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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttcattttggcatattgttatcacctattcaacttaattatgtttgttctagtatgttgttaagttgcttgattacttctttatgaactccctagcaaagtaagaatcaacttttgccagaaatgactggagaattcaactatcactcacttcaagaactctcttatatgttgccttctttcctgcagGGATATTTCTTGCTTTCAGAAGGGGCCAAAGTTCGTCATGGTGTTCGGACTATAAATATCACAATTTCTGCTCGAAATCCTTGCTTTGGAAATAG

Basic information

species Oryza sativa
transcript LOC_Os03g45770.2
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|29624463|gb|CB629474.1|CB629474
EST:     AGAGACGAAGCAAAGCATTTGAACCTACCTATTTATATGGTGTGGAGAAG                         GGATATTTCTTGC
genomic: AGAGACGAAGCAAAGCATTTGAACCTACCTATTTATATGGTGTGGAGAAGgtaaggttca ... tttcctgcagGGATATTTCTTGC
EST: gi|157650552|gb|EX450186.1|EX450186
EST:     GGTGTGGAGAAG                         GGATATTTCTTGCTTTCAGAAGGGGCCAAAGTTCGTCATGGTGTTCGGACT
genomic: GGTGTGGAGAAGgtaaggttca ... tttcctgcagGGATATTTCTTGCTTTCAGAAGGGGCCAAAGTTCGTCATGGTGTTCGGACT

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: 56 (upstream exon), 75 (downstream exon)
Score: 15

TACAGTGGTTTGAGAGACGAAGCAAAGCATTTGAACCTACCTATTTATATGGTGTGGAGAAGgtaaggttca ... tttcctgcagGGATATTTCTTGCTTTCAGAAGGGGCCAAAGTTCGTCATGGTGTTCGGACTATAAATATCACAATTTCTGCTCGAAATCCTTGCTTTGGAAATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaactatcactcacttcaagaactctcttatatgttgccttctttcctgcagGGATATTTCTTGCTTTCAGAAGGGGCCAAAGTTCGTCATGGTGTTCGGACTATAAATATCACAATTTCTGCTCGAAATCCTTGCTTTGGAAATAG
          cactcac  putative branch site (score: 15)
                                   tgttgccttctttcct  putative PPT
                              ttatatgtt  TA-rich tract