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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcacaagtacttgatcattcaggccttgttgattcatgtagcggtaacaatatggtgtatagcaaccaagtgacattcacctctcttgtttgttcagGTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGCGCACGCAGGCCCGGCATTCTGATGTCCACATTGAGGGCTCTCGACAGCC

Basic information

species Oryza sativa
transcript LOC_Os01g70310.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 2
--tctgcacaagtacttgatcattcaggccttgttgattcatgtagcggtaacaatatggtgtata-gcaaccaagtgacat-tcacctctcttgtttgtt-cagGTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGCGCACGCAGGCCCGGCATTCTGATGTCCACATTGAGGGCTCTCGACAGCC
  |||   |    |  || |||  || ||  ||       ||| | ||||| | || ||    | | |  ||  || ||    | ||     ||||| ||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| || || ||||| ||||| ||| |||| ||| ||| ||| ||||||||||
tttctttcctgagaaatgttcaggcaagcactgc-----aatgcaacggtaccgatctgtatgacatgagactgagcgaggcattactctctttgttcgtttcagGTCGAAGTCAGGATGAGGGAAGGGCATGCAGTCAATATCCACATGTTCTGTGCGCGTAGGCCAGGCATCCTGCTGTCGACAATGACGGCCCTCGACAGCC
















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|88240391|gb|CI239553.1|CI239553
EST:     AGGAACTTTGCCCAACCTCATTTCCAAGCCCTAGTGGTCAACAAGCCACG                         GTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGC
genomic: AGGAACTTTGCCCAACCTCATTTCCAAGCCCTAGTGGTCAACAAGCCACGgttagtcaaa ... gtttgttcagGTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGC
EST: gi|86601405|gb|CI253733.1|CI253733
EST:     AGGAACTTTGCCCAACCTCATTTCCAAGCCCTAGTGGTCAACAAGCCACG                         GTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGC
genomic: AGGAACTTTGCCCAACCTCATTTCCAAGCCCTAGTGGTCAACAAGCCACGgttagtcaaa ... gtttgttcagGTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGC
EST: gi|86594391|gb|CI251263.1|CI251263
EST:     AGGAACTTTGCCCAACCTCATTTCCAAGCCCTAGTGGTCAACAAGCCACG                         GTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGC
genomic: AGGAACTTTGCCCAACCTCATTTCCAAGCCCTAGTGGTCAACAAGCCACGgttagtcaaa ... gtttgttcagGTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaacaatatggtgtatagcaaccaagtgacattcacctctcttgtttgttcagGTCGAAGTTAGGATGAGGGAAGGTCATGCAGTCAATATCCACATGTTCTGCGCACGCAGGCCCGGCATTCTGATGTCCACATTGAGGGCTCTCGACAGCC
 cggtaac  putative branch site (score: 3)
                                 ttcacctctcttgttt  putative PPT
      aatat  TA-rich tract