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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgcactcctagtttatttctgtgcctatgacgtgctagtactcattggtattttgtaaaattgttgtgggtatgtctaactgattattcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG

Basic information

species Oryza sativa
transcript LOC_Os04g59494.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 23
acatgcactcctagtttatttctgtgcctatgacgtgctagtactcattggtattttgtaaaattgttgtgggtatgtctaactgat----tattcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG
   |  | |    | |  |     || || |||| | |  ||||| |||||||||| || || || | ||   ||| | | |   ||    ||||  |||||||||||||||||||||  |||||||||| ||||| |||||||| |||||| |  | ||  ||||||| || |||
-attttattgtgtgctcttagtaatgtct-tgacatacaggtactgattggtattt-gtgaagtt-tcgtacatatatgtgatatatattttatttgtttccagATTGGCAAAGAAATAGCACCTGTGGTGATCACCGTTGTTTCGTGCTTGATTACCATCCTAAAATCCCCAGAG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM5G869572_T01 (Zea mays), 3'ss of exon 3
acatgcact----cctagtttatttctg--tgcctatgacg-tgctagtactcattggtattttgtaaaattgttgtgggtatgtctaactgattattcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG
||  || |     |  || |||||||    |    ||| |  | | |||| |  |||||||||   ||  || ||     |||||         |||   |||||||||||||||||||||  | |||||||| ||||| |||||||| |||||||| || ||| ||||||| || |||
accagccccagaacagagcttatttcctcttagtaatgccactaccagtagtggttggtatttatgaagtttcttacatatatgt-------gatatctgtttccagATTGGCAAAGAAATAGCGCCTGTGGTGATCACCGTTGTTTCGTGCTTGGTTCCCATTCTAAAATCCCCAGAG
















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|58608072|gb|CK036105.1|CK036105
EST:     TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG                         ATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG
genomic: TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAGgttttgtacc ... tcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG
EST: gi|58671684|gb|CK060370.1|CK060370
EST:     TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG                         ATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG
genomic: TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAGgttttgtacc ... tcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG
EST: gi|86850485|gb|CI307714.1|CI307714
EST:     TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG                         ATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG
genomic: TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAGgttttgtacc ... tcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG
EST: gi|58592654|gb|CF990962.1|CF990962
EST:     TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG                         ATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG
genomic: TGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAGgttttgtacc ... tcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggtattttgtaaaattgttgtgggtatgtctaactgattattcctttccagATTGGCAAAGAAATTTCACCTGTGGTTATCACTGTTGTTTCTTGCTTGGTGCCTATTTTAAAATCTCCTGAG
                                         ttattcctttcc  CT-rich tract
      tattttgtaaaattgt  TA-rich tract