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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaagagaatagtgttgaggacaaactacatctttagtaaaatttactatgttttcatgaactaatgatatttgtacatctttcaatatgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGAACGTTCCCCTAGATGTTGACAATTTGCATAATTTGTTTTCTCCGGAATG

Basic information

species Oryza sativa
transcript LOC_Os03g64400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G140874_T01 (Zea mays), 3'ss of exon 2
gtgagaagagaatagtgttgaggacaaactacatctttagtaaaatttactatgttttcatgaactaatgatatttgtacatctttcaatatgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGAACGTTCCCCTAGATGTTGACAATTTGCATAATTTGTTTTCTCCGGAATG
       |||    || | || |  ||  |  || | | |   | |  |  ||  ||   | |  | |||  |||  |     || |||||| ||||||||| | ||||||||||| |||||||| ||||||||||| ||||||||||||||  | ||   ||||||| |  |    ||||  |||||||| || ||  |
-----gtgaggcatgtctcgaagctaagtt-tatgtatggattagtgaatcatcattgtgtaatgttatgtcattcatgttcattccaatatacccatagGCCTAGCAGAAGCTGGATTGATTTCTAGCAAGCTTTCAAGATCTGATATGAATATCCCAGAAGATGTTCATGACAATCATATCTTGTTTTCCCCTGAGAG

upper sequence: LOC_Os03g64400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G077222_T01 (Zea mays), 3'ss of exon 5
gtgagaagagaatagtgttgaggacaaactacatctttagtaaaatttactatgttttcatgaactaatgatatttgtacatctttcaatatgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGAACGTTCCCCTAGATGTTGACAATTTGCATAATTTGTTTTCTCCGGAATG
       | ||    |||   |   || |||  | | | |||    ||| |   |  | ||    |||||  |||  |     || ||||||  |||||||| | ||||||||||| |||||||| ||||||||||| ||||||||||||||  | ||   ||||||| |  |    ||||  |||||||| || ||  |
-------gtgaggcatgtctcg---aagctaagtttat-gtatggattagtgaatcattattgtgtaatgtcattcatgttcattccaatatatccatagGCCTAGCAGAAGCTGGATTGATTTCTAGCAAGCTTTCAAGATCTGATATGAATATCCCAGAAGATGTTCATGACAATCATATCTTGTTTTCCCCTGAGAG

upper sequence: LOC_Os03g64400.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G077222_T02 (Zea mays), 3'ss of exon 5
gtgagaagagaatagtgttgaggacaaactacatctttagtaaaatttactatgttttcatgaactaatgatatttgtacatctttcaatatgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGAACGTTCCCCTAGATGTTGACAATTTGCATAATTTGTTTTCTCCGGAATG
               |||   |   || |||  | | | |||    ||| |   |  | ||    |||||  |||  |     || ||||||  |||||||| | ||||||||||| |||||||| ||||||||||| ||||||||||||||  | ||   ||||||| |  |    ||||  |||||||| || ||  |
------------gcatgtctcg---aagctaagtttat-gtatggattagtgaatcattattgtgtaatgtcattcatgttcattccaatatatccataggcctagCAGAAGCTGGATTGATTTCTAGCAAGCTTTCAAGATCTGATATGAATATCCCAGAAGATGTTCATGACAATCATATCTTGTTTTCCCCTGAGAG

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|58689870|gb|CK078557.1|CK078557
EST:     TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAG                         GCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA
genomic: TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAGgtgagaagag ... atgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA
EST: gi|58669049|gb|CK057735.1|CK057735
EST:     TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAG                         GCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA
genomic: TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAGgtgagaagag ... atgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA
EST: gi|58669849|gb|CK058535.1|CK058535
EST:     TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAG                         GCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA
genomic: TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAGgtgagaagag ... atgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA
EST: gi|58611882|gb|CK039594.1|CK039594
EST:     TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAG                         GCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA
genomic: TGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATACAAGgtgagaagag ... atgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactatgttttcatgaactaatgatatttgtacatctttcaatatgcccatagGCTTGGCAGAAGCTGGGTTGATTTCCAGCAAGCTTTCGAGATCTGATATGAACGTTCCCCTAGATGTTGACAATTTGCATAATTTGTTTTCTCCGGAATG
                 aactaat  putative branch site (score: 2)
                 aactaatgatattt  TA-rich tract