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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtttctacttaatgttgtccgtagccgtaatactcctgcattttttaattatatctggtaatttattttttgctgcaaatgtattctattggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGAAACTATCATGGATGCCAACTCCAGTTTAAATGAGCAAAAGTCTGAAGAA

Basic information

species Oryza sativa
transcript LOC_Os05g11550.2
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|58663416|gb|CK052102.1|CK052102
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|88722240|gb|CI745750.1|CI745750
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GAATTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|88402728|gb|CI613176.1|CI613176
EST:     CGGGCCGCGCCACGACGCTGTCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|58672770|gb|CK061456.1|CK061456
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|88356730|gb|CI619216.1|CI619216
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|29630243|gb|CB635252.1|CB635252
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|58671706|gb|CK060392.1|CK060392
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|29681334|gb|CB677609.1|CB677609
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|66920389|gb|CX107237.1|CX107237
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA
EST: gi|88692699|gb|CI736274.1|CI736274
EST:     CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCAC                         GACTTGAAATTCTGTGTATGAAGTAGCATTTANTGGAGAAAGCTCAAGGGA
genomic: CGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaattatatctggtaatttattttttgctgcaaatgtattctattggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGAAACTATCATGGATGCCAACTCCAGTTTAAATGAGCAAAAGTCTGAAGAA
 ttttaat  putative branch site (score: 3)
                                         ttctatt  putative PPT
     attatatctggtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtttctacttaatgttgtccgtagccgtaatactcctgcattttttaattatatctggtaatttattttttgctgcaaatgtattctattggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGAAACTATCATGGATGCCAACTCCAGTTTAAATGAGCAAAAGTCTGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- tgtttct
- - - - - - - atgttgt
- - - - - - - - - - - - - - - - - -ctcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgcaa