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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaaataaccatgactttttttgaaaagcacatttcacacaatccgattaggtactcaagaaaatatacttcttttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG

Basic information

species Oryza sativa
transcript LOC_Os09g36190.1
intron # 4
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|58674241|gb|CK062927.1|CK062927
EST:     TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTG                         CTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
genomic: TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTGgtataaaaat ... ttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
EST: gi|86831839|gb|CI303279.1|CI303279
EST:     TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTG                         CTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
genomic: TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTGgtataaaaat ... ttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
EST: gi|29628540|gb|CB633551.1|CB633551
EST:     TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTG                         CTGAACATCAAGTCGATGCAGCTGCAAAAAATGCTCGAAGG
genomic: TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTGgtataaaaat ... ttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
EST: gi|25801297|gb|CA757258.1|CA757258
EST:     TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTG                         CTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
genomic: TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTGgtataaaaat ... ttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
EST: gi|29682192|gb|CB678467.1|CB678467
EST:     TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTG                         CTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
genomic: TGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTGgtataaaaat ... ttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG

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: 73 (upstream exon), 41 (downstream exon)
Score: 99

AGCAATGCTAGTTTGGATGTTGATGACAAGGTTAAATCTGAAAACAGTTCTGCAGAACATGAGTTATCACTGACAGATAAAACACCCAAGGATGATACTGgtataaaaat ... ttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttcacacaatccgattaggtactcaagaaaatatacttcttttctgtgcagCTGAACATCAAGTCGATGCACCTGCAAAAAATGCTCGAAGG
                                   tatacttcttttct  CT-rich tract
                               aaaatatacttctttt  TA-rich tract