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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctctcgattattactaaacttacgtgtacgagagaaaggttgtgtatttagcttgacctttttagtttcttatgacagTGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTACTACAGGGCTAAAGGCGTAAAATTTATAAAAGGAACGGTTTTGACATCATTTGA

Basic information

species Arabidopsis thaliana
transcript AT3G27820.1
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|124998242|gb|EL070511.1|EL070511
EST:     TGACGATGGTTTTCCCAGAGGCTCACTGCA                         TGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTACTACA
genomic: TGACGATGGTTTTCCCAGAGGCTCACTGCAgtaagttctc ... cttatgacagTGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTACTACA
EST: gi|124845366|gb|EH929803.1|EH929803
EST:     AGTGATCAACAAAATCAATGTGACGATGGTTT-CCCAGAGGCTCACTGCA                         TGGCACGTCTCTTTACGCCCAAG
genomic: AGTGATCAACAAAATCAATGTGACGATGGTTTTCCCAGAGGCTCACTGCAgtaagttctc ... cttatgacagTGGCACGTCTCTTTACGCCCAAG
EST: gi|125063910|gb|EL131719.1|EL131719
EST:     CAAAATCAATGTGACGATGGTTTTCCCAGAGGCTCACTGCA                         TGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTACTACA
genomic: CAAAATCAATGTGACGATGGTTTTCCCAGAGGCTCACTGCAgtaagttctc ... cttatgacagTGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTACTACA
EST: gi|125102679|gb|EL157355.1|EL157355
EST:     AGTGATCAACAAAATCAATGTGACGATGGTTTTCCCAGAGGCTCACTGCA                         TGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTAC
genomic: AGTGATCAACAAAATCAATGTGACGATGGTTTTCCCAGAGGCTCACTGCAgtaagttctc ... cttatgacagTGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtacgagagaaaggttgtgtatttagcttgacctttttagtttcttatgacagTGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTACTACAGGGCTAAAGGCGTAAAATTTATAAAAGGAACGGTTTTGACATCATTTGA
                           gcttgac  putative branch site (score: 4)
                                 cctttttagtttctt  CT-rich tract
                                   tttttagtttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctctcgattattactaaacttacgtgtacgagagaaaggttgtgtatttagcttgacctttttagtttcttatgacagTGGCACGTCTCTTTACGCCCAAGATTGCAAGTTTGTATGAAGACTACTACAGGGCTAAAGGCGTAAAATTTATAAAAGGAACGGTTTTGACATCATTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA