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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag

Basic information

species Oryza sativa
transcript LOC_Os01g17260.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctct-ctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
||||   |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||| ||||| || ||||| || ||||||||||||||||| ||||||  |    | || ||    | |   ||| |    || || | |  |        ||  | || ||         |||   || |||        | |||  ||                                                         
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctc-----ccaaaaagaatgctcatcttgcatttcag---------------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G39050.1 (Glycine max), 5'ss of exon 11
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgt--actaaatcctctttatcttttccac---tatatgaag-
 ||||| || ||||| ||| | || || |||||||| |||||||| |||||||| ||||||||||| || || ||||| ||||||   ||| ||   ||||||   | || || ||| |     |      ||| |   | || | | | ||    |   ||  ||||        |||  || || |  |  || ||||   | | |  | |  |||  |||      ||| |   || || || |||         || ||||  
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaacttttcttactcacatgtacgcgatcagtttggttcatttttctcaaa---gaaaatgctctt-------tcatacagcatttcatg-gcagattattg-atatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaag

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 5
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggag-tatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
 |   | || || || ||  ||||||| ||||||||  ||||||| |||||  | ||||||||||| |||||||| || ||||||   || |||| ||||||||  |  |||| |  |||   ||| || |     || ||   | |       || |  |||     |       || | || | || | ||   |  ||  | | |  |                                                   
GCCCAGCTCATCAGGCTCCCCGGGAAATGTGGCAAATAACATGGGTCAAATAACTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCTCCAGgtacgctcattttccggtctaattctgtttt--ctcaacttccatct------ttttgaaataa----agagaactcaggaagctttgaattaactgagtttaatttatttg--------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G31050.2 (Glycine max), 5'ss of exon 9
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagt-atgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
 |   |  | || || ||  ||||||| |||||||  |||||||| |||||||| ||||||||||| |||||||| || |||||    || |||||||||||||  |  |||| |  |||   ||| || |          || | | | ||     |  |||     |       || | ||  |  | | | | |  ||  |                                                          
ACCCAGCACATCAGGCTCCTCGGGAAATGTGGCAAGTTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACTCTTGATGGGTTTCTTCGCCAGgtacgctcattttccggtctaattctgttttctcaacttccatctttttgaaataaagagataa----agagaactcaggaagcttagaattaagtgagttaaa----------------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 9
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag-
 ||||| || ||||| ||| | || || |||||||| |||||||| |||||||| ||||||||||| || || ||||| ||||||   ||| ||   ||||||      |  || |||  ||| | | | |    | | ||  |||  ||   ||     | | |  | |    | || | | |   | | |      |   |  ||||   | |   ||| |    |||     || ||||| |||      || ||||  
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGATTCATTAAGCAGgta------tgcttttcttactcacatgtgtgcgatcagtttggtacatatttctcaaagaaaatgctctttcataca-gcatttcatggcagattattgataacaaacatcactattaaaata---acttggctctgtttatttttgtggtcatttgaaag

