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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttcaaagattgcaactgttgttgcctatgcataatttgccagtctgttttggcctaccgatctgacttttattgtcttcgtgtattttatttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGCATAGATTCATCACTGAGTGCCTCTCCTTCTCGTTGGCCTATTGATTTTG

Basic information

species Oryza sativa
transcript LOC_Os08g43400.2
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|313083968|gb|HO213751.1|HO213751
EST:     AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAG                         CAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
genomic: AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAGgtaatcatgt ... atttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
EST: gi|33793306|gb|CF322532.1|CF322532
EST:     AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAG                         CAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
genomic: AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAGgtaatcatgt ... atttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
EST: gi|29657638|gb|CB653913.1|CB653913
EST:     AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAG                         CAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC
genomic: AGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAGgtaatcatgt ... atttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGC

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: 71 (upstream exon), 70 (downstream exon)
Score: 14

CGCAGAACAAGAAACTCTCACCAGTGACATCAGTTGTCTCACCAAGTTGAAGAAGACTGATAGTGACCATGAGGATGAACTTGATGAGTATCAGGATCAGgtaatcatgt ... atttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGCATAGATTCATCACTGAGTGCCTCTCCTTCTCGTTGGCCTATTGATTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttggcctaccgatctgacttttattgtcttcgtgtattttatttgtgcagCAGTCTATTAGAGATGGATCTACAACCTTGAGAACTGTCAAAGATGTTGGCATAGATTCATCACTGAGTGCCTCTCCTTCTCGTTGGCCTATTGATTTTG
                atctgac  putative branch site (score: 14)
                                         ttttattt  putative PPT
                                     tgtattttatttgt  TA-rich tract