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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCGGCGTCATCTTCGCCGCCCGCGACACCACCGCCAGCGTCCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgcctcctcatatctcatagtatatcaaagtccttgatggtgaggctgaccgcgggtgccatggatggaacag

Basic information

species Oryza sativa
transcript LOC_Os02g47470.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G179147_T02 (Zea mays), 5'ss of exon 2
CATCGGCGTCATCTTCGCCGCCCGCGACACCACCGCCAGCGTCCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgcctcctcatatctcatagtatatcaaagtcc-ttgatggtgag-gctgaccgcgggtgccatggatggaacag-------------
 ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||  |||  | |  |   |  |   |   |     | ||  | | | ||   ||||| | |  |  || || ||               
GATCGGCGTCATCTTCGCCGCCCGCGACACCACCGCCAGCGTGCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCATCgtaagttcttctctccctgccggctcatgcctggcaccagatcgactgcgtgcgcccgccgcgcg-gagactgacgggacgagctggtgttgtag

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G126505_T02 (Zea mays), 5'ss of exon 2
CATCGGCGTCATCTTCGCCGCCCGCGACACCACCGCCAGCGTCCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgcctcctcatatctca---tagtatatcaaagtccttgatggtgaggctgaccgcgggt--gccatggatggaacag-----------------------------------
 ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||| |||| ||| ||||  ||  | |    |      | || |||       | | |   || ||  | |||| |    |  |  ||  ||                                       
GATCGGCGTCATGTTCGCCGCCCGCGACACCACCGCCAGCGTGCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCGGCGGTCCTCAAGGCGGTCATCgtgagttgtccctcccggtcccgggtcttgtttattgggtggcatcaaactgcgggcgcccgccgcgcggagacagactgactgacgggatgagctggtgtgtgtgtgtgttgcgaacag

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G35250.1 (Glycine max), 5'ss of exon 3
CATCGGCGTCATCTTCGCCGCCCGCGACACCACCGCCAGCGTCCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgcctc----ctcatatctcatagtatatcaaagtccttgatggtgaggctgaccgcgggtg--ccatggatggaacag---------------
 || |||||||| ||||| || || |||||||||||||| || || || ||||| ||||||| |||||| ||  |||||   |||||  | || || |  ||||||    ||      |  | ||||| || | ||  | |     |    | |   |        ||    ||   |||   |                 
TATTGGCGTCATTTTCGCAGCTCGTGACACCACCGCCAGTGTGCTGACGTGGATCGTCAAGTACCTCGGTGAAAACCCCAGTGTCCTAGAAGCTGTTAATgtaagtgtctcttgttttttctttctcaaagaaaattgaggctgagggca-taaaaatagtaaaaagtagttcaaaaatgattcttcgacacctcaaaaga

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ30794 (Selaginella moellendorffii), 5'ss of exon 4
CATCGGCGTCATCTTCGCCGCCCGCGACACCACCGCCAGCGTCCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgcctcctcatatctcatagtatatcaaagtccttgatggtgaggctgaccgcgggtgccatggatggaacag----
 ||||| ||||||||||| ||||  ||||||||||||||||||||||| ||| |  ||||||  |||   ||  |||||||  ||||| || | ||||| |||    |     ||| |      ||| | | | |||  |||  | ||| | |||||||||  |  | ||   |   | |    
GATCGGTGTCATCTTCGCGGCCCAGGACACCACCGCCAGCGTCCTCACTTGGCTCCTCAAGTATCTCAAGGAGAACCCCGCGCTCCTCGAGTCTGTCACGgta----caaactctcgt------tagaaaaacgaagaacttc-tcgtg-gactgaccgcgt-tttcgtgttcgtcgctggcag

upper sequence: LOC_Os02g47470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ22851 (Selaginella moellendorffii), 5'ss of exon 4
CATCGGCGTCATCTTCGCCGCCCGCGACACCACCGCCAGCGTCCTCACCTGGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgcctcctcatatctcatagtatatcaaagtccttgatggtgaggctgaccgcgggtgccatggatggaacag----
 ||||| ||||||||||| ||||  ||||||||||||||||||||||| ||| |  ||||||  |||   ||  |||||||  ||||| |  | ||||| |||    |     ||| |      ||| | | | |||  |||  | ||| | |||||||||  |  | ||   |   | |    
GATCGGTGTCATCTTCGCGGCCCAGGACACCACCGCCAGCGTCCTCACTTGGCTCCTCAAGTATCTCAAGGAGAACCCCGCGCTCCTCGACTCTGTCACGgta----caaactctcgt------tagaaaaacgaagaacttc-tcgtg-gactgaccgcgt-tttcgtgttcgtcgctggcag

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|66914874|gb|CX101722.1|CX101722
EST:     GGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACC                         GAAGAGCAGCTGCAGATTGCCAAGGAGAAAGAGGCGTCGGGCGAGCCGCTG
genomic: GGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgc ... gatggaacagGAAGAGCAGCTGCAGATTGCCAAGGAGAAAGAGGCGTCGGGCGAGCCGCTG
EST: gi|58599154|gb|CK009682.1|CK009682
EST:     GGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACC                         GAAGAGCAGCTGCAGATTGCCAAGGAGAAAGAGGCGTCGGGCGAGCCGCTG
genomic: GGATGGTCAAGTTCCTCGGCGACCACCCCGCCGTCCTCAAGGCCGTCACCgtaagttcgc ... gatggaacagGAAGAGCAGCTGCAGATTGCCAAGGAGAAAGAGGCGTCGGGCGAGCCGCTG