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 11
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggag-tatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
 |   | || || || ||  ||||||| |||||||| |||||||| |||||||| ||||||||||| |||||||| || ||||||   || |||| ||||||||  |  |||| |  |||   ||| || |     || ||   | |       || |  |||     |       || | || | || | |||  |  ||  | | |  |                                                   
GCCCAGCTCATCAGGCTCCTCGGGAAATGTGGCAAATTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcattttccggtctaattctgtttt--ctcaacttccatct------ttttgaaataa----agagaactcaggaagctttgaattatctgagtttaatttatatg--------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G26280.1 (Glycine max), 5'ss of exon 11
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaacc--ttgggtatagtcttatgatgtc-catggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
 | ||  || ||||| ||| | || || |||||||  |||||||| |||||||| ||||||||||| ||||| ||||| || ||    ||| |||  |||||||  | || ||| |  | ||    |  | |  ||    |   |  || ||    |  ||   |||||| |  |    | | || |   || |||    |||                                                             
ACCTGCCTCATCTGGTTCATCAGGGAATGTGGCAAGTTACATGGGTCAAATGGCCATGGCCATGGGCAAGCTAGGGACACTAGAAGGGTTCATTCAACAGgtacattcttctttgttgcacttgtatgccaatagtttgctgcattagtgaataggtgaggacgagtcttttagtccagccttgatttcctaatatt---att-------------------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 7
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaacc--ttgggtatagtcttatgatgtc-catggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
 | ||  || ||||| ||| | || || |||||||| |||||||| |||||||| ||||||||||| ||||| ||||| |||||    ||| |||  |||||||  | || ||| |  | ||    |    |  ||    ||  |  || ||    |   | | | |||| |  |    | | || |   || |||    |||                                                             
ACCTGCCTCATCTGGTTCATCAGGGAATGTGGCAAATTACATGGGTCAAATGGCCATGGCCATGGGTAAGCTAGGGACACTTGAAGGGTTCATTCAACAGgtacttttttctttgttgcacttgtatacaaatagtttgctacattggtgaataagtgaagaagaatcttttagtccagccttgatttcctaatatt---att-------------------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 11
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctct-ctctcttttctagtgtaaattatgta-tgtaaaccttgggtatagtcttatgatgtccatggagtatgt-agtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
|||||| |||||||| ||| | ||||| ||||||||||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||   ||  |||| ||||||     | |    | |    | ||||| ||      ||  ||  | | |  | | |   ||| ||||  | |||  ||   || | || || |   |||                                                               
TCTTGGCTCTTCTGGTTCATCTGGAAATGTGGCAAACTATATGGGTCAAATGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttctaaagttttgattttctttcctgacaataagaataaaatcttgatcatat-tatggtctgtttatgatcaaccagaaagttaggaaatgga---------------------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 10
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtctta-tgatgtcca-tggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
 | |||  | ||||||||| | || || ||||||||||| |||||||| ||||| ||||| ||||| ||||| ||||| ||||||   || ||||| ||||||          |||| || |   |||  | |      | | | ||| ||| ||||  |  |     | || || | | |  | |   |  | |     ||    | ||                                                     
ACCTGGCCCATCTGGATCATCAGGGAATGTGGCAAACTATATGGGCCAGATGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaa---------tctcccttttagtttagtggaagttgtaaggaatg-aaaacttgaatgcatcagcagtggtggcaaataaaattatttatttattttttgctatcaa-----------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ18699 (Selaginella moellendorffii), 5'ss of exon 2
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgta-tgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
|   || |||   |||    |    ||||| || ||||||||||| |||||||| ||||| ||||| ||||| || || || ||||| ||  ||||||||||| |  |      | |  ||| |||||     ||  |||| | |   | |                                                                                                               
TGCCGGCTCTCTGGGAAACTCCCCCAACGTAGCGAACTACATGGGACAAATGGCCATGGCAATGGGAAAGCTCGGAACTCTCGAGAACTTTGTTCGCCAGgtaacgcgag---ccgcgatctttctttctcgctgataattctttggcgcag--------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ22847 (Selaginella moellendorffii), 5'ss of exon 5
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
    || ||    ||  |  ||   ||||| |||||||||||||| || ||||| ||||||||||||||||| || || || || || ||  |||| ||||||         |  |   |||   ||||  | |   |    | | | |    ||||       |   ||||      ||   || ||  |   | | ||                                                             
CTCGGGATCGCTGGGGGCCTCGTCCAACGTCGCAAACTACATGGGACAGATGGCTATGGCCATGGGGAAGCTCGGCACTCTGGAAAACTTTGTTCGTCAGgtaaagccaaactctttcttcttcttttttcatttccagcagtttttcttggtcttgctctccata--atgaaagttctgcctta-gttttccacagcttttt----------------------------------------------------------

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ30797 (Selaginella moellendorffii), 5'ss of exon 6
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgta---ccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag
    || ||    ||  |  ||   ||||| |||||||||||||| || ||||| ||||||||||||||||| || || || || || ||  |||| ||||||   |||   | |||||   ||| |  | | |      | || |   | |    ||||       |   ||||      ||   || ||  |   | | ||                                                             
CTCGGGATCGCTGGGGGCCTCGTCCAACGTCGCAAACTACATGGGACAGATGGCTATGGCCATGGGGAAGCTCGGCACTCTGGAAAACTTTGTTCGTCAGgtaaagccaaactctttcttcttcttttctcttttccagcagtttt---tcttggtcttgctctccata--atgaaagttttgcctta-gttttccacagcttttt----------------------------------------------------------

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|55434868|gb|CV730559.1|CV730559
EST:     TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAG                         GCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
genomic: TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgtt ... ctatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
EST: gi|32948334|gb|BP184906.1|BP184906
EST:     TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAG                         GCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
genomic: TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgtt ... ctatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
EST: gi|16574217|gb|BI801513.1|BI801513
EST:     TGGCAAT-GCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAG                         GCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
genomic: TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgtt ... ctatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
EST: gi|55434870|gb|CV730560.1|CV730560
EST:     TTGAGAATTTCCTTCGCCAG                         GCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
genomic: TTGAGAATTTCCTTCGCCAGgtaccatgtt ... ctatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
EST: gi|58659223|gb|CK047903.1|CK047903
EST:     TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAG                         GCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
genomic: TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgtt ... ctatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
EST: gi|58670245|gb|CK058931.1|CK058931
EST:     TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAG                         GCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC
genomic: TGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgtt ... ctatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACC