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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcaatatgaacactggtttgcactttaattattgaaaacagcataaatccagtcaatgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g05200.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05200.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G107651_T01 (Zea mays), 3'ss of exon 13
gttagcaatatgaacactggtttgcact-ttaattattga-------------------aaacagcataaa-tccagtcaa-tgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG
|||||||||| ||||| || | |  ||  ||||| |||                     | ||| | |||| |||| |  | | || ||    ||   | |||||||||| |||||||| ||||||||||| || ||||| ||||||||||| ||  |||||||| |||||
gttagcaatacgaacattgttctctacccttaataattatgttctttgttagttcacttagacatcgtaaaatccatttgagtaatgttagccctgaatgatcagGTTTCTTTGCTTCTGAAAGACAGTTTCATTGATTCGTTCCCCTCAAATGATAGACCATTTATAAAG

upper sequence: LOC_Os03g05200.2 (Oryza sativa), 3'ss of exon 15
lower sequence: AT2G20320.1 (Arabidopsis thaliana), 3'ss of exon 17
---gttagcaatatgaacactggtttgcactttaattattgaaaacagcat----aaatccagtcaatgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG
    |||   ||||    |||    |  |   | |  |   |  ||   ||    |  ||    |||   | |   |  |   ||||||||||||  | |||||||| |||||||||||||||||||| ||    |  || ||||| ||  | |||
gtacttacttatatagctactctcctcgaagctgaacaagaactactttatttctatctctcaccaactctctaaatctttctttatcagGTTTCTCTACTTCTAAAGGACAGTTTTATCGATTCATTTCCTGGTAGAGATCGACCCTTCATTAAG
















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|29624630|gb|CB629641.1|CB629641
EST:     CTGACCTGCGATCTCATACCATCACCAATGTACAGTCAAATAATGACAGG                         GTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC
genomic: CTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATAATGACAGGgttagcaata ... atcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC
EST: gi|29614852|gb|CB619865.1|CB619865
EST:     CTGACCTGCGATCTCATACCATCACCAATGTACAGTCAAATAATGACAGG                         GTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC
genomic: CTGACCTGCCATCTCATACCATCACCAATGTACAGTCAAATAATGACAGGgttagcaata ... atcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattattgaaaacagcataaatccagtcaatgatatttcttctatcttatcagGTTTCGTTGCTTCTAAAAGACAGTTTTATCGATTCATTCCCCTCAAAGGACCGACCATTTGTAAAG
 ctttaat  putative branch site (score: 4)
                                     tttcttctatcttatc  putative PPT
                              aatgatattt  TA-rich tract