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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCACCCCGCCCTCCATCGCCGGCGGGCCACCCCGCGCTTCGTTGGTTCGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttcggtttccctgccctcctttttgctgcatgtttgaccagcggttgcgcgagtcagttttcaactcttggatttgttggttttctaagaaaa...

Basic information

species Oryza sativa
transcript LOC_Os05g11550.1
intron # 1
splice site 5'
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 75 (downstream exon)
Score: 14

GGGCCACCCCGCCCTCCATCGCCGGCGGGCCACCCCGCGCTTCGTTGGTTCGGGCCGCGCCACGACGCTGCCTCGGCTCCCTTCTCCCTCCAGGCTGCACgtaatgtttc ... attggtacagGACTTGAAATTCTGTGTATGAAGTAGCATTTACTGGAGAAAGCTCAAGGGAAACTATCATGGATGCCAACTCCAGTTTAAATGAGCAAAAGTCTGAAGAA




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