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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactacttacccgttatttacttttaggtctttaatgtgctcaaactggtacctagtctgccaagcataagcagaatttttttttttttggtattgtcc...

Basic information

species Oryza sativa
transcript LOC_Os09g12550.1
intron # 14
splice site 5'
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|86482193|gb|CI124826.1|CI124826
EST:     CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
EST: gi|29627251|gb|CB632262.1|CB632262
EST:     CAGGATAATTCAAAACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
EST: gi|87014906|gb|CI271505.1|CI271505
EST:     CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
EST: gi|86842980|gb|CI342205.1|CI342205
EST:     CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
EST: gi|66915004|gb|CX101852.1|CX101852
EST:     CANGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
EST: gi|29673906|gb|CB670181.1|CB670181
EST:     CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
EST: gi|22305127|gb|BQ906349.1|BQ906349
EST:     AGGATAATTCAACACCAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: AGGATAATTCAACA-CAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
EST: gi|58653118|gb|CK041798.1|CK041798
EST:     CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAG                         GAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC
genomic: CAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGC

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), 73 (downstream exon)
Score: 18

GAAGGAAAGCTCAGGATAATTCAACACAATGTTGCAGACTACTAGGGGAAATATTCTTGAGgtactactta ... cttttcgcagGAACTTATCTCCACAGATTCATATGCCCAATGAATCATATCCCATCCCAGCTAAATCATGGTGGTCAATTTTGAAGGACCAACATGCAGATGTTCGCCTT




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