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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAGgtcagatacactctgaggtgagatgtgccatggacatgaagtatcacgcatcttggtgtctaccagcaactgatagtgttctttagcaggcatggtgctggtttaagttgataggtacctggcccatcatagaaattttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g41100.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179097_T02 (Zea mays), 5'ss of exon 7
CAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCA--------TTCTGAATCTATGAGgtcagatacactctgaggtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttagcaggcatggtgctggtttaagttgataggtacctggcccatcatagaaattttgttgcag
                        |||||||||||| |||  |||| |||| |||||  || |   |||| ||||| |||| |||        | |||| |  ||||||| |||||   |||||||||||  |||||||||||||||||||||||  | ||| |||||||| ||||||||||||||||||||||||||                                                         
------------------------CTTTTTGGCTGAACTAGAAGCA-CTTGATTGGGTCCTGTCCGTCCTAACTGTTATGCTTCACACTGAAATCCTGAGTTCATGAGGTTAGATATCTTCTGAGgtgag--gtgccatggacatgaagtatcacatcttctcggtgtctagcagcaactgatagtgttctttagcag---------------------------------------------------------

upper sequence: LOC_Os04g41100.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179097_T08 (Zea mays), 5'ss of exon 7
CAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCA--------TTCTGAATCTATGAGgtcagatacactctgaggtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttagcaggcatggtgctggtttaagttgata-ggtacct------ggcccatcatagaaattttgttgcag
                        |||||||||||| |||  |||| |||| |||||  || |   |||| ||||| |||| |||        | |||| |  ||||||| |||||   |||||||||||  |||||||||||||||||||||||  | ||| |||||||| |||||||||||||||||||||||||||| |||| | ||||||| | |||| |||  ||      ||||||||||||||||||||||||||
------------------------CTTTTTGGCTGAACTAGAAGCA-CTTGATTGGGTCCTGTCCGTCCTAACTGTTATGCTTCACACTGAAATCCTGAGTTCATGAGGTTAGATATCTTCTGAGgtgag--gtgccatggacatgaagtatcacatcttctcggtgtctagcagcaactgatagtgttctttagcaggcttggtaccggtttaaatggataaggtttctccttgtggcccatcatagaaattttgttgcag

upper sequence: LOC_Os04g41100.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179097_T01 (Zea mays), 5'ss of exon 8
CAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATG-AGgtcagatacactctgaggtgagatgtgccatggacatgaagtatcacgcatcttggtgtctaccagcaactgatagtgttctttagcaggcatggtgctggtttaagttgataggtacctggcccatcatagaaattttgttgcag-
                                        | ||     |  ||| |  | ||  ||    | | |  ||||  |||     |  ||  || ||    | |     |  |   || | ||     ||| | || |   || | ||||  | ||   |  ||    ||| |    |    || |     ||   | || |  ||       |||  | |  || | | | |   |    
----------------------------------------TAAGGTTTCTCCTTGTGGCCCATC-ATAGAAATTTTGTTGCAGGATTAACGCTTCATCCAGATCGATCATAAAAGCAAATATAATCTACCTGCATCATAAGgtgtg--gcgtgttggcttttattggttac-accagtttcacct--ttggaacttctctatgtaaaat--attccagattggtacgttgtaaacaatgtccagtgtg

upper sequence: LOC_Os04g41100.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 7
CAAGGGAACATTGGCAACCGTGGTCTTTTTGGCTGAGCTATTAGCAACTTGTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAGgtcagatacactctgaggtgagatgtgccatggacatgaagtatcacg-catcttggtgtctaccagcaactgatagtgttctttagcaggcatggtgctggtttaagttgataggtacctggcccatcatagaaattttgttgcag
                 |||||| |||||||||||| |||  || |  |  || |    || |   | || ||||| |||| |||  ||||||| | ||||||||||    |||||||||||  |||||||||||||||||||||||  | ||| |||||||| |||| |||||||||||||||||||||                                                         
-----------------CCGTGGGCTTTTTGGCTGAACTAAGAGTACTTGATTGGATTCCTGTCCGTACTAACTGTTATGCTTCACCCTGAATCCACGAGGTCAGATGTCTTCTGAGgtgag--gtgccatggacatgaagtatcacatcttctcggtgtctagcagcgactgatagtgttctttagcag---------------------------------------------------------

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|29628989|gb|CB634000.1|CB634000
EST:     GTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAG                         GATTAACTCCAACCAGATTGATCATAAAAGCAGTCTAATCTGCCTGCATCG
genomic: GTTTGGGCTCTATTGATCCTGACTGTCATGCATCATTCTGAATCTATGAGgtcagataca ... tttgttgcagGATTAACTCCAACCAGATTGATCATAAAAGCAGTCTAATCTGCCTGCATCG