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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccaaaaccgccttatttctctgttacatatgcttcttgttttatttaaaagaacaacttttcatccagatatactctaacgaaagcattttgtatgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTATCACTGGCTCGACTGTTTACGTTGACAATGGACTCAATACAATGGGGCT

Basic information

species Oryza sativa
transcript LOC_Os08g23810.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23810.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 11
gtccaaaacc-gccttatttctctgttacatatg-cttcttgttt--------tatttaaaaga--acaac--ttttcatccagatatactctaac------gaaagcattttgtatgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTATCACTGGCTCGACTGTTTACGTTGACAATGGACTCAATACAATGGGGCT
|||  |     | ||  |  || |||||| | || |||  |||||        ||||| ||||    ||||  ||||| ||    |   ||||           ||| ||  | | ||| ||||||| || |||||||||||||| ||||||||||| ||| |||||||||| || ||||| |||||||||||||| ||||||||||| |||||||||||||||||
gtcagagttttgactcctccctttgttacttgtgacttgctgtttcatccccctatttgaaaggtggcaacctttttcttcacagtgctctcttttttcttaacaagtatgctct-tgttgaacagATGAGGTGGGGAACACAGCTGCATTCCTGGTTTCTTCATTGGCTTCTGCCATCACCGGCTCGACTGTTTATGTTGACAATGGGCTCAATACAATGGGGCT

upper sequence: LOC_Os08g23810.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 10
gtccaaaaccgc---cttatttctctgttacata-tgcttcttgttt-tatttaaaagaacaa--cttttcatccagata-------tactctaacgaaagcattttgtatgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTATCACTGGCTCGACTGTTTACGTTGACAATGGACTCAATACAATGGGGCT
   || |   ||   |||  ||   ||| || |  || ||| |     ||||| ||||  | |  |||||  | || |         |  | |||| || | | | |   ||| | ||||| || |||||||||||||| ||||||||||| ||| |||||||||| || |||||||||||||||||||| |||||||||||||||||||||||||||||
-gtcagagttgcatactttgttacttgtcacttgctgtttcctccccgtatttgaaaggtccaacctttttcttcaaacgctgtcttttttttaacaaatgtactct---tgttggacagATGAGGTGGGGAACACAGCTGCATTCCTGGTTTCTTCATTGGCTTCTGCCATCACTGGCTCGACTGTTTATGTTGACAATGGACTCAATACAATGGGGCT
















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|88487859|gb|CI425130.1|CI425130
EST:     GAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|88672973|gb|CI727088.1|CI727088
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|29613729|gb|CB618742.1|CB618742
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|3767353|gb|AU031463.1|AU031463
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAA-TGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|33691059|gb|CF319298.1|CF319298
EST:     GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
EST: gi|88262025|gb|CI365601.1|CI365601
EST:     GATAGAATACTCTTATGTTAATCCACCGTTCCAGAAAGAACTGTTGGCAG                         ACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA
genomic: GATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAGgtccaaaacc ... tgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacaacttttcatccagatatactctaacgaaagcattttgtatgtcgaacagACGAAGTGGGGAACACAGCAGCATTCCTGGTGTCTCCATTGGCTTCCGCTATCACTGGCTCGACTGTTTACGTTGACAATGGACTCAATACAATGGGGCT
                        ctctaac  putative branch site (score: 2)
                                     attttgtat  TA-rich tract