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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATATTAGTTCTGTTTCAAGCAATGGTACAAACAGTACTGAGGTGGAACAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatctttccaatttgcctctacagatataattctgtcattccaaggttcttgcagttccaacagccttttctttggcagtactgggctactggc...

Basic information

species Oryza sativa
transcript LOC_Os01g15490.3
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|218485756|gb|FG955738.1|FG955738
EST:     TCGATCATTGTAGTTGGTGATGAAATATT                         G-TCGGCACAGTTGAGGATAAGCTA-GTGCAGGCTTGTGCAAGAAGCTTCA
genomic: TCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatc ... ggtatttcagGTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
EST: gi|25798023|gb|CA753984.1|CA753984
EST:     CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATT                         GTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
genomic: CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatc ... ggtatttcagGTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
EST: gi|58690912|gb|CK079599.1|CK079599
EST:     CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGACGAAATATT                         GTTCGGCACAGTTGAGGATAAG
genomic: CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatc ... ggtatttcagGTTCGGCACAGTTGAGGATAAG
EST: gi|58691625|gb|CK080312.1|CK080312
EST:     CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGACGAAATATT                         GTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
genomic: CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatc ... ggtatttcagGTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
EST: gi|58605964|gb|CK033997.1|CK033997
EST:     GACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGACGAAATATT                         GTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
genomic: GACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatc ... ggtatttcagGTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
EST: gi|29670775|gb|CB667050.1|CB667050
EST:     CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATT                         GTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA
genomic: CAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatc ... ggtatttcagGTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCA

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: 64 (upstream exon), 60 (downstream exon)
Score: 11

AGAATATTAGTTCTGTTTCAAGCAATGGTACAAACAGTACTGAGGTGGAACAGACGATCTCACGCTCAGCGTCGATCATTGTAGTTGGTGATGAAATATTgtgagtaatc ... ggtatttcagGTTCGGCACAGTTGAGGATAAGCTAGGTGCAGGCTTGTGCAAGAAGCTTCATGCAATTGGCTGGCGAGTTTCTCATGTAGCAGTTGTTTCCAATGAA




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