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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATGATTTCACACCGAAAGTGTCTGATTTCGGACTGGCCAGGACTGCAAGGGGGGAGGGGAACCAGCACATCTCCACTCGTGTCATGGGAACATTTGGgtatgaatcatatccctcatccctctgtgttctgatggaatcacaatttctaatgcataatatgactatgtctttcttctcag

Basic information

species Oryza sativa
transcript LOC_Os01g09860.1
intron # 13
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|58665542|gb|CK054228.1|CK054228
EST:     GGGGGTGAGGGGAACCAGCACATCTCCACTCGTGTCATGGGAACATTTGG                         ATATGTTGCAC
genomic: GGGGG-GAGGGGAACCAGCACATCTCCACTCGTGTCATGGGAACATTTGGgtatgaatca ... ttcttctcagATATGTTGCAC
EST: gi|58676156|gb|CK064843.1|CK064843
EST:     GGGAACATTTGG                         ATATGTTGCACCGGAGTATGCCATGACAGGACATCTCCTTGTCAAGAGCGA
genomic: GGGAACATTTGGgtatgaatca ... ttcttctcagATATGTTGCACCGGAGTATGCCATGACAGGACATCTCCTTGTCAAGAGCGA
EST: gi|428954|gb|D25110.1|D25110
EST:     AGGGGGGAGGGGAACCAGCACATCTCCACTCGTGTCATGGGAACATTTGG                         ATATGTTGCACCGGAGTATGCCATGACAGGACATCTCCTTGTCAAGAGCGA
genomic: AGGGGGGAGGGGAACCAGCACATCTCCACTCGTGTCATGGGAACATTTGGgtatgaatca ... ttcttctcagATATGTTGCACCGGAGTATGCCATGACAGGACATCTCCTTGTCAAGAGCGA

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), 65 (downstream exon)
Score: 9

AGCATGATTTCACACCGAAAGTGTCTGATTTCGGACTGGCCAGGACTGCAAGGGGGGAGGGGAACCAGCACATCTCCACTCGTGTCATGGGAACATTTGGgtatgaatca ... ttcttctcagATATGTTGCACCGGAGTATGCCATGACAGGACATCTCCTTGTCAAGAGCGATGTGTACAGCTATGGAGTAGTGTTGCTTGAGCTCCTCACCGGTAGAAAG




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