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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataattatacttggattcaagattggcaatttaagctcacaggaccgaacattgttgttgctatacttgtagtggtagcaattttggactggtaaaatctattgtgatttctttcccatttcaatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGAAATGCACTTGGTTTCATAATCCTCCCGTTCTTCATAGGCGTGCACAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g56360.1
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|29672385|gb|CB668660.1|CB668660
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|30226790|gb|CB964682.1|CB964682
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|30228254|gb|CB966145.1|CB966145
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|58690336|gb|CK079023.1|CK079023
EST:     TTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: TTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|163927643|gb|EG712439.1|EG712439
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|58608842|gb|CK036875.1|CK036875
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|29680740|gb|CB677015.1|CB677015
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|29678634|gb|CB674909.1|CB674909
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|30228465|gb|CB966355.1|CB966355
EST:     GTTTGAGATCGATCCTCCTTGTCGATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
EST: gi|38468635|gb|CF952766.1|CF952766
EST:     GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT                         GCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA
genomic: GTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGA

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: 74 (upstream exon), 67 (downstream exon)
Score: 12

GTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCATgtaataatta ... caatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGAAATGCACTTGGTTTCATAATCCTCCCGTTCTTCATAGGCGTGCACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaattttggactggtaaaatctattgtgatttctttcccatttcaatggccagGCATACGTAGATATGATCAATTCTGGCAGAGAGGATGAAGTGAAATGGGGAAATGCACTTGGTTTCATAATCCTCCCGTTCTTCATAGGCGTGCACAAAG
                               tttctttcccatttc  CT-rich tract
                taaaatctatt  TA-rich tract