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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattggtcgctccttctgtttcatcttctaacatggattggcgtatcatatgcatattccatctcactgttttcctgcattgactctccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACACATGTCATTGAGAAATAAGACTCAGGAGTACATTTGGCGGCAAAATTAT

Basic information

species Oryza sativa
transcript LOC_Os08g25310.1
intron # 14
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|89168356|gb|CI109560.1|CI109560
EST:     GAGGCAGCTAAGG                         AGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATGAACAACA
genomic: GAGGCAGCTAAGGgtaaaattgg ... ccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
EST: gi|89173446|gb|CI041339.1|CI041339
EST:     ATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGG                         AGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATGAACAACA
genomic: ATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGGgtaaaattgg ... ccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
EST: gi|163929216|gb|EG713065.1|EG713065
EST:     AACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGG                         AGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
genomic: AACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGGgtaaaattgg ... ccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
EST: gi|29682931|gb|CB679206.1|CB679206
EST:     AACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGG                         AGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
genomic: AACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGGgtaaaattgg ... ccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
EST: gi|86874658|gb|CI318217.1|CI318217
EST:     GGAGGCAGCTAAGG                         AGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
genomic: GGAGGCAGCTAAGGgtaaaattgg ... ccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
EST: gi|29675315|gb|CB671590.1|CB671590
EST:     AACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGG                         AGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA
genomic: AACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGGgtaaaattgg ... ccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACA

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), 72 (downstream exon)
Score: 21

GTGCTGCAAGCTACCGTGATGAAGCAACTGGAAATTGCAGAATCAATAGAGGAAGTGATTAGGAGGCAGCTAAGGgtaaaattgg ... ccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACACATGTCATTGAGAAATAAGACTCAGGAGTACATTTGGCGGCAAAATTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcatatgcatattccatctcactgttttcctgcattgactctccttacacagAGACGAAGATTTTGTGCGTAATAAAGAGACCTAACTCCAGAATTAACAACACATGTCATTGAGAAATAAGACTCAGGAGTACATTTGGCGGCAAAATTAT
                                            tccttac  putative branch site (score: 21)
                                         ctctccttac  CT-rich tract
           atatt  TA-rich tract