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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaagcagaacttgctctgtttgtccagttgttaatactgtacagtagtattagtactaggactacaagctaatcctcctgaggaagtgaagtga...

Basic information

species Oryza sativa
transcript LOC_Os01g63770.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63770.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G127949_T01 (Zea mays), 5'ss of exon 6
GCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaagcagaacttgctctgtttgtccagttgttaa--tactgtacagtagtattagtactaggactacaagctaatcctcctgaggaag-tgaagtga--
||||||||| |  | ||| |||| || |||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    ||   ||       | | |    ||  |||||   | |||||  |||| || |   ||  ||||   || ||   | || |  ||     
GCCGAAGGCGTGGCGCACTCCGGCCCCACCAAGCTCGTGCTCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaagcctt-ctctttcccacaaccaactcaacaaattactgactactagta--agtagtacg--cacgtgctaccacttctactgcagctttagcagga

upper sequence: LOC_Os01g63770.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G01240.2 (Arabidopsis thaliana), 5'ss of exon 4
GCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaagcagaacttgctc-tgtttgtccagttgttaatactgtacagtagtattagtactaggactacaagctaatcctcctgagga-agtgaagtga
|| || ||  | || ||  |||||||||||||||| ||| ||||||| ||||| ||||||||||||||||| |||||||| || ||||| || || ||||||| |      |  || ||| ||  | | || ||  |  ||   | ||  |  | | | |  ||   | ||  |  | |   || |  | |||    |  
GCGGAGGGTGTGACACATTCCGGTCCAACCAAGCTTGTGTTGTACTTTACCGGAGCCACCAACATCCTCTATACCTTCGGTGGACACGCTGTGACCGTgtaagtatttttaatatttctcatggattttcaattaattgtataatcca-caacaattggaaaagtgatgcattcctaacaaactaattatagttggata-

upper sequence: LOC_Os01g63770.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 5'ss of exon 5
GCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaagcaga-acttgctctgtttgtccagttgttaatactgtacagtagtattagtactaggactacaagctaatcctcctgag--gaagtgaagtga------------------------------------------------
 ||   ||| | || ||||  || ||      |  |||  | |||||||| || || |||||||| ||||||||||| ||  ||||||| || |||||||||| |||  ||  |  | |||    ||  |   | | ||   | | ||     ||   | || |   |     | |    |  ||    |      | |||                                                
ACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGTgtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaacttcctaattactattgccag

upper sequence: LOC_Os01g63770.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ18760 (Selaginella moellendorffii), 5'ss of exon 5
GCCGAAGGCATCACCCACACCGGTCCAACCAAGCTGGTGCTGTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaagcagaacttgctctgtttg--tccagttgttaatactgtacagtagtattagtactaggactacaag---ctaatcctcctgaggaagtgaagtga--------------------------------------------------------------------------------------
| |  |||  | |  ||  | |  ||||  || || || |  || ||||| || |||||||||||| | |||||||| || ||||| |||||||| |||||||   | ||  | |  | | |      |    ||| |  |||  ||   |   ||   | |      |        ||  || |||||   |  | || | |                                                                                      
GACCCAGGTGTAAAGCATTCGGCCCCAAATAATCTCGTCCAATATTTCACTGGAGCCACCAACATCTTGTACACCTTTGGTGGCCATGCCGTCACTGTgtaagtcgatcatgattctcacggcaccactttgcttgatcctacgatatcattccatcgattccctcctttttctttcctgttcttcctgctcagatcaaatcatacccctccggatcaaatcaagttttttcttacttctttttgcaagaccagatgatataactaagttgtttgtggttttcttgcag

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|58661448|gb|CK050128.1|CK050128
EST:     ACCGGCGCCACCAACATCCTCTACACCTTCGGTGGCCACGCCGTCACAGT                         GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCT
genomic: ACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaag ... attggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCT