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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttcaaggatcacagatgactgttttttatttgatatcactgtagagtctttgtccttctgcccttctccatcattgtttatgtaggatgcaattcattatgctatggtttcaggtatttttcttctatcagtagtagtgcttgaaatgtagatctctgtcatacag

Basic information

species Oryza sativa
transcript LOC_Os01g44040.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA05G25780.1 (Glycine max), 5'ss of exon 10
AAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttcaaggatcacagatgactgttttttatttgatatcactgtagagtctttgtccttctgcccttctccatcattgtttatgtaggatgcaattcattatgctatggtttcaggtatttttcttctatcagtagtagtgcttgaaatgtagatctctgtcatacag
|||  |  |  | || |   ||||||||||||||||| ||||||| |||||||| || || ||||| ||||||||||| |||||||| || |||||||||||||           || |  || |||   |||| |  |   ||| ||   | | ||| |  |       ||   |    |  ||||  |  ||   | ||||  ||   |                                                              
AAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGCCTATTTTCATCCAAATgtaa-----------tctcgaat-actagcttttgta-gtggtcattgggtaattttttttatataatagttggtccagctattttaaatttgaaatatttcaccatctcag-------------------------------------------------------------

upper sequence: LOC_Os01g44040.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G08730.1 (Glycine max), 5'ss of exon 10
AAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttcaaggatcacagatgactgttttttatttgatatcactgtagagtctttgtccttctgcccttctccatcattgtttatgtaggatgcaattcattatgctatggtttcaggtatttttcttctatcagtagtagtgcttgaaatgtagatctctgtcatacag
|||  |  |  | || |   ||||||||||||||||| ||||||| |||||||| || || ||||| ||||||||||| ||||||||||| ||||||||||||| | | |||   |  |   ||  || |  | ||| | |||   |      | | |    ||  | ||  ||         ||||  |  ||   | ||||  ||   |                                                              
AAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGCCTACTTTCATCCAAATgtaa-tctccaatactagcttgtg--tggtggtcattgggtattttt------tttataatatttagtccagctat-------tttaaatttgaaatatttcaccatctcag-------------------------------------------------------------

upper sequence: LOC_Os01g44040.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT2G34410.1 (Arabidopsis thaliana), 5'ss of exon 9
AAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttcaaggatcacagatgactgttttttatttgatatcactgtagagtctttgtccttctgcccttctccatcattgtttatgtaggatgcaattcattatgctatggtttcaggtatttttcttctatcagtagtagtgcttgaaatgtagatctctgtcatacag
 ||| || |  ||||||| || ||||| ||||| ||| |||| || ||||| || || |||||||| ||||||||||| |||||||| |||||||| | ||||| | || ||     |||   | ||  |  || ||| |||||     |    |  |    ||      || |    |||| || || |  |                                                                                
TAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGCCTATTTCCATCCCACTgtaactcttgaa--cctaca---gccttctcgttttttcatatcttctcatgaaccctacgattaaaatattttttgacatt-ttcatttcag--------------------------------------------------------------------------------

upper sequence: LOC_Os01g44040.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 5'ss of exon 10
AAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttcaaggatcacagatgactgttttttatttgatatcactgtagagtctttgtccttctgcccttctccatcattgtttatgtaggatgcaattcattatgctatggtttcaggtatttttcttctatcagtagtagtgcttgaaatgtagatctctgtcatacag
 ||  |  |  | |  | | ||||||| ||||| ||  |||| ||||||||||| || |||||||| || |||||||| |||||||| |  || |||| |||||||| | |    |  ||  |   |   |||| | |  | ||  ||||       |   ||||    |||    |||||| | ||                                                                                      
CAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGCCTATTATCACCCAACTgtaagttctta---cttccatttttttccgttttttgtagtgtcgatgtaa------taaacttcaaaacttggg-atcattctctag-------------------------------------------------------------------------------------

upper sequence: LOC_Os01g44040.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S74_21V6.1 (Physcomitrella patens), 5'ss of exon 9
AAAAGCAAACT-TACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttcaaggatcacagatgactgttttttatttgatatcactgtagagtctttgtccttctgcc-cttctccatcattgttta-tgtaggatgcaattcattatgctatggtttcaggtatttttcttctatcagtagtagtgcttgaaatgtagatctctgtcatacag
 ||||    ||   ||  || | || || ||||||||| ||||||| || || || ||||| ||||||||||| ||| |||||||||| || ||||| |  ||| ||  |   |     |   | || ||     | | | | |   |  |     |  |      ||   | | |||    |   ||| |  || ||   ||| ||  ||| |  ||||      |||  | |   | |  |    |  |||  |  || || | |         
-AAAGAGCCCTGCGCCTTTGCTTCACGAATGGCATTTCAGATCTGGGCTCGACCGATATATCTGGATTATTGGCATGCTCTATGCCTATTTTCATCCTACGgtatgtcgttttgaccaccttctaaccgtagaaaaat-ggtttggttagatcccgtaagagtgagtgttgcctttccgctgtgacttactacagaattgtatttat--tgcaaaagtttgtaa-gtttcgcatgattgaacatctttatttgtgaactacatgtttccag-----

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|87006678|gb|CI285712.1|CI285712
EST:     ATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAAT                         GTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG
genomic: ATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttc ... tgtcatacagGTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG
EST: gi|88721652|gb|CI744951.1|CI744951
EST:     ATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAAT                         GTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG
genomic: ATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttc ... tgtcatacagGTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG
EST: gi|29659100|gb|CB655375.1|CB655375
EST:     TTATATATGGATTATGGGAATGATCTATGCCTACTTCCATCCAAAT                         GTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG
genomic: TTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttc ... tgtcatacagGTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG
EST: gi|86502826|gb|CI145459.1|CI145459
EST:     ATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAAT                         GTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG
genomic: ATCGTTATATATGGATTATTGGAATGATCTATGCCTACTTCCATCCAAATgtaagttttc ... tgtcatacagGTTGAAAGATGGATGGAAAAGCTTGAAGAATCTGAAACTAAGGTTAGGTTG