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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACTgtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcag

Basic information

species Oryza sativa
transcript LOC_Os11g25980.2
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g25980.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G479163_T01 (Zea mays), 5'ss of exon 3
GGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACTgtaagtcaaacttagtctggcatctttttgct-tatttgagttcttaatgcaa--tagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcag
|| |||||||||| |||||||| ||||| ||||| || || || || || || ||||| |||||||||||||||||||||||||||||||| ||||||||||||| || |    ||| |   |  | ||    || |||      || ||     |||| ||||   |    | || | |    | |||| |                                           
GGTTGATTCTTGTTCATGGGCGGTACTCCTACAATCGCACTGCCTTCCTGTCGCAGTACTCTTTCTACAAGTCATTGTTAATTTGCTTTATTCAGATACTgtaagccataaaccgtccgtacttgtattatggtagttggacgtatagtgtgtgctagttttcttgatt-gctcatat-tctgtgcatgcag-------------------------------------------

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GLYMA13G37090.1 (Glycine max), 5'ss of exon 21
GGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACTgtaagtcaaacttagtc-tggcatc--tttttgcttatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcag
|  | ||||| |||||||| || ||||| |||||||||||||| ||||||||||| ||||| ||||| |||||  |  | || ||||| ||||| || |||| |||   | | |    |||| |   |||||  |||  ||| | |  | |  |||  | ||   | |   |    |||    | |    ||| ||  || |                                 
GATTAATTCTGGTCCATGGCCGCTACTCTTACAACCGTACAGCATTTCTTTCTCAATATTCATTCTATAAGTCCCTACTGATATGCTTCATCCAAATCCTgtgagtttcattgaacaatggctttcatttttctttacctga-tacgcagta-aattatttttaaattaggtgcccctgccggaaaggcttgggtagctgtt---------------------------------

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GLYMA12G33340.1 (Glycine max), 5'ss of exon 21
GGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACTgtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcag
|  | ||||| |||||||| || ||||| |||||||||||||| ||||||||||| ||||| ||||| |||||  |  | || ||||| ||||| ||  ||| |||   | | |         |||| |  |||  ||| |    |    |||  | ||   | |  ||    |||  | | |    ||| ||  || |  |                              
GATTAATTCTGGTCCATGGCCGCTACTCCTACAACCGTACAGCATTTCTTTCTCAATATTCATTCTATAAGTCCCTACTGATATGCTTCATCCAAATCTTgtgagtttcattgaac--aatggctttctctttacctga-taagcagca-aattattttgaaaatagatgcccctgccagaaaggattgggtagctgttgataa----------------------------

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 5'ss of exon 21
lower sequence: AT5G44240.2 (Arabidopsis thaliana), 5'ss of exon 20
GGCTGATTCTTGTCCATGGGCGATACTCATACAACCGTACAGCTTTTCTTTCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACTgtaagtcaaacttagtctggcatctttttgct------tatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcag
| ||||||||||| |||||| | || ||||| ||||| ||||| ||| | || |||||||| |||||||| || ||||| || ||||| ||||||||  |||||||  |  |   || |  || || |   |       |||  |||  || ||| |||| |     |||   || ||| |                                                         
GACTGATTCTTGTTCATGGGAGGTATTCATATAACCGGACAGCATTTTTGTCCCAGTATTCCTTCTACAAATCGTTGTTGATATGCTTCATCCAGATTTTgtaagttta-ttatctcagatatgttctcagtagatatcattcaagtcgttcatgaaatactgacaacag--aatctatgtag-------------------------------------------------------

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|163929268|gb|EG711029.1|EG711029
EST:     TCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACT                         TTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAG
genomic: TCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACTgtaagtcaaa ... atgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAG