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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTCGGCCACGTGGAACCGGCCGCCAAGGACCCCATCCTCGGCGTCACCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatctgttcccttcctcctcctcctccgtttcatcatgaattgtctcgattgatccccgagctgtgtgtgtgtgtgttcgccgcag

Basic information

species Oryza sativa
transcript LOC_Os06g35540.1
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|66917395|gb|CX104243.1|CX104243
EST:     CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTC                         GGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
genomic: CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatct ... ttcgccgcagGGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
EST: gi|58607841|gb|CK035874.1|CK035874
EST:     CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTC                         GGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
genomic: CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatct ... ttcgccgcagGGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
EST: gi|13807574|gb|AU181996.1|AU181996
EST:     CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTC                         GGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
genomic: CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatct ... ttcgccgcagGGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
EST: gi|88406564|gb|CI599057.1|CI599057
EST:     CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTC                         GGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
genomic: CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatct ... ttcgccgcagGGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
EST: gi|88392405|gb|CI612879.1|CI612879
EST:     CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTC                         GGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
genomic: CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatct ... ttcgccgcagGGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
EST: gi|88403459|gb|CI573182.1|CI573182
EST:     CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTC                         GGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC
genomic: CCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatct ... ttcgccgcagGGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGC

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: 75 (upstream exon), 53 (downstream exon)
Score: 22

GTGGTTCGGCCACGTGGAACCGGCCGCCAAGGACCCCATCCTCGGCGTCACCGAGGCGTTCCTCGCCGACCCCTCCCCGGACAAAGTCAACGTCGGCGTCgtgcgtatct ... ttcgccgcagGGCGCGTACCGGGACGACAGCGGGAAGCCCGTGGTGCTGGAGTGCGTGCGCGAGGCGGAGCGGCGGATCGCCGGGAGCATGAACAT




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