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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgtagctctctcctcccctccgttgctccccctcaattgctgggtttgggtttgggtttgggtggcgtctcatcgatccccctgtgtag

Basic information

species Oryza sativa
transcript LOC_Os01g10290.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 2
CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgta-gctctctcctcccctccgtt-gctccccctcaat-tgctgggtttgggt--ttgg-gtttgggtggc-gtctcatcgatccccc-tgtgtag-----------
|| ||||||| || || |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||  | ||||   ||| ||||  | ||||  ||||  | |    | ||| |||  |||  | |||| |||  | || || ||||     ||| | |           
CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaggtggttgctgattggttggttgactgattgatctggtgtgtttcgtgtgttcacag

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G818887_T01 (Zea mays), 5'ss of exon 1
CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgta-gctctctcctcccctccgtt-gctccccctcaat-tgctgggtttg---ggtttgggtttgggtggc-gtctcatcgatccc-cctgtgtag-----------
|||||||||| || || |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||  | ||||   ||| ||||  | ||||  ||||  | |    | |||    ||||   | |||| |||  | || || ||||     ||| | |           
CGCGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaagtggttgctgattggttggttgactgattgatctggtttgtttcgtgtgttcacag

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G062635_T01 (Zea mays), 5'ss of exon 1
CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgta-gctctctcctcccctccgtt-gctccccctcaat-tgctgggtttgggt--ttgg-gtttgggtggc-gtctcatcgatccccc-tgtgtag-----------
|||||||||| || || |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||||||  | ||||   ||| ||||  | ||||  ||||  | |    | ||| |||  |||  | |||| |||  | || || ||||     ||| | |           
CGCGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaggtggttgctgattggttggttgactgattgatctggtgtgtttcgtgtgttcacag

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA09G36540.1 (Glycine max), 5'ss of exon 1
CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgtagctctctcctcccctccgttgctccccctcaattgctgggtttgggtttgggtttgggtggcgtctcatcgatccccctgtgtag----------------------------------
| || ||||| || ||||||   || || || || |||   ||| |||||||| ||  ||||||||| || |||||  |||| ||||||||||||||||||||  |||    | |  |     |      |   |||      ||    ||  |  |    | || | ||    |||||  | || |                                   
CCCGAACCGTTTCCGCCTTCAAAGAAAAAGGAGTTCTCAGTGTCTCCGAGTTCGTCACCGCCGGCGATAATCTCGTTGCCAAATGCCCCACCTGGTCCTGgtaattctaattttcatttttccgtcttttcctgattat---attcaaatt--gcctcttttagcctttcga-aatcccaatttgaatgatttagtaaatgtgtgattctgttttccaatag

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ14759 (Selaginella moellendorffii), 5'ss of exon 1
CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgtagctctctcctcccctccgttgctccccctcaattgctgggtttgggtttgggtttgggtggcgtctcatcgatccccctgtgtag
| ||||| || ||||| ||| |||| || ||||| ||  |   | | || ||| |||  ||||| ||||| |||||| |||||||||| ||||||||||||||     | |  ||       |     ||||   || |    |||     |    ||    |  |                      
CTCGCACGGTCTCGGCATTCGTCGAGAAAGGCGTGCTGACTCCCGCGGAATTCGTCCAGGCCGGTGACAATCTCGTCGCCAAGTGCCCTACCTGGTCCTGgtatgatacgctacc-------taaagtcccttgtttacctattttcttcctcctctttctcgcag----------------------

upper sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ26505 (Selaginella moellendorffii), 5'ss of exon 1
CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgtagctctctcctcccctccgttgctccccctcaattgctgggtttgggtttgggtttgggtggcgtctcatcgatccccctgtgtag
| ||||| || ||||| ||| |||| || ||||| ||  |   | | || ||| |||  ||||| ||||| |||||| |||||||||| ||||||||||||||     | |  ||       |     ||||   || |    |||     |    ||    |  |                      
CTCGCACGGTCTCGGCATTCGTCGAGAAAGGCGTGCTGACTCCCGCGGAATTCGTCCAGGCCGGTGACAATCTCGTCGCCAAGTGCCCTACCTGGTCCTGgtatgatacgctacc-------taaattcccttgtttacctattttcttcctcctctttctcgcag----------------------

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|29638206|gb|CB643215.1|CB643215
EST:     TTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTG                         GGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCACCTGACAAGCA
genomic: TTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgtagctctct ... ccctgtgtagGGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCACCTGACAAGCA
EST: gi|38477977|gb|CF962110.1|CF962110
EST:     TTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTG                         GGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCACCTGACAAGCA
genomic: TTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgtagctctct ... ccctgtgtagGGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCACCTGACAAGCA