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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaattaacaatctatccaaataaaataagtacttcattttttataaaattcttagcttttatctgatcatattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTA

Basic information

species Oryza sativa
transcript LOC_Os01g53880.2
intron # 3
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|29675176|gb|CB671451.1|CB671451
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|86842279|gb|CI335208.1|CI335208
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29672643|gb|CB668918.1|CB668918
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29679028|gb|CB675303.1|CB675303
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|88830109|gb|CI074781.1|CI074781
EST:     AGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: AGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|4715467|gb|AU056584.1|AU056584
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|88831238|gb|CI082048.1|CI082048
EST:     GGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: GGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|88831004|gb|CI080428.1|CI080428
EST:     GTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: GTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29643256|gb|CB648263.1|CB648263
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29675174|gb|CB671449.1|CB671449
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|29639753|gb|CB644762.1|CB644762
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
EST: gi|89177420|gb|CI250869.1|CI250869
EST:     TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAG                         CTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA
genomic: TGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACA

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: 68 (upstream exon), 48 (downstream exon)
Score: 22

GATGGGATCCCTATTGGAAGGAAAATAGACCTTGCAGCCTATAACAGCTATGATGGGCTATCGTCAGCTGTCAAACAACTCTTCCATGGGTTTCTTCAAGgtagaaatta ... catattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataagtacttcattttttataaaattcttagcttttatctgatcatattgcagCTCAAAAGGACCAAACTAATGCGCAAATTGCACAGCAAGGTGCAGATGACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTA
                                      atctgat  putative branch site (score: 22)
          ttcattttttataaaa  TA-rich tract