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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g11840.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgtt--ttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtt----tcctaacctgttctatttttcag
||||||||||||||||||||| |||||||||||||| |||||| |||| ||||||||||||||||||||||||||||||| | ||||||||||||||||||||   | |||||||||||||  |  | || ||||||   |  |||  |   | ||     |    |||| | |||||  |||||| ||
AGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAGCATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAGgttgcctttgttcaccatgctgctgcgatgtaaacttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgtt--ttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtt----tcctaacctgttctatttttcag
||||||||||||||||||||| |||||||||||||| |||||| |||| ||||||||||||||||||||||| ||||||| | ||||||||||||||||||||   | |||||||||||||| |||| || ||||||   |  |||  |   | ||     |    |||| |  ||||  |||||| ||
AGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAGCATAATGAAATCCAAACTGTTAACATCAAGAGTGTTGGTGCAGACAATGAGgttgcctttgttcaccatgctattatgatgtaaacttagtaagcttgttataaggtttctctgtggtccttaattgtttcattttttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcag----------------------------
||||||||| ||||||||||||| ||| || ||||| || ||||| || ||||||||||| || ||||| ||||| || | | | || |||||    ||||| |    |     || |   | | ||       ||||  | || |    | |   ||||    ||  | |  |  |||| ||                            
AGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctgttattcctttttttttttgggctgtataatttgcgagcaagaagtgtt----aagttctctttatttttagtgacatgtgcaagtactatgcttcttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACA-------ATGAGgttttctgttcaccatgcta-----atatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcag--------
||| ||||| ||||||||||||| |||||| ||||| || ||||| || ||||||||||| || ||||| ||||| || | | | || |||||         ||| | | |  | ||||   |  |      |||  |||  | |  | | |  |   || | | | || |||  | |  |||   | |  |  |        
AGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgtatgggctctattattcatttttttggctgtataatttgcgagcaagaagtgttaagttct-ctttatttttagtgagatgtgtaagtactatgcttcttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctgttcaccat--gctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcag-----------
| ||||||| |||||||||||||  |  ||||||||||||||| | || ||||||||||| |||||||  || ||||| | ||||||||||||  | |||||   |     ||      ||  |||  ||     | | |  || |  || |   |  | ||||      || |   |||||              
AATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACTGCAAACATCAAAAGTATTGGTGCAGATTACGAGgtacacgccatacttgtaactcttatactgtggcataggatgacctatttgttttttgtttttcgcctgatgataagtttttgttctgtaacttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgtttt-ctgttcaccatg-ctaatatgttgaaaacttgtaatactttctt-atacgtcatgtttcctaacctgttctat--ttttcag
| ||||||| |||||||||||||| || ||||||||||||||| | || ||||||||||| ||||| |  || ||||| | |||||||||||   | ||||| |  ||  | |   |  ||  | | ||      | | || || | | | |  |  |   ||   |   |||    ||  |||| ||
AATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACCGCAAACATCAAAAGTATTGGTGCAGGTTACGAGgtctagctcctaattgtaactcttgtattctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttt----tctgttcaccatgctaatatgttg-------aaaacttgtaatactttcttatacgtc-atgtttcctaacctgttctatttttcag-------------
| ||||||| |||||||||||||| || ||||||||||||||| | || ||||||||||| ||||| |  || ||||| | |||||||||||   | ||||| |     ||  |    |  ||  |||  ||       ||||| ||    |||    |||   |   |  | ||| |    ||  |  |||||              
AATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAGCATAATGAAATTCAAACCGCAAACATCAAAAGTATTGGTGCAGGTTACGAGgtctagctcctaattgtaactcttgtattctggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaagctttcatctctctaccttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttt-----tctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcag---------------
||| ||||| || || ||||||| |||||||||||| |||||| | || ||||||||||| || ||||| ||||| |||| | | || |||||   ||||||||     |   |||| | |  |   || |||   || ||  ||     ||||   |  |  |     |   |    | | ||||                 
AGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAGCATAATGAAATTCAGACTGTGAATATAAAGAGTGTGGGAGCAGATTTTGAGgtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 10
AGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAACATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgt--------tttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcag------------------------------------------------------------------------------
 |  || ||||||||||||||  | ||||| |||||||||||| ||||||| |||||||| || ||||| ||| ||||| |  ||||||| ||    |||||         | ||||| |  |     ||      |||  | ||  || ||  || ||     | ||||||   |  |  || || |||                                                                               
GGCACCAGTTGCTAGCATGGATGGTAGTGGTAAAATCATATGGGCAAAACACAATGAAATACAGACTGTCAATGTCAAGGCAGTTGGTGCTGATTTCGAGgtggcgcctactcctgtttaaaaattagattcaaataaagttagttgtatttgttt-tatactttctttcctgtgcaatgttagttatcattagctatatttagaactatcatgtagtaatatcaaataactgaagctttttcatgtttttatttttatttttgtgcag

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|88299886|gb|CI579947.1|CI579947
EST:     ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAG                         ATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGACTATTGGTGCAGACAATGAGgttttctgtt ... tatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGT