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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTCTTCTGCATAAACATCGTGCTCGGAAATGTCAGCCTGCGCTACATCCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcattttgcacctccttacatcatcactattccatattcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcag

Basic information

species Oryza sativa
transcript LOC_Os04g59550.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G127591_T02 (Zea mays), 5'ss of exon 1
TTTGTCTTCTGCATAAACATCGTGCTCGGAAATGTCAGCCTGCGCTACATCCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcattttgcacctccttacatcatcactattccatattcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcag
|| ||||||||||||||||| ||||| |||||||||||| |||||||||||||||||||||| |||||||| |||||||||||||| ||||||||||| |||| |     ||   |   ||| || |  |   | || | |  |   | |||| |  | | ||| |||||  | || | || ||   ||                                      
TTCGTCTTCTGCATAAACATTGTGCTGGGAAATGTCAGCTTGCGCTACATCCCAGTCTCCTTCATGCAGACAATCAAATCTTTCACTCCTGCAACCACAGgtatat---cttgatataccctcactttgtgtatcttgcttgcttgctgtcgtatcatcatcatcatcatcat-ctcctgcttggttcag-------------------------------------

upper sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G11850.1 (Glycine max), 5'ss of exon 2
TTTGTCTTCTGCATAAACATCGTGCTCGGAAATGTCAGCCTGCGCTACATCCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcattttgcacctccttacatcatcactattccatattcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcag
||||| ||||| || ||||| || || || ||||| ||||| || ||||| ||||| || ||||||||||| || ||||| ||||| ||||| ||||| |||||  | |||    |     |   | |||  ||    ||||||   |  |   | |||   |||   |  |||  |    || ||   |      || ||  |||   |                 
TTTGTGTTCTGTATTAACATAGTTCTGGGGAATGTGAGCCTACGATACATTCCAGTTTCTTTTATGCAGACAATAAAATCATTCACACCTGCCACCACAGgtaggtttatt----aatcggtgttaacatttctgccacatatttgctacc---tgctttatattgagac-ttg--aggatatttacatctgatattggtgaactggcacag---------------

upper sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G03210.1 (Glycine max), 5'ss of exon 2
-------------------------------------------------------------------TTTGTCTTCTGCATAAACATCGTGCTCGGAAATGTCAGCCTGCGCTACATCCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcattttgcacctccttacatcatcactattccatattcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcag
                                                                   ||||| ||||| || ||||| ||||| || ||||| |||||  | ||||| || || || ||||||||||| || ||||| |||||||||||||| || |                                                                                                                               
GCTGAAGCTTAAACCACTGATAACTGTTGACCCTGAAGACCGCTGGAGAAGAATCTTTCCTATGTCATTTGTGTTCTGTATTAACATTGTGCTAGGGAATgtgagcctaagatacataccggtttcttttatgcagacaataaaatcattcacccctgcaacaacag-------------------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G21870.1 (Arabidopsis thaliana), 5'ss of exon 2
TTTGTCTTCTGCATAAACATCGTGCTCGGAAATGTCAGCCTGCGCTACATCCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcattttgcacctccttacatcatcactattccatattcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcag
||||| ||||| || ||||| ||| | || ||| | || ||  | ||||| || ||||| ||||||||||||||||||||||| || |||||||| || |||  ||   ||||        | | ||    | | || || | | |  |  | ||| ||   ||| |  |  |         |||||     |      ||                          
TTTGTGTTCTGTATCAACATTGTGTTGGGGAATATTAGTCTTAGATACATTCCTGTCTCTTTTATGCAGACTATCAAATCTTTAACTCCTGCAACAACAGgtttagggttttt-------ttaagattgagaatttttcaaaataaagt--gatttttttttattgttctgattggtttttgtgtaatggttttttgagtgcag-----------------------

upper sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S60_175V6.3 (Physcomitrella patens), 5'ss of exon 4
TTTGTCTTCTGCATAAACATCGTGCTCGGAAATGTCAGCCTGCGCTACATCCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcattttgcacctccttacatcatcactattccatattcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcag
|| ||||| ||  | ||||||||||| ||||| |||||||| || ||||| || || ||||||||||| || ||||| || ||||| ||||| ||||| ||||  | |   |||    |  | |  |  | | || |     || ||     |||| |||  ||| | |       |||  || ||||  |||  |||  | ||  ||  || | |           
TTCGTCTTTTGTGTTAACATCGTGCTTGGAAACGTCAGCCTTCGTTACATACCTGTTTCCTTTATGCAAACCATCAAGTCCTTCACACCTGCCACCACAGgtat-gccgaattg----ttttaaatttctgagtactttgacttgatgg--atttttttactattttaa-------acaaaat-taacctcctaactgccgctcc-ctgtcatttc-----------

upper sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S6_175V6.1 (Physcomitrella patens), 5'ss of exon 3
TTTGTCTTCTGCATAAACATCGTGCTCGGAAATGTCAGCCTGCGCTACATCCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcattttgcacctccttacatcatcactattccatattcattttcgttttcttagcattatcatattgctacagcatgtaacaccctccctgatggtctgcttccaatccatgtcatgcag
 | || || ||| | || || ||||| ||||| ||||||||||| ||||| ||  | ||||| ||||||||||||||||| ||||| ||||| || || ||||  | ||| |||   |    ||   | | ||| ||   | |  | ||| |||||| |  | ||| |   |        ||| | || |   |     |||                         
ATCGTTTTTTGCGTCAATATAGTGCTTGGAAACGTCAGCCTGCGTTACATACCTATTTCCTTCATGCAGACTATCAAATCCTTCACACCTGCCACTACAGgtac-gccatgttgttgcaagctattgcgt-act-tttgttctcgaatttagttttcgtttcgttaactggtcctgctctcatttcactcttccttaactgga------------------------

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|33801646|gb|CF326695.1|CF326695
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|58675889|gb|CK064576.1|CK064576
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|218485011|gb|FG955777.1|FG955777
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|3760530|gb|C97784.1|C97784
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|29660579|gb|CB656854.1|CB656854
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|2311307|gb|C27462.1|C27462
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|33674856|gb|CF303095.1|CF303095
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|38476272|gb|CF960405.1|CF960405
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|218483001|gb|FG956129.1|FG956129
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|58679490|gb|CK068177.1|CK068177
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|218497812|gb|FG965091.1|FG965091
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|58675642|gb|CK064329.1|CK064329
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
EST: gi|3107880|gb|D43611.1|D43611
EST:     CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGG                         TTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG
genomic: CCCAGTCTCCTTTATGCAGACTATCAAATCTTTCACCCCTGCAACCACGGgtagagtcat ... tgtcatgcagTTATTCTGCAGTGGTTAGTTTGGAGCAAGCATTTTGAGTGGCGCATATGGG