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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcattgagacgtccatctgcaatttatacacgatataatttcttacagttgatcttttttttttcagATAGCATTTCTGTCTAGCATATATCCTTCTTTGGTGCTCACTTATGCTGGGCAAACAGCATACCTTATAAACAATGTCAATGACTTTGGTGATGGTTTCT

Basic information

species Oryza sativa
transcript LOC_Os09g27580.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g27580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G088964_T01 (Zea mays), 3'ss of exon 6
-------------------------------------gttagtttcattgaga--cgtccat-ctg----caattta--tacacgatataatttcttacagttgatcttttttttttcagATAGCATTTCTGTCTAGCATATATCCTTCTTTGGTGCTCACTTATGCTGGGCAAACAGCATACCTTATAAACAATGTCAATGACTTTGGTGATGGTTTCT
                                     | |  | || ||| ||   || ||| ||     || || |  || |||      | ||      |||   ||||| |||||||||||||||||||||||||||||| |||||| |||||||||| || |||||||||||||| ||||| || ||||| ||||| |||||  |||| || ||||
gttgtttattttcatcaacactacactgcaactttgagatcctctccttgtgagctgttcatgctatggccagttcagctaaacgccgccgtgtccgtgtcttg--ttttttgttttcagATAGCATTTCTGTCTAGCATATACCCTTCTCTGGTGCTCACATACGCTGGGCAAACAGCGTACCTCATCAACAACGTCAACGACTTCAGTGACGGATTCT

upper sequence: LOC_Os09g27580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S166_51V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------gttagtttcattgagacgtccatctgcaattt-atacacgat--ataatttcttacagttgatctttttt-----ttttcagATAGCATTTCTGTCTAGCATATATCCTTCTTTGGTGCTCACTTATGCTGGGCAAACAGCATACCTTATAAACAATGTCAATGACTTTGGTGATGGTTTCT
                   ||   ||| | ||   | ||  | | || ||| | |||   |   |||| |     |    ||| ||  |     ||| ||| | || ||    | |    | ||||| ||  || | || ||||||||||||||||||||||| || |||||| |   | |  ||| |   || || ||||
aattgtgcttccactacgtgtctcttttaatgcc-cttcagtgtacattttgagacaaagttggtaatgttactgaacctatccttagtcaatatttgcagTTGGCTTTCTCCTTTTTAGTGTATCCATCCGTGCTCCTTACTTATGCTGGGCAAACAGCATATCTCATAAACCACCCCGAGAACTATTTAGAGGGATTCT
















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|58610501|gb|CK038213.1|CK038213
EST:     CTGAAGCTATGTTCGCAGATCTTGGGCACTTCAGCAAAAAGGCTATTCAG                         ATAGCATTTCTGTCTAGCATATATCCTTCTTTGGTGCTCACTTATGCTGG
genomic: CTGAAGCTATGTTCGCAGATCTTGGGCACTTCAGCAAAAAGGCTATTCAGgttagtttca ... tttttttcagATAGCATTTCTGTCTAGCATATATCCTTCTTTGGTGCTCACTTATGCTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatctgcaatttatacacgatataatttcttacagttgatcttttttttttcagATAGCATTTCTGTCTAGCATATATCCTTCTTTGGTGCTCACTTATGCTGGGCAAACAGCATACCTTATAAACAATGTCAATGACTTTGGTGATGGTTTCT
                                    ttgatctttttttttt  CT-rich tract
        aatttatacacgatat  TA-rich tract