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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatgtttttgtagtgtaacataattcttcattgaaggaaataattaagttttcccttgtagctgatgtttacctgtgtgattattaatgtaattgcagATTCTCAAGGCTATGGGCTTTTCAAAGACTTCATCAGCTGCTCTAAAGATCCTTATAAATATTGGATACTTCCCTGTGCATGTCAATCTTGATCTTTACA

Basic information

species Oryza sativa
transcript LOC_Os01g62440.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62440.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G082260_T01 (Zea mays), 3'ss of exon 6
caaatgtttttgtagtgtaacataattcttcattgaaggaaataa----ttaagttttcccttgtagctgatgtttacctgtgtgattattaatgtaattgcagATTCTCAAGGCTATGGGCTTTTCAAAGACTTCATCAGCTGCTCTAAAGATCCTTATAAATATTGGATACTTCCCTGTGCATGTCAATCTTGATCTTTACA
||||    ||| || | ||  |  |||||| |||||| ||  |      ||   | ||    |||   ||| |||    | | |  |||  ||| |||| |||||||||||| |||||||| ||  | | ||| |||||||||||||||||| | ||||||||| |||||||||||||||||||||||||||| || |||| ||
caaacacattt-taattta-taccattctttattgaatgaggtgcagttttccatcttttgatgtctgtgaagttggtttttattttta--aatttaatggcagATTCTCAAAGCTATGGGATTCACGAGGACATCATCAGCTGCTCTAAAGCTTCTTATAAATGTTGGATACTTCCCTGTGCATGTCAATCTCGACCTTTTCA
















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|33679223|gb|CF307462.1|CF307462
EST:     CATATGCAGTTGATGCATGTGATGATGAACAAAGGAGAACGGCAGGAAAC                         ATTCTCAAGGCTATGGGCTTTTCAAAGACTTCATCAGCTGCTCTAAAGATC
genomic: CATATGCAGTTGATGCATGTGATGATGAACAAAGGAGAACGGCAGGAAACgtaacatatt ... gtaattgcagATTCTCAAGGCTATGGGCTTTTCAAAGACTTCATCAGCTGCTCTAAAGATC
EST: gi|58670594|gb|CK059280.1|CK059280
EST:     CATATGCAGTTGATGCATGTGATGATGAACAAAGGAGAACGGCAGGAAAC                         ATTCTCAAGGCTATGGGCTTTTCAAAGACTTCATCAGCTGCTCTAAAGATC
genomic: CATATGCAGTTGATGCATGTGATGATGAACAAAGGAGAACGGCAGGAAACgtaacatatt ... gtaattgcagATTCTCAAGGCTATGGGCTTTTCAAAGACTTCATCAGCTGCTCTAAAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagttttcccttgtagctgatgtttacctgtgtgattattaatgtaattgcagATTCTCAAGGCTATGGGCTTTTCAAAGACTTCATCAGCTGCTCTAAAGATCCTTATAAATATTGGATACTTCCCTGTGCATGTCAATCTTGATCTTTACA
                                      tattaat  putative branch site (score: 2)
                                  tgattattaatgtaat  TA-rich tract