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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttcattctttcctttgaaatatccagtatcatggtaacatgctctctattatctgcacttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGCCATTTGCTGAATCAACTTTGCTAGG

Basic information

species Oryza sativa
transcript LOC_Os06g48770.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48770.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 13
------gtatgtttt----tcattctttcctttgaaatatccagtatcatggtaacatgctctctattatctgc------acttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGCCATTTGCTGAATCAACTTTGCTAGG
      || || |||    | | || ||||| | |  |||||||| || |  | ||||    |   |||| |        | |  |||||| || ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||
gtatgtgtttgatttgggcttactcgttcctctcaggtatccagtgtcttaatgacatttatttatttatttttttaaaaaatcctgcagGTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG

upper sequence: LOC_Os06g48770.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 12
----------------gtatgtttttcattctttcctttgaaatatccagt--atcatggta----acatgctctcta-ttatctgcact------tatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGCCATTTGCTGAATCAACTTTGCTAGG
                 ||    |||   || ||   |  ||  ||    |  ||||| |||    || |  ||| || |||| |    |      |||  ||| || ||| |  |  | |||||| |||| |||||||| ||||||||||| |||||||| |||||   | || ||||
gtataatttatgaatcatactactttacctcattatgtcaaaggatttgctcaatcatagtactttactttttctttacttatttattttgtcgactatttagGACTTTCATCTACTATGAATGTTCGGATTGTTTATCTGGACATCATGAGACCATTTGCCGAATCTGTTCTGTTAGG
















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|58606319|gb|CK034352.1|CK034352
EST:     TTTCCCTGGTGATGCAATTATATTCAGGGGGGTTTTGAATCTTCTTAGAG                         GGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGC
genomic: TTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTTCTTAGAGgtatgttttt ... acttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGC
EST: gi|29679895|gb|CB676170.1|CB676170
EST:     TTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTTCTTAGAG                         GGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGC
genomic: TTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTTCTTAGAGgtatgttttt ... acttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGC
EST: gi|58590136|gb|CF988444.1|CF988444
EST:     GCAATTATATTCATGAGGGTTTTGAATCTTCTTAGAG                         GGTTATCAGCATCACTAAGATGTTAGGATAGTTTATCTAGACATCATGAGG
genomic: GCAATTATATTCATGAGGGTTTTGAATCTTCTTAGAGgtatgttttt ... acttatgcagGGCTATCAGCATCACTAA-ATGTTAGGATAGTTTATCTAGACATCATGAGG
EST: gi|87005733|gb|CI316152.1|CI316152
EST:     TTTCCCTGGTGATGCAATTATATTCATGA-GGTTTTGAATCTTCTTAGAG                         GGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGC
genomic: TTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTTCTTAGAGgtatgttttt ... acttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgaaatatccagtatcatggtaacatgctctctattatctgcacttatgcagGGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGCCATTTGCTGAATCAACTTTGCTAGG
                    tggtaac  putative branch site (score: 2)
                                 tctattat  TA-rich tract