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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctgaacttcgcaattttgcctcaaattttaacttgttcctgtccgttgtctgctcgctaatgaagttgttccctctccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCCGGTGCTTTTGTGAAGTTGTAGCTTCTGCCAAGTTTAATTTACCTCAGGC

Basic information

species Oryza sativa
transcript LOC_Os01g56520.2
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|88956618|gb|CI092818.1|CI092818
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|86482881|gb|CI125514.1|CI125514
EST:     CAGTGACGATGTTTGGTTGCCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88223563|gb|CI223412.1|CI223412
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88992801|gb|CI035763.1|CI035763
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|86425351|gb|CI070448.1|CI070448
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|3759682|gb|C96940.1|C96940
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACNCCTTAGGAACNTTGCGGTAGACAAGAACTGGANCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88908465|gb|CI091058.1|CI091058
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88510138|gb|CI437644.1|CI437644
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|8930555|gb|BE225319.1|BE225319
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGCAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88268046|gb|CI378818.1|CI378818
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|86432137|gb|CI085748.1|CI085748
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAGAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|58590658|gb|CF988966.1|CF988966
EST:     AGTGACGATAGTTTGGGTGGCAGTCAGCCTACCTACTCTCAAGCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGCAGACAAGAACTGGAGCC
genomic: AGTGACGAT-GTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|86872406|gb|CI342030.1|CI342030
EST:     CAGTGACGATGTTT-GGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|86507304|gb|CI149937.1|CI149937
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|86259576|gb|CI065449.1|CI065449
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88282616|gb|CI404012.1|CI404012
EST:     CAGTGACGATNTTTGGGTTGCAGTCAGCCTACGTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|33663698|gb|CF294665.1|CF294665
EST:     CAGTGACGATGTTTGGGTGGCAGTCANCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTANGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88848672|gb|CI087194.1|CI087194
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|109712254|gb|CI104862.1|CI104862
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88846728|gb|CI373496.1|CI373496
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88292223|gb|CI535017.1|CI535017
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|89180192|gb|CI044471.1|CI044471
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88275470|gb|CI395321.1|CI395321
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACTTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88903439|gb|CI088977.1|CI088977
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
EST: gi|88476741|gb|CI414012.1|CI414012
EST:     CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAG                         GCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC
genomic: CAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCC

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: 50 (upstream exon), 26 (downstream exon)
Score: 1

CCACGCCGTCCTGACCTGGTATTGCCGGAGGGCGCGACCGTTCTTCCTTTCAGTGACGATGTTTGGGTGGCAGTCAGCCTACCTACTCTCAACCATTAAGgtattctgaa ... ccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCCGGTGCTTTTGTGAAGTTGTAGCTTCTGCCAAGTTTAATTTACCTCAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttcctgtccgttgtctgctcgctaatgaagttgttccctctccaaatgcagGCAGAAGAAAACTACGCCTTAGGAACGTTGCGGTAGACAAGAACTGGAGCCGGTGCTTTTGTGAAGTTGTAGCTTCTGCCAAGTTTAATTTACCTCAGGC
                       cgctaat  putative branch site (score: 1)
                                  ttgttccctctcc  putative PPT
                          taatgaa  TA-rich tract