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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g19510.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G119725_T02 (Zea mays), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgt-------tcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag
|||||||||| || ||||||||||| |||||||||||| ||||||| ||||| ||||||||||||||||| |||||||| ||||||||||| ||||||||||||| ||| ||| |||         |  | | |||||| | |  ||||||   |||  |   ||    ||  || |  ||| |||
GGTATGCAAAACGATTTTTGCATCCCGATGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAGCATTTCAACGCAGAGAAgtaagcactacatatttccattcttgttttctttctgttcagcaggtgttcattttgattaaaatgtccttcctatt--tttacag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G006507_T02 (Zea mays), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgt-------tcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag
|||| ||||| || ||||||||||| || ||||||||| ||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||||||||||| ||| ||| ||||        |  | | |||||| |  | ||||||   ||   |  |||    ||  || |  ||| |||
GGTACGCAAAACGATTTTTGCATCCCGACGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAACATTTCAATGCAGAGAAgtaagcactacatatttgcattcttgttttctttctgttcagttggtgttcatttttattaagatgcccttgctatt--tttacag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag
||||||||||| | ||||||||||||||||||||  |    ||||| || ||||| || |||||||| || || || || ||||| ||||||||||| | ||  ||| | | | | ||    | ||  ||  || |  |||     |||   | | ||| |  || ||    |||||||
GGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGATAGgt--gaattacttgtctgaaattgtagttgcagatca-gtgacaatctt---tacaatttttattttaaa--ttttcag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgac--cttgtgttccacttgggtgcgattatg----tttgtactctttttcag------------
||||||||||  |||| ||||||||||||||||||||    ||||| || || || || |||||||| ||||||| |||  |||| ||||||| |||||||||||       ||||| | || | | |   |||    |  || || | |||       |||      |||||  |||  ||| |            
GGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAGAAgtaag-------tttttttcccataaaccagtgatagttcctggtcaaattgaaaatttttacacttctttgtgttctgcttccgatgatcttccag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag---------------------------------------------------------------------------------------------
||||||| |||||||||||||| || ||||| || || |  ||||| ||||| ||||| ||||||||||| || | | |   |||||| ||| |  ||| | ||| ||  |  |   ||   ||  || |   | ||  |    |  ||  ||         |  | |   |||   ||                                                                                             
GGTATGCCAAGCGGTTTTTGCACCCCGATGTAGTGGCGCCGTATGAGTACATCTTCATTTGGGATGAGGATCTTGATTTGAGGCATTTTAATCCTAAGAGgcaagtacatc--tgccgtatattactccgactagctcattcgtcgatttagtaaagcctcatacgcatgttttagaaggattccttttcgcggttgctctcaaagagaaaagtgagacttgaaacttctgaagattttggatttattgatacgggtggactggcttcgcag

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|38475807|gb|CF959940.1|CF959940
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|33795503|gb|CF323621.1|CF323621
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|33675555|gb|CF303794.1|CF303794
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|86906524|gb|CI294647.1|CI294647
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT