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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgccggacccaccattccatttattctgattgtagtaatacatttaaataattgatagtgtgtgcctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g54100.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G095634_T01 (Zea mays), 5'ss of exon 2
ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgccggacccaccattccatttattctgattgtagtaatacatttaaataattgat----agtgtgtgcctgcag
|||||| |||||||  |||||| | ||||||||||||||||||||||| || |||||||| ||||||||||| ||  |||||||||||||||||||||||||||      ||| || |||  ||| || |  |||||  ||| ||  || |   || |||||    | | ||   ||  ||
ACATCTTGGGAGAACAGGTAGCAGGAGGGATGATTTAGAATCTCTAGCATATACACTAGTCTTTCTTCTACGAGGATGTCTACCTTGGCAAGGTTATCAGgtaaaatataggatcctccag-ccacttgtattgatttgagtgatgtatatgtgtacttgatgtttattttgcatctatag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 9
ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgccggacccaccattccatttattctgattgtagtaatacatttaaataat-tgatagtgtgtgcctgcag
 ||||| || ||||  |||||| | || ||||| || |||||||| |||||||| || || |||||||| || || || |||||||||||||| || ||||| |||   |   |  |   |    ||  | || || |||     | || | | |  | ||||  | | ||  | |||
CCATCTTGGTAGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTTCGTGGTCGGCTACCTTGGCAAGGATACCAGgttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgt-tacag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 9
ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgccggacccaccattccatttatt-ctgattgtagtaatacatttaaataattgatagtgtgtgcctgcag
 ||||| ||  |||  |||||| | || ||||| || |||||||| |||||||| || || |||||||| || || || |||||||||||||| |||||||| |||    |   | |  | ||  |||| | || ||||||     | || | | |  |    |   | |   | |||
TCATCTTGGTCGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTTCGTGGTCGGCTACCTTGGCAAGGATATCAGgttatt-attgtttcaaatagtcattttagtactaattgtaaatgaaaatatgactcttatgaaactttttgttacag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA04G09070.1 (Glycine max), 5'ss of exon 9
ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgccggacccaccattccatttatt-ctgattgta-gtaatacatttaaataattgatagtgtgtgcctgcag
 ||||| || ||||  |||||  | || ||||| ||||||||||| |||||||| || || |||||||| |||||  | |||||||||||||| |||||||| |||    |   | |  | ||  || | | || || ||| || | | || | | |  |      | | |   | |||
TCATCTTGGTAGAACAGGTAGTAGGAGAGATGACTTAGAATCTCTTGCTTACACTCTTGTCTTTCTTCTTCGGGGTAGGCTACCTTGGCAAGGATATCAGgttatt-attgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 9
ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgccggacccaccattcc-atttattctgattgtagtaatacatttaaataattgatagtgtgtgcctgcag------------------------------------------------------
 ||| | |||||||  || ||  | || |||||||| |||||||| |||||||| ||  |||| || || || || |||||||||||||||||||||||||   || ||   |  |    |||| ||  | | || |  |  |  |  |||| ||     ||||   | ||      |                                                      
TCATTTGGGGAGAACTGGCAGTAGGAGAGATGATTTGGAATCTCTTGCTTACACTCTTATTTTCCTCCTCCGTGGTCGTCTACCTTGGCAAGGTTATCAGg---ttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaatcccatatatag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 9
ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgta---attcgccggacccaccattccatttattctgattgtagtaatacatttaaataattgatagtgtgtgcctgcag
 || || || || |  || ||| |||| |||||||| |||||||| |||||||| ||  |||||||||| || || || || |||||||||||||| |||||    | |  ||  ||  |  ||   ||||  | | || ||  |  |  |  | | |  |  |      |   ||  ||
TCACCTTGGAAGGACTGGAAGCAGAAGAGATGATTTGGAATCTCTTGCTTACACCCTCATTTTTCTTCTCCGTGGACGGCTGCCTTGGCAAGGTTACCAGgttgacagtttccaaacttaa-ataggattttcttttat-gtgattctgtacatca-ttctgaaccaacagcttctttag

upper sequence: LOC_Os01g54100.2 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 9
ACATCTAGGGAGAATCGGTAGCCGAAGGGATGATTTAGAATCTCTAGCTTACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgccggacccaccattccatttattctgattgtagtaatacatttaaataattgatagtgtgtgcctgcag---------------------------------------------------------------------------------------------------------
|||| | || || |  || ||  | ||||| || || ||||| || ||||||||  | || || ||||| ||||| ||||| ||||||||||||||||||||| |  |    ||        | | |   |      | ||| ||  || | ||  |||  |  | | | ||  ||                                                                                                          
ACATTTGGGAAGGACTGGGAGTAGGAGGGACGACTTGGAATCACTGGCTTACACTTTGGTATTCCTTCTGCGGGGTCGTCTTCCTTGGCAAGGTTATCAGgtact--gattaactttgtgg-ctagtagctaacgaggaagtgatcaatgtgaa--atttttcttttcttcccacatcccacatcccactttttttgtattttgtttgttttgttttgttttgttttttctttttcctctcactatttttcatttggacgtgctatatatttggttttgtag

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|58680661|gb|CK069348.1|CK069348
EST:     ACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAG                         GGTGAAAACAAGGGTTTCCTTGTGTGCAAAAAGAAAATGGCTACGTCTCCA
genomic: ACACACTAGTTTTTCTTCTACGGGGGCGTCTACCTTGGCAAGGTTATCAGgtaattcgcc ... gtgcctgcagGGTGAAAACAAGGGTTTCCTTGTGTGCAAAAAGAAAATGGCTACGTCTCCA