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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTCCATATAACAAGATTTCTTACAGCGACATAGTTCACAAAGgtgtgtgtttattatttaagtaactgtttctgaatttctcagaaagagcctttattaaattttttatggtcatatag

Basic information

species Oryza sativa
transcript LOC_Os01g71590.1
intron # 7
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|29680927|gb|CB677202.1|CB677202
EST:     CTGTCCATATAACAAGATTTCTTACAGCGACATAGTTCACAAAG                         ATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGNNN
genomic: CTGTCCATATAACAAGATTTCTTACAGCGACATAGTTCACAAAGgtgtgtgttt ... ggtcatatagATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGAAA
EST: gi|88839237|gb|CI000709.1|CI000709
EST:     GATTTCTTACAGCGACATAGTTCACAAAG                         ATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGAAG
genomic: GATTTCTTACAGCGACATAGTTCACAAAGgtgtgtgttt ... ggtcatatagATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGAAA
EST: gi|27554312|gb|CA998212.1|CA998212
EST:     CTGTCCATATAACAAGATTTCTTACAGCGACATAGTTCACAAAG                         ATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGNNN
genomic: CTGTCCATATAACAAGATTTCTTACAGCGACATAGTTCACAAAGgtgtgtgttt ... ggtcatatagATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGAAA
EST: gi|33801197|gb|CF326472.1|CF326472
EST:     GATTTCTTACAGCGACATAGTTCACAAAG                         ATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGNNN
genomic: GATTTCTTACAGCGACATAGTTCACAAAGgtgtgtgttt ... ggtcatatagATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGAAA
EST: gi|88845066|gb|CI083991.1|CI083991
EST:     CGACATAGTTCACAAAG                         ATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGNNN
genomic: CGACATAGTTCACAAAGgtgtgtgttt ... ggtcatatagATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGAAA

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: 63 (upstream exon), 56 (downstream exon)
Score: 105

CTGTCCATATAACAAGATTTCTTACAGCGACATAGTTCACAAAGgtgtgtgttt ... ggtcatatagATGTAACCAAGGCTGTTGCACAAATGTCTACTTCTCTGCCTGCTGCAGAAAAAAAG




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