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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgaatggcttgcatgcttgatgcaccatcagttgcaaagttgcatgtttttttttcctttttcctcaattcactttgaattgacaaacttgtgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGCAGTTATCATGAACTTCGTAGTGAGGTAGGGCGCCTTTTTGGCCTTGAGG

Basic information

species Oryza sativa
transcript LOC_Os02g06910.1
intron # 12
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|29613687|gb|CB618700.1|CB618700
EST:     GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
EST: gi|29666700|gb|CB662975.1|CB662975
EST:     GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
EST: gi|58685183|gb|CK073870.1|CK073870
EST:     GTTCAGAT-ATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
EST: gi|29666699|gb|CB662974.1|CB662974
EST:     GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
EST: gi|29656950|gb|CB653225.1|CB653225
EST:     GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
EST: gi|58654954|gb|CK043634.1|CK043634
EST:     GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
EST: gi|29663502|gb|CB659777.1|CB659777
EST:     GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGGTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: GTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
EST: gi|29663501|gb|CB659776.1|CB659776
EST:     TGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAG                         GTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC
genomic: TGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGC

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: 68 (upstream exon), 70 (downstream exon)
Score: 30

TCAAACACTAACTACTCCGGGCTGCTTAGATGAATCAGGATATGTTCCATGTTCAGATAATGCTGATCAAGTGAAGCGACCGCATGCAACCTTTGTGAAGgtgagtgaat ... tgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGCAGTTATCATGAACTTCGTAGTGAGGTAGGGCGCCTTTTTGGCCTTGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttcctttttcctcaattcactttgaattgacaaacttgtgtcctatagGTTTACAAATCTGGAACCGTTGGAAGGTTGCTCGACATCACTAGATTTAGCAGTTATCATGAACTTCGTAGTGAGGTAGGGCGCCTTTTTGGCCTTGAGG
                               aattgac  putative branch site (score: 30)
                           tttgaatt  TA-rich tract