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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATCCACCGTCGCCTCCGCCGTCCGGCAGTTCGCCGACGCCGACAGCACCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatacataaaaatattacaataaattataattttttcaattgtgatatatattttgttagaattttaattaagtttaattaattttctattataatatttttggttaattag

Basic information

species Oryza sativa
transcript LOC_Os11g10460.1
intron # 1
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|88311970|gb|CI580135.1|CI580135
EST:     CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAG                         GGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
genomic: CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
EST: gi|88693106|gb|CI736681.1|CI736681
EST:     CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAG                         GGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAA
genomic: CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAA
EST: gi|88346392|gb|CI635870.1|CI635870
EST:     CCATCCTCCCCGCCCTTGTTCGTATCCAGTTCCACGACTGCTTCGCCAAG                         GGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
genomic: CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
EST: gi|88328101|gb|CI649903.1|CI649903
EST:     CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAG                         GGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
genomic: CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
EST: gi|88346377|gb|CI635855.1|CI635855
EST:     CATCCTCCCCGCCCTTGCTTCGTCTCCAGTTCCACGACTGCTTCGCCAAG                         GGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
genomic: CATCCTCCCCGCCCTTG-TTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
EST: gi|88692557|gb|CI736132.1|CI736132
EST:     CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAG                         GGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
genomic: CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
EST: gi|88346378|gb|CI635856.1|CI635856
EST:     CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAG                         GGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG
genomic: CCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTG

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: 67 (upstream exon), 65 (downstream exon)
Score: 14

TGAATCCACCGTCGCCTCCGCCGTCCGGCAGTTCGCCGACGCCGACAGCACCATCCTCCCCGCCCTTGTTCGTCTCCAGTTCCACGACTGCTTCGCCAAGgtacatatac ... ggttaattagGGGTGTGATGGGTCGGTGCTGATCAAGGGAGTGGGGAATAACGCGGAGGTGAACAACAACAAGCACCAGGGGCTGCGTGGGCTTGACGTGGTGGACAGCA




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