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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatagtacattttactagatgctttgcaatgttgagaaagttctcttcatagattcttctttccctaacaggagttttatctataaatggattttgcagGTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGGTAAGTTGATCAAGTTTGCACAG

Basic information

species Oryza sativa
transcript LOC_Os06g10880.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g10880.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G033413_T01 (Zea mays), 3'ss of exon 3
---agatagtacattttactagatgctttgcaatgttgagaaagttctcttcatagattcttctttccctaacaggagttttatctataaatggattttgcagGTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGGTAAGTTGATCAAGTTTGCACAG
   |     | ||| ||  |  |  ||  | ||||  |      |||     ||   || || |||| || |||  || ||  ||| ||||||| ||||||||||| ||||| | ||||     |||| |||||||||||||||||   ||||||| || || || |||||||| ||||||||   || | ||| ||||||| 
ttgatgcgctgcatattcatcaa--ctgggaaatgacggttcccttcagacaatgtgtttttttttcactcacaaaagcttc-tctgtaaatggtttttgcagGTCCTGGAGCGTATCAACAGCCAACATGGACCAAAGGCAAAGAAGCTTTGCCTGCGCCGCACCCTGACTGGCCCATGGTAGCCTGCTGAAGCTTGCACAA
















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|89193034|gb|CI050332.1|CI050332
EST:     GTGGAAATGATACAGAAGCAAAATGATGAG                         GTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGC
genomic: GTGGAAATGATACAGAAGCAAAATGATGAGgtaatgacct ... gattttgcagGTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGC
EST: gi|87029295|gb|CI276563.1|CI276563
EST:     GTGGAAATGATACAGAAGCAAAATGATGAG                         GTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGC
genomic: GTGGAAATGATACAGAAGCAAAATGATGAGgtaatgacct ... gattttgcagGTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGC
EST: gi|86258557|gb|CI064910.1|CI064910
EST:     ATGATACAGAAGCAAAATGATGAG                         GTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGC
genomic: ATGATACAGAAGCAAAATGATGAGgtaatgacct ... gattttgcagGTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatagattcttctttccctaacaggagttttatctataaatggattttgcagGTCATGGAGAGAATCACTCAGCAACTTGGACCAAAGGCAAAGAGATTTTGCCTCCGACGAACACTGACTGGTCCATGGTAAGTTGATCAAGTTTGCACAG
                  ccctaac  putative branch site (score: 2)
                              ttttatctataaatgg  TA-rich tract