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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACCACTAGGCAGTCTGCCCGTGCGCTTCTTGTGATAAGCGATTACTCTTCGC

Basic information

species Oryza sativa
transcript LOC_Os01g17260.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G030280_T02 (Zea mays), 3'ss of exon 8
gtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtac-taaatcctctttatcttttccactatatg----aagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACCACTAGGCAGTCTGCCCGTGCGCTTCTTGTGATAAGCGATTACTCTTCGC
                                                            | | |||    ||| |  |    ||||||  |  | ||   || ||    | ||  |||  |   || | