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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGGCGGCGGCGGTGGCCGTGATGCTCCTCCTTGCGCAGGTGTCAGCGGCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgttgccacagcgtttctctttttcatcgtttcaagcctgagatcccttttgctagatatgtatgaatgtattaataatgttaacgatttttag...

Basic information

species Oryza sativa
transcript LOC_Os12g03060.1
intron # 2
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|29618674|gb|CB623686.1|CB623686
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88415912|gb|CI594024.1|CI594024
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88828089|gb|CI778654.1|CI778654
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|86904894|gb|CI310687.1|CI310687
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|33653554|gb|CF276168.1|CF276168
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|58668824|gb|CK057510.1|CK057510
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88734622|gb|CI758130.1|CI758130
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88736919|gb|CI760427.1|CI760427
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88718196|gb|CI741706.1|CI741706
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88337398|gb|CI629688.1|CI629688
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|86910179|gb|CI292983.1|CI292983
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|29657293|gb|CB653568.1|CB653568
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|66920771|gb|CX107619.1|CX107619
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88356178|gb|CI627626.1|CI627626
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|25798686|gb|CA754647.1|CA754647
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88733588|gb|CI756765.1|CI756765
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88402485|gb|CI596346.1|CI596346
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|29686826|gb|CB683101.1|CB683101
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|58597158|gb|CK007686.1|CK007686
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88337316|gb|CI629606.1|CI629606
EST:     GCGGNTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC

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: 75 (upstream exon), 75 (downstream exon)
Score: 61

CCTGGGCGGCGGCGGTGGCCGTGATGCTCCTCCTTGCGCAGGTGTCAGCGGCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG




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