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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacactttcaaatcacacagtattagaccagaaatatttgtaccttttcaattctttgccttcctagctaacacattttggtcctctattcagATGAGCGTAACGGTGTGCCAATTGGGAAACAG

Basic information

species Oryza sativa
transcript LOC_Os12g23170.1
intron # 8
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|27546972|gb|CA765065.2|CA765065
EST:     CAACAAGACATCCATCAGCTATCTCAATGATTGGGATGTGAAAATTTCAT                         ATGAGCGTAACGGTGTGCCAATTGGGGAAACAG
genomic: CAACAAGACATCCATCAGCTATCTCAATGATTGGGATGTGAAAATTTCATgtatgacact ... ctctattcagATGAGCGTAACGGTGTGCCAATTGGG-AAACAG
EST: gi|66916200|gb|CX103048.1|CX103048
EST:     CAACAAGACATCCATCAGCTATCTCAATGATTGGGATGTGAAAATTTCAT                         ATGAGCGTAACGGTGTGCCAATTGGGAAACAG
genomic: CAACAAGACATCCATCAGCTATCTCAATGATTGGGATGTGAAAATTTCATgtatgacact ... ctctattcagATGAGCGTAACGGTGTGCCAATTGGGAAACAG
EST: gi|87007240|gb|CI277315.1|CI277315
EST:     CAACAAGACATCCATCAGCTATCTCAATGATTGGGATGTGAAAATTTCAT                         ATGAGCGTAACGGTGTGCCCATTGGGAAACAG
genomic: CAACAAGACATCCATCAGCTATCTCAATGATTGGGATGTGAAAATTTCATgtatgacact ... ctctattcagATGAGCGTAACGGTGTGCCAATTGGGAAACAG

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: 32

GATTATATTGCGATCAACCATTACACAACTTATTATGTCAGTCACCACGTCAACAAGACATCCATCAGCTATCTCAATGATTGGGATGTGAAAATTTCATgtatgacact ... ctctattcagATGAGCGTAACGGTGTGCCAATTGGGAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaccttttcaattctttgccttcctagctaacacattttggtcctctattcagATGAGCGTAACGGTGTGCCAATTGGGAAACAG
                           agctaac  putative branch site (score: 32)
                                           tcctctattc  putative PPT
      ttttcaatt  TA-rich tract