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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGGAAAAAGAAAACTGCTAAGGAAATTGTTGAAACTCCAACAAGATCAAAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatataaaagagaccttgcttctttttaattacatgatcattattgtgatgactgcataactaacatctttttttcttag

Basic information

species Oryza sativa
transcript LOC_Os01g55090.2
intron # 4
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|86865592|gb|CI330997.1|CI330997
EST:     AA-GTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|29675819|gb|CB672094.1|CB672094
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|88483397|gb|CI420668.1|CI420668
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|88256058|gb|CI358446.1|CI358446
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|86540363|gb|CI180569.1|CI180569
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|86866361|gb|CI336957.1|CI336957
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|88517006|gb|CI444660.1|CI444660
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
EST: gi|86540334|gb|CI180540.1|CI180540
EST:     AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAG                         TCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA
genomic: AAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACA

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: 54 (upstream exon), 22 (downstream exon)
Score: 1

CTAGGAAAAAGAAAACTGCTAAGGAAATTGTTGAAACTCCAACAAGATCAAAGGTTGCTAGAGTTCAATTAGTTGATAGCCCTGCTCGAGTCACTAGGAGgttaggatat ... tttttcttagTCAAACAAGGACAACTGGAACACCAACTATTGCTAGAGAAGGATGCTCACAAGATTCACCTGGACCAGTGACAAGGAGGCGCTTGGCTATGACTGAAGCA




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