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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGTACGTTCCCTTGAACGTCTTTTACAGTATGGCGAGCAGAATATTAGAAGGGCGGTTCCTCTAGCTCTGGGCTTGCTTTGCATATCCAATCCAAAGgtatggtacatgatttgttatttttgtagtaacgtcaaatgtttgttatctttgtgccgttgcacacaatcattcaatatatagaattgctgataaagaa...

Basic information

species Oryza sativa
transcript LOC_Os09g15750.1
intron # 19
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|86901593|gb|CI310355.1|CI310355
EST:     GAAGGGCGGTTCCTCTAGCTCTGGGCTTGCTTTGCATATCCAATCCAAAG                         GTAAATGTTATGGACACAATGAGCAGACTGAGCCATGAT
genomic: GAAGGGCGGTTCCTCTAGCTCTGGGCTTGCTTTGCATATCCAATCCAAAGgtatggtaca ... tgtcaattagGTAAATGTTATGGACACAATGAGCAGACTGAGCCATGAT
EST: gi|29644400|gb|CB649407.1|CB649407
EST:     GAAGGGCGGTTCCTCTAGCTCTGGGCTTGCTTTGCATATCCAATCCAAAG                         GTAAATGTTATGGACACAATGAGCAGACTGAGCCATGATGCAGATGCGGAA
genomic: GAAGGGCGGTTCCTCTAGCTCTGGGCTTGCTTTGCATATCCAATCCAAAGgtatggtaca ... tgtcaattagGTAAATGTTATGGACACAATGAGCAGACTGAGCCATGATGCAGATGCGGAA
EST: gi|218478818|gb|FG953673.1|FG953673
EST:     GAAGGGCGG-TCCTCTAGCTCTGGGTTTGCTTTGCATATCCAATCCAAAG                         GTAAATGTTATGGACACAATGAGTAGACTGAGCCATGATGCAGATGCGGAA
genomic: GAAGGGCGGTTCCTCTAGCTCTGGGCTTGCTTTGCATATCCAATCCAAAGgtatggtaca ... tgtcaattagGTAAATGTTATGGACACAATGAGCAGACTGAGCCATGATGCAGATGCGGAA

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: 75 (upstream exon), 56 (downstream exon)
Score: 19

GGCTGTACGTTCCCTTGAACGTCTTTTACAGTATGGCGAGCAGAATATTAGAAGGGCGGTTCCTCTAGCTCTGGGCTTGCTTTGCATATCCAATCCAAAGgtatggtaca ... tgtcaattagGTAAATGTTATGGACACAATGAGCAGACTGAGCCATGATGCAGATGCGGAAGTTTCTATG




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