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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttactttattcagtagctacagcaaactaattgctgtatccattattattgtcctaattattcagtagatcagaaaactcacatgttggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTCTTTTCCCTGGAGTGGCCTGCTTCCTTGTTGCAGTCATTCTTGGCTCTGC

Basic information

species Oryza sativa
transcript LOC_Os12g31850.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g31850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G091891_T01 (Zea mays), 3'ss of exon 1
agtttactttattcagtagctacagcaaactaattgctgtatccattattattgtcctaattattcagtagatcagaaaactcacatgttg-gatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTCTTTTCCCTGGAGTGGCCTGCTTCCTTGTTGCAGTCATTCTTGGCTCTGC
    ||  ||  |   | | |  | |   || ||| ||| ||   ||   ||   || |            ||||  ||    |  || || ||| ||||||||| || ||||| || ||||||||||||||||||||||| ||||||||||| || || || ||||| |||||||||||||| ||||| |||||||||||
---gtatgttgctagcttgtttgaactc-ctgatttctgaat--gtttacatacacccagca---tgacgaatcatcaataatatgtgctgtgattttcagGCACGACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTCTGTTTCCCGGCGTGGCATGCTTCCTTGTTGCTGTCATCCTTGGCTCTGC

upper sequence: LOC_Os12g31850.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G025528_T04 (Zea mays), 3'ss of exon 2
--------agtttactttattcagtagctacagcaaactaattgctgtatccattattattgtcctaattattcagtagatcagaaaactcacatgttggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTCTTTTCCCTGGAGTGGCCTGCTTCCTTGTTGCAGTCATTCTTGGCTCTGC
        ||   |  ||        | |    ||   |       | |   |   |  ||||  | |||     ||    ||    | ||   |||    ||||||||||| || ||||| || ||||||||||||||||||||||| ||||||||||| |||||||| ||||| |||||||| || || ||||| |||||||| ||
tgtctgacagaccaagtttcgtttctgttctgtcagctttgaaatggaagaaaaagtctttgttttgatttccacgtcttcca----attcttgtgt----tcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTCTGTTCCCTGGTGTGGCGTGCTTCCTCGTCGCCGTCATCCTTGGCTCCGC
















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|218496842|gb|FG946818.1|FG946818
EST:     TGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAG                         GCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
genomic: TGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAGgtaggtaaaa ... ggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
EST: gi|29614658|gb|CB619671.1|CB619671
EST:     AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAG                         GCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
genomic: AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAGgtaggtaaaa ... ggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
EST: gi|88299367|gb|CI572319.1|CI572319
EST:     AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAG                         GCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
genomic: AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAGgtaggtaaaa ... ggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
EST: gi|29665274|gb|CB661549.1|CB661549
EST:     AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAG                         GCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
genomic: AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAGgtaggtaaaa ... ggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
EST: gi|29614656|gb|CB619669.1|CB619669
EST:     AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAG                         GCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC
genomic: AGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAGgtaggtaaaa ... ggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattattgtcctaattattcagtagatcagaaaactcacatgttggatcttcagGCACAACACTGAATTATTTCCTGGACAACCGCATCAACAGAGCAGAGATTCTTTTCCCTGGAGTGGCCTGCTTCCTTGTTGCAGTCATTCTTGGCTCTGC
                                 aactcac  putative branch site (score: 2)
                                                tcttc  putative PPT
            taattattca  TA-rich tract