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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcattaactcttcagatggagattttttctgtggagtaaacttctagatgtaacgctggagcttgtgaggtgatttagtactgtgaggtcaaaccaaccatatatttgtcgttgcagGCTTGTGGTTCCATGAAGAGTTGGAGCTCATTCTGGGGTGTCAATTGAAGATACAAGGGAGGTCACACTTTTCCGTACTCAAGTAAAGTCCATTATACAA

Basic information

species Oryza sativa
transcript LOC_Os01g01150.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01150.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G056145_T03 (Zea mays), 3'ss of exon 2
gtactcattaactcttcagatggagattttttctgtggagtaaacttctagatgtaacgctggagcttgtgaggtgatttagtactgtgaggtc-aaaccaaccatatatttgtcgttgcagGCTTGTGGTTCCATGAAGAGTT---GGAGCTCATT-CTGGGGTGTCAATTGAAGATACAAGGGAGGTCACACTTTTCCGTACTCAAGTAAAGTCCAT-TATACAA-
||| ||     ||| | |  | ||||||   ||  ||||| ||||||||| |||||| ||||| | |||| ||| |||||  ||| |||||||  ||||||||||| ||||||||||| ||||||  || ||||||||||||||   ||||| |||| ||||| ||||  |||||||||||||||||   ||||||       |||||||||||| ||  ||||||| 
gtattc-----ctcattaacttgagattcgctccttggagcaaacttctaaatgtaaagctggtg-ttgtaaggcgatttcatacagtgaggtagaaaccaaccatgtatttgtcgtttcagGCTCATGATTCCATGAAGAGTTCTTGGAGCACATTTCTGGGATGTCGGTTGAAGATACAAGGGAGTATACACTTC------CTCAAGTAAAGTACACATATACAAG

upper sequence: LOC_Os01g01150.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G056145_T04 (Zea mays), 3'ss of exon 2
gtactcattaactcttcagatggagattttttctgtggagtaaacttctagatgtaacgctggagcttgtgaggtgatttagtactgtgaggtc-aaaccaaccatatatttgtcgttgcagGCTTGTGGTTCCATGAAGAGTT---GGAGCTCATT-CTGGGGTGTCAATTGAAGATACAAGGGAGGTCACACTTTTCCGTACTCAAGTAAAGTCCATTATACAA
||| ||     ||| | |  | ||||||   ||  ||||| ||||||||| |||||| ||||| | |||| ||| |||||  ||| |||||||  ||||||||||| ||||||||||| ||||||  || ||||||||||||||   ||||| |||| ||||| ||||  |||||||||||||||||   ||||||   |                          
gtattc-----ctcattaacttgagattcgctccttggagcaaacttctaaatgtaaagctggtg-ttgtaaggcgatttcatacagtgaggtagaaaccaaccatgtatttgtcgtttcagGCTCATGATTCCATGAAGAGTTCTTGGAGCACATTTCTGGGATGTCGGTTGAAGATACAAGGGAGTATACACTTCCTCAA------------------------

upper sequence: LOC_Os01g01150.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132936_T03 (Zea mays), 3'ss of exon 3
gtactcattaactcttcagatggagattttttctgtggagtaaacttctagatgtaacgctggagcttgtgaggtgatttagtactgtgaggtc-aaaccaaccatatatttgtcgttgcagGCTTGTGGTTCCATGAAGAGTTG---GAGCTCATT-CTGGGGTGTCAATTGAAGATACAAGGGAGGTCACACTTTTCCGTACTCAAGTAAAGTCCATTATACAA-------
||| ||     ||| | || | ||||||   ||  ||||| |||||| || ||||||| |||||| |||| ||| |||||  ||| |||||||  ||||||||||| ||||||||||| ||||||| || |||||||||||||||   |||| |||| ||||| ||||  |||||||||||||| ||          | |  ||||||||||||||||| ||||||       
gtattc-----ctcattagcttgagattcgctccttggagcaaacttttaaatgtaacactggag-ttgtaaggcgatttcatacagtgaggtagaaaccaaccatgtatttgtcgtttcagGCTTATGATTCCATGAAGAGTTGTTGGAGCACATTTCTGGGATGTCGGTTGAAGATACAAGGAAG----------TACACACTCAAGTAAAGTCCAT-ATACAAGACTATA

upper sequence: LOC_Os01g01150.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132936_T01 (Zea mays), 3'ss of exon 2
gtactcattaactcttcagatggagattttttctgtggagtaaacttctagatgtaacgctggagcttgtgaggtgatttagtactgtgaggtc-aaaccaaccatatatttgtcgttgcagGCTTGTGGTTCCATGAAGAGTTG---GAGCTCATT-CTGGGGTGTCAATTGAAGATACAAGGGAGGTCACACTTTTCCGTACTCAAGTAAAGTCCATTATACAA
||| ||     ||| | || | ||||||   ||  ||||| |||||| || ||||||| |||||| |||| ||| |||||  ||| |||||||  ||||||||||| ||||||||||| ||||||| || |||||||||||||||   |||| |||| ||||| ||||  |||||||||||||| ||  ||||||                               
gtattc-----ctcattagcttgagattcgctccttggagcaaacttttaaatgtaacactggag-ttgtaaggcgatttcatacagtgaggtagaaaccaaccatgtatttgtcgtttcagGCTTATGATTCCATGAAGAGTTGTTGGAGCACATTTCTGGGATGTCGGTTGAAGATACAAGGAAGTACACACTCAA----------------------------

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|66923717|gb|CX110565.1|CX110565
EST:     ACATGGAGAACTTGAGTGCTGATCGAAGTGTTCATCTGATCTATAAAAAT                         GCTTGTGGTTCCATGAAGAGTTGGAGCTCATTCTGGGGTGTCAATTGAAGA
genomic: ACATGGAGAACTTGAGTGCTGATCGAAGTGTTCATCTGATCTATAAAAATgtactcatta ... gtcgttgcagGCTTGTGGTTCCATGAAGAGTTGGAGCTCATTCTGGGGTGTCAATTGAAGA
EST: gi|88838132|gb|CI372700.1|CI372700
EST:     ACATGGAGAACTTGAGTGCTGATCGAAGTGTTCATCTGATCTATAAAAAT                         GCTTGTGGTTCCATGAAGAGTTGGAGCTCATTCTGGGGTGTCAATTGAAGA
genomic: ACATGGAGAACTTGAGTGCTGATCGAAGTGTTCATCTGATCTATAAAAATgtactcatta ... gtcgttgcagGCTTGTGGTTCCATGAAGAGTTGGAGCTCATTCTGGGGTGTCAATTGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgaggtgatttagtactgtgaggtcaaaccaaccatatatttgtcgttgcagGCTTGTGGTTCCATGAAGAGTTGGAGCTCATTCTGGGGTGTCAATTGAAGATACAAGGGAGGTCACACTTTTCCGTACTCAAGTAAAGTCCATTATACAA
                                     atatatttgt  TA-rich tract