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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCTGCTCCGCCTACCCGACCTCCGGTGGCCTCTACTACTGGAGTGCCAAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTGgtgagtacgtgtatgtattgtgaattgtccgtctctcatgaacttctcgttccaagaaatgaggaaagccttgcaaaaatttcatactccagcatctttt...

Basic information

species Oryza sativa
transcript LOC_Os01g71720.1
intron # 2
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|58611354|gb|CK039066.1|CK039066
EST:     AAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTG                         GTTTAACATCACGGGACAG
genomic: AAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTGgtgagtacgt ... tgctttgcagGTTTAACATCACGGGACAG
EST: gi|66923657|gb|CX110505.1|CX110505
EST:     AAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTG                         GTTTAACATCACGGGACAG
genomic: AAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTGgtgagtacgt ... tgctttgcagGTTTAACATCACGGGACAG
EST: gi|88421312|gb|CI569157.1|CI569157
EST:     AAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTG                         GTTTAACATCACGGGACAG
genomic: AAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTGgtgagtacgt ... tgctttgcagGTTTAACATCACGGGACAG

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: 72 (upstream exon), 65 (downstream exon)
Score: 3

AGATCTGCTCCGCCTACCCGACCTCCGGTGGCCTCTACTACTGGAGTGCCAAGCTCGCCGGCAACGACTGGGCTCCCTTTGCTTCTTGGATCACTGGCTGgtgagtacgt ... tgctttgcagGTTTAACATCACGGGACAG




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