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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaatttacctgatattctgattcttttgtgaagGTATGGATTATTGG

Basic information

species Oryza sativa
transcript LOC_Os12g26290.6
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 7
lower sequence: AC205471.4_FGT004 (Zea mays), 3'ss of exon 4
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGG--------------------------------------------------------------------------------------
||||||||  ||| ||||||||||||||||||||  ||||||||| ||         || | || |||||||||||||||||||||||||||||||||||||||| ||||||||||||||| ||||||||| ||||||||| |||||||   ||||| |||||||||||||||||||| |||||||                                                                                      
gtgaggatatatt-atctcattttctcatatttgttgaaagaaaacaa---------ttaacgctggtattacttttccaagtggaaattttatttacatctgcatattcaaattaattaa-ttagtgagattgtgtacaaatttacct--cattctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAGATACATTTGGTCACATAGGAGGACCGACATTAGGTGGGCTCGTGGGGTTGAAGAAGCCGATCAACCATGGC

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G818450_T01 (Zea mays), 3'ss of exon 2
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGG--------------------------------------------------------------------------------------
||||||||  ||| ||||||||||||||||||||  ||||||||| ||         || | || | ||||||||||||||||||||||||||||||||| | || ||||||||||||||| ||||||||| ||||||||| |||||||   ||||| |||||||||||||||||||  |||||||                                                                                      
gtgaggatatatt-atctcattttctcatatttgttgaaagaaaacaa---------ttaacgctgatattacttttccaagtggaaattttatttacatgt-catattcaaattaattaa-ttagtgagattgtgtacaaatttacct--cattctaattcttttgtgaagGTATGATTTATTGGGTAAGAAAATAAAAGATACATTTGGTCACATAGGAGGACCGACATTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGGC

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G100724_T01 (Zea mays), 3'ss of exon 4
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGG--------------------------------------------------------------------------------------
||||||||  ||| ||||| ||||||||||||||  ||||||||| ||         || |  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| ||||||||| |||||||    |||| |||||||||||||||||||| |||||||                                                                                      
gtgaggatatatt-atctcgttttctcatatttgttgaaagaaaacaa---------ttaacactggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaa-ttagtgagattgtgtacaaatttacct--cgttctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAAGATACATTTGGTCACATAGGAGGACCGACGTTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGG

upper sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G312997_T01 (Zea mays), 3'ss of exon 6
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGG--------------------------------------------------------------------------------------
||||||||  ||| ||||||||||||||||||||  ||||||||| ||         || | || ||||||||||||||||||||||||||||||||||||||||||||||||| |||||| ||||||||| ||||||||| ||||||| ||||||| |||||||||||||||||||| |||||||                                                                                      
gtgaggatatatt-atctcattttctcatatttgttgaaagaaaacaa---------ttaacgctggtattacttttccaagtggaaattttatttacatctgcaaattcaaataaattaa-ttagtgagattgtgtacaaatttacctcatattctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAGATACATTTGGTCACATAGGAGGACCGGCATTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGGC

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|29673790|gb|CB670065.1|CB670065
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTG                         GTATGGATTATTGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGG
EST: gi|29677261|gb|CB673536.1|CB673536
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTG                         GTATGGATTATTGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGG
EST: gi|29629207|gb|CB634218.1|CB634218
EST:     TCGAGCTTCTCAAGACAAAAACCATGAGAGCTGNCA-TGCGCGCAAATTG                         GTATGGATTATTGG
genomic: TCGAGCTTCTCAAGACAAAAACCATGAGAGCTG-CAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaattagtgagaatgtgtacaatttacctgatattctgattcttttgtgaagGTATGGATTATTGG
                                    ttctgat  putative branch site (score: 3)
                                          ttcttttgt  CT-rich tract
                    tacaattta  TA-rich tract