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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgaatttaatttccatttatgtgctgcttatcaattacaactagctgagttcatcttcagtatttctacttaatctgtagttttgcttaacctttgcttgtttatttcagGAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGATGATATCAAATCCACGCCTATCTGCTCCAGCCACGGCACTATACCTTAAC

Basic information

species Oryza sativa
transcript LOC_Os01g67500.1
intron # 5
splice site 3'
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|58603236|gb|CK013764.1|CK013764
EST:     CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAG                         GAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT
genomic: CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAGgtattgaatt ... tttatttcagGAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT
EST: gi|58670104|gb|CK058790.1|CK058790
EST:     CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAG                         GAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT
genomic: CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAGgtattgaatt ... tttatttcagGAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT
EST: gi|86900707|gb|CI302124.1|CI302124
EST:     CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAG                         GAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT
genomic: CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAGgtattgaatt ... tttatttcagGAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT
EST: gi|88412069|gb|CI566798.1|CI566798
EST:     CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAG                         GAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT
genomic: CAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAGgtattgaatt ... tttatttcagGAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGAT

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), 32 (downstream exon)
Score: 3

CACTAGTTCAGTTCTTGAGGAACGCTGTGCAAGATGGAAATGAGAAGGCACAGGAAATTGGTGCCATGGCTCTTTTTAACCTTGCTGTCAACAATAACAGgtattgaatt ... tttatttcagGAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGATGATATCAAATCCACGCCTATCTGCTCCAGCCACGGCACTATACCTTAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtatttctacttaatctgtagttttgcttaacctttgcttgtttatttcagGAACAAGGGACTTTTATTGTCTGCTGGAGTAATCGATCAACTTGAGCAGATGATATCAAATCCACGCCTATCTGCTCCAGCCACGGCACTATACCTTAAC
                             gcttaac  putative branch site (score: 3)
                                             tttatttc  putative PPT
     tatttctacttaat  TA-rich tract