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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAAGGAGACGCCTTGGTAACAAAATTAGTGTACAGGGGAATGTTGACCCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaaacttcattgtgcattttcattttctgttcatttaagtttctaatacttacatttgagaatgcttcatcagtgaggtctccaaattgtcca...

Basic information

species Oryza sativa
transcript LOC_Os01g43390.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43390.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G365644_T02 (Zea mays), 5'ss of exon 4
ATGGAAGGAGACGCCTTGGTAACAAAATTAGTGTACAGGGGAATGTTGACCCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaaacttcattgtgcattttcattttctgttcatttaagtttctaatacttacatttgagaatgcttcatcagtgaggtctc-caaattgtcca---
|||||||||  |||||||||||   |||||||||||| |||||||| || ||||||||||| || || ||||||||||||||||  ||||||||||||||||||||||| |||  |     |||||  | ||| ||||  |||  |||| |  |  | |   |   |     ||||| | |||| |  |  |||  |       
ATGGAAGGAAGCGCCTTGGTAATGGAATTAGTGTACAAGGGAATGTGGATCCAGCATTTCTGTTCTCACCATTACCAGTACTGATTGATGAAATTCATAGgttagttaagactaaaaaaatcattt--aatttatgttattttgggtttttggt--taatgctcatgtgcaattcattaatgagataacataaaacgctgcctg

upper sequence: LOC_Os01g43390.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G025031_T02 (Zea mays), 5'ss of exon 1
ATGGAAGGAGACGCCTTGGTAACAAAATTAGTGTACAGGGGAATGTTGACCCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaaacttcattgtgcattttcattttctgttcatttaagtttctaatacttacatttgagaatgcttcatcagtgaggtctcc-aaattgtcca-
|||||||||| |||||||||||    ||||||||||| |||||||| || ||||||||| | || || ||||||||||||||||| |||||||||||||||||||| ||  ||  |   |     || | |||  |||  |||  |||| |  |  | |   |   |     ||||| | |||| || || ||| ||     
ATGGAAGGAGGCGCCTTGGTAATGGCATTAGTGTACAAGGGAATGTGGATCCAGCATTTTTGTTCTCACCATTACCAGTACTGACTGATGAAATTCATAGgttagtaaaggctcaaagatttccatttaatttacgttattttgtgtttttgct--taatgctcatgtgcaattcattaatgagatcacctaaagtgctgct

upper sequence: LOC_Os01g43390.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G377609_T03 (Zea mays), 5'ss of exon 4
ATGGAAGGAGACGCCTTGGTAACAAAATTAGTGTACAGGGGAATGTTGACCCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaaacttcattgtgcattttcattttctgttcatttaagtttctaatacttacatttgagaatgcttcatcagtgaggtctc-caaattgtcca---
|||||||||  |||||||||||   |||||||||||| |||||||| || ||||||||||| || || ||||||||||||||||| |||||||||| |||||||||||| |||  |   | |||||  | ||| ||||  ||| ||||| |  |  | |   |   |     ||||| | |||| |  |  |||  |       
ATGGAAGGAAGCGCCTTGGTAATGGAATTAGTGTACAAGGGAATGTGGATCCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaagactaaaaaattcattt--aatttatgttattttgagtttttggt--taatgctcatgtgcaattcattaatgagataacataaaacgctgcctg

upper sequence: LOC_Os01g43390.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G024738_T03 (Zea mays), 5'ss of exon 4
ATGGAAGGAGACGCCTTGGTAACAAAATTAGTGTACAGGGGAATGTTGACCCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaaacttcattgtgcattttcattttctgttcatttaagtttctaatacttacatttgagaatgcttcatcagtgaggtctcc-aaattgtcca-
|||||||||| |||||||||||    ||||||||||| |||||||| || ||||||||| | || || ||||||||||||||||| |||||||||||||||||||| ||  ||  |   |     || | |||  |||  |||  |||| |  |  | |   |   |     ||||| | |||| || || ||| |||    
ATGGAAGGAGGCGCCTTGGTAATGGCATTAGTGTACAAGGGAATGTGGATCCAGCATTTTTGTTCTCACCATTACCAGTACTGACTGATGAAATTCATAGgttagtaaaggctcaaagatttccatttaatttacgttattttgtgtttttgct--taatgctcatgtgcaattcattaatgagatcacctaaagtgttgct

upper sequence: LOC_Os01g43390.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G088533_T01 (Zea mays), 5'ss of exon 4
ATGGAAGGAGACGCCTTGGTAACAAAATTAGTGTACAGGGGAATGTTGACCCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaaacttcattgtgcattttcattttctgttcatttaagtttctaatacttacatttgagaatgcttcatcagtgaggtctc-caaattgtcca---
|||||||||  |||||||||||   ||| |||||||| |||||||| || ||||||||||| || || ||||||||||||||||| |||||||||| |||||||||||| |||  |   | |||||  | ||| ||||  |||  |||| |  |  | |   |   |     ||||| | |||| |  |  |||  |       
ATGGAAGGAAGCGCCTTGGTAATGGAATCAGTGTACAAGGGAATGTGGATCCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaagactaaaaaattcattt--aatttatgttattttgggtttttggt--taatgctcatgtgcaattcattaatgagataacataaaacgctgcctg

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|86838508|gb|CI329036.1|CI329036
EST:     CCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAG                         GGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGG
genomic: CCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaa ... tgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGG