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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcactgaaacaggagcacgatgcaaagctaaagcaacaacttgttttgtgttacacctggcacacattttttggagcttattgatacctttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGATCAGAATAAGTACAAGTCAATGCTTATCCGTACATATTCTACAGTATGGA

Basic information

species Oryza sativa
transcript LOC_Os01g55360.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------gtca-ctgaaaca--ggagcacgatgcaaagctaaagcaacaacttgttttgtgttacacctggcacacattttttggagcttattgatacctttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGATCAGAATAAGTACAAGTCAATGCTTATCCGTACATATTCTACAGTATGGA
                                                                      ||| || | |||  | |||| | | ||| |||| |||| || | |||||   ||      |  |  ||   | ||||                ||| ||||||||||  |||||||||||||| | |||||||   | |||||||||||||||||||| || || || |||||||||| |||||| ||||||||||||||||
gttagtaatttcttgttccttttgctctttattgcgctctgctctctctctctctctctctctctagatttcagctaatacactgaagcatggttcaa-gctagagcagcagcctgtttcaggtgctcttttacgtactaatcttgg-------------tcattttttcagGCTACCACAGATGGGAATAGAGCTAATGGACAGCCATTGCTTGTCAATGATCAGAACAAATATAAATCAATGCTTACCCGTACGTATTCTACAGTATGGA

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031052_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------gtca-ctgaaaca--ggagcacgatgcaaagctaaagcaacaacttgttttgtgttacacctggcacacattttttggagcttattgatacctttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGATCAGAATAAGTACAAGTCAATGCTTATCCGTACATATTCTACAGTATGGA
                                                                  ||| || | |||    | || | | ||| |||| |||| |||| ||||||  ||                ||||| |  || ||      | |||| ||||||||||  |||||||||||||| | ||||||| | | |||||||||||||||||||| || || || |||||||||| || ||| ||||||| ||||||||
gttagtaatttcttgttccttttgctctttattgagctttgctctctctctctccctctttagatttcagctaatacactaaaacatggttcaa-gctagagcagcaacctgttttaggt------------gttctttttcgtactaatcttggtcatttt-ttcagGCTACCACAGATGGGAATAGAGCTAATGGACAACCATTGCTTGTCAATGATCAGAACAAATATAAATCAATGCTTACCCATACGTATTCTATAGTATGGA

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G049447_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------gtcactgaaacaggagcacgatgcaaagctaaagcaacaacttgttttgtgttacacctggcacacattttttggagcttattgatacctttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGATCAGAATAAGTACAAGTCAATGCTTATCCGTACATATTCTACAGTATGGA
                                                        ||  |  |        |  |  |  |   |  |    | || |    |    | |  |         ||||| |  || ||      | ||||  | |||||||  ||||||||||||   | ||||||| | | |||||||||||||||||||| || || || |||||||||| || ||| ||||||||||||||||
gttagtaatttcttgtttcttttgctctttattgcgctttgctctctctctctccctctttatatttcagctaatacactgaaacatggttcaatctagagcagcagcatattttaggtgttcttttttgtactaatcttggtcatttt--ttagGCTACCACAGATGGGAATAATGCTAATGGACAACCATTGCTTGTCAATGATCAGAACAAATATAAATCAATGCTTACCCATACGTATTCTACAGTATGGA

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------------gtcactgaaacaggagcacgatgcaaagctaaagcaacaacttgttttgtg--ttacacctggcacacattttttggagcttattgatacctttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGATCAGAATAAGTACAAGTCAATGCTTATCCGTACATATTCTACAGTATGGA
                                                                                |||  ||||| |     ||  | |   |  |    |||| |    |     |    | ||  | | ||||| | | || ||    | | |||| ||||||||||  |||||||||||||| | ||||||| | | |||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||||||||
gttagtaaattcttcttccatttgctctttattgcgctctgttctttctagatttcagccaatatataagcatggttcaaactagaacagcaagctaatatacaagcatggttcaaactagagcagcagcctgtttcaggtgctcttttttcgtaactaatcatgatcattttcttcagGCTACCACAGATGGGAATAGAGCTAATGGACAACCGTTGCTTGTCAATGATCAGAACAAGTATAAATCAATGCTTATCCGTACATATTCTACAGTATGGA

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G890512_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------gtca-ctgaaaca--ggagcacgatgcaaagctaaagcaacaacttgttttgtgttacacctggcacacattttttggagcttattgatacctttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGATCAGAATAAGTACAAGTCAATGCTTATCCGTACATATTCTACAGTATGGA
                                                                     ||| || | |||  | | || | | ||| |||| |||| || | ||||||  ||                ||||| |  || ||      | |||| ||||||||||  |||||||||||||| | ||||||| | | |||||||||||||||||||| || || || |||||||||| || ||| ||||||||||||||||
gttagtaatttcttgttccttttgctcttttattgcgctttgctctctctctctctccctctttagatttcagctaatacactgaaacatggttcaa-gctagagcagcagcctgttttaggt------------gttctttttcgtactaatcttggtcatttt-ttcagGCTACCACAGATGGGAATAGAGCTAATGGACAACCATTGCTTGTCAATGATCAGAACAAATATAAATCAATGCTTACCCATACGTATTCTACAGTATGGA

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|29681974|gb|CB678249.1|CB678249
EST:     AGGACGTGCCACCCTGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: AGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
EST: gi|58661284|gb|CK049964.1|CK049964
EST:     TGTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
EST: gi|29673386|gb|CB669661.1|CB669661
EST:     TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
EST: gi|29679197|gb|CB675472.1|CB675472
EST:     TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgttacacctggcacacattttttggagcttattgatacctttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGATCAGAATAAGTACAAGTCAATGCTTATCCGTACATATTCTACAGTATGGA
                                  tattgat  putative branch site (score: 3)
                                          cctttttgttc  CT-rich tract
                   acatttttt  TA-rich tract