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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgagaatccattaaagtcatattcatgctgctgataccagcttaataatgttgagattgagataattgatgatccttaaatttttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGACCCAAGTGGCCATTGAATGGGCTCGATGGCTATCTGACTGATGTTTGGC

Basic information

species Oryza sativa
transcript LOC_Os07g25710.1
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|89164048|gb|CI101136.1|CI101136
EST:     AGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGAGAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: AGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|25805355|gb|CA761316.1|CA761316
EST:     CGTGAAGGATGTTCCAGAAAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|29673026|gb|CB669301.1|CB669301
EST:     CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|86864674|gb|CI344223.1|CI344223
EST:     TCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: TCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|88993115|gb|CI108743.1|CI108743
EST:     GATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: GATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|88276417|gb|CI397021.1|CI397021
EST:     GAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: GAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|86260267|gb|CI066140.1|CI066140
EST:     CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|89189637|gb|CI049176.1|CI049176
EST:     CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCCAACCAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|88966647|gb|CI365870.1|CI365870
EST:     GTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGA-GGTCTCTCCAAGATGTGGA
genomic: GTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|32948129|gb|BP184701.1|BP184701
EST:     CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
EST: gi|89198566|gb|CI016651.1|CI016651
EST:     CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAG                         AATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA
genomic: CGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGA

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: 20

ACCTCAGCAGAAGGAACAAAGCCATCTTCTGATCTTCCAGAATCTTCTGCCGTGAAGGATGTTCCAGAGAACAGTCAGAACGGAATAGCCAAACAAACAGgcatgagaat ... tttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGACCCAAGTGGCCATTGAATGGGCTCGATGGCTATCTGACTGATGTTTGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcttaataatgttgagattgagataattgatgatccttaaatttttgtttcagAATCAGGTGACAGATAATGAGGATGTGATGAGGGTCTCTCCAAGATGTGGACCCAAGTGGCCATTGAATGGGCTCGATGGCTATCTGACTGATGTTTGGC
                          aattgat  putative branch site (score: 20)
                                           tttttgtttc  putative PPT
                                      ttaaatttttgtttca  TA-rich tract