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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttcttcagtcatctttctgctgtttgcatgtgcacaagtgaaatttatttatccagaatgaaaatgacttaacttatcaggatggttttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAACACCATCACAGAGAGACGAGAGGAAAAGCTTGTGAAGAAGTAACTCAAA

Basic information

species Oryza sativa
transcript LOC_Os01g66970.3
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|88963723|gb|CI031075.1|CI031075
EST:     ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|58694156|gb|CK082843.1|CK082843
EST:     ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|88966199|gb|CI013075.1|CI013075
EST:     ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|86536682|gb|CI176888.1|CI176888
EST:     TAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: TAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|14192139|gb|AU184350.1|AU184350
EST:     GTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: GTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|86889269|gb|CI315880.1|CI315880
EST:     ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|88268805|gb|CI377709.1|CI377709
EST:     ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|88263819|gb|CI367593.1|CI367593
EST:     ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
EST: gi|702921|gb|D49212.1|D49212
EST:     ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAG                         GTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA
genomic: ATGTTATAGCCCGTTCTTGTTATGCTTTTCAACACCGGAGGCGAAGACAGgtatacttcc ... ttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatttatccagaatgaaaatgacttaacttatcaggatggttttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAACACCATCACAGAGAGACGAGAGGAAAAGCTTGTGAAGAAGTAACTCAAA
                        acttaac  putative branch site (score: 3)
                                           ttttctctgc  putative PPT
              aatgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttcttcagtcatctttctgctgtttgcatgtgcacaagtgaaatttatttatccagaatgaaaatgacttaacttatcaggatggttttctctgcagGTTTAGGGGCCACCTGAACCTGGCTGGAAGCATTTACTCAAAACAACTCAACACCATCACAGAGAGACGAGAGGAAAAGCTTGTGAAGAAGTAACTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT