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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctcttttatttgtgcaaacttgtaatcttgcaaaaggtagacttgcacgtaagtgaactgtcatggatctctgtggtaacaacggctgccttttcatgttttgctctttgacaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTCGAGCCAGATAACTCAAACAAATTGCAAGATCAACCATCGGTGCACCAGA

Basic information

species Oryza sativa
transcript LOC_Os06g38470.1
intron # 6
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|86832858|gb|CI332464.1|CI332464
EST:     AGGGCACAGAACCTCCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|86523321|gb|CI163527.1|CI163527
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|58674694|gb|CK063381.1|CK063381
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACCAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|5455320|gb|AU075563.1|AU075563
EST:     AGGGCACAGAA-CTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|66925626|gb|CX112474.1|CX112474
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88252041|gb|CI350469.1|CI350469
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACAGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|55408752|gb|CV721128.1|CV721128
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88265007|gb|CI368781.1|CI368781
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88843364|gb|CI372264.1|CI372264
EST:     TCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: TCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|29685767|gb|CB682042.1|CB682042
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88272015|gb|CI388068.1|CI388068
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88510493|gb|CI437999.1|CI437999
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88459569|gb|CI519630.1|CI519630
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88255777|gb|CI353648.1|CI353648
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|89181796|gb|CI113302.1|CI113302
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88506074|gb|CI433580.1|CI433580
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88481000|gb|CI418271.1|CI418271
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|86911312|gb|CI317632.1|CI317632
EST:     GGGCACAGAACCTGCGGCTGATGGACGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGGCCATAGACGAACCAGGCTCCCTGAAAGT
genomic: GGGCACAGAACCTGCGGCTGATGGA-GTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGAT-GGCCATAGACGAACCAGGCTCCCTGAAAGT
EST: gi|86834547|gb|CI344478.1|CI344478
EST:     CTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: CTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|87009873|gb|CI277374.1|CI277374
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|86430977|gb|CI083400.1|CI083400
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|86867560|gb|CI337930.1|CI337930
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88457166|gb|CI531765.1|CI531765
EST:     CTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: CTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|86499424|gb|CI142057.1|CI142057
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88258870|gb|CI359260.1|CI359260
EST:     AGGGCACAGAACCTTCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|29680280|gb|CB676555.1|CB676555
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
EST: gi|88256779|gb|CI359167.1|CI359167
EST:     AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTT                         CCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC
genomic: AGGGCACAGAACCTGCGGCTGATGGAGTTGGTTCCTCGAAACAAACTGTTgtaagtgctc ... acaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctctgtggtaacaacggctgccttttcatgttttgctctttgacaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTCGAGCCAGATAACTCAAACAAATTGCAAGATCAACCATCGGTGCACCAGA
                         ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgctcttttatttgtgcaaacttgtaatcttgcaaaaggtagacttgcacgtaagtgaactgtcatggatctctgtggtaacaacggctgccttttcatgttttgctctttgacaactgcagCCTACCGATGCAAGTGCGATGGCCATAGACGAACCAGGCTCCCTGAAAGTCGAGCCAGATAACTCAAACAAATTGCAAGATCAACCATCGGTGCACCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA