAAAGAGCTTGAGGAGAAAGCGGAGACT
                               atctgat  putative branch site (score: 4)
                                              tttcttc  putative PPT
          aattttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacattttcgtcttttcttgtatggaattttcatagatctggagagatctgatttttatggtttcttcagGGATATGGAGTGGGGGATGGAGGAGTATAGGCGGACGTTGGAGGAGATGGAGAGGATGGAGGCGGCGGAGCTGAAAGAGCTTGAGGAGAAAGCGGAGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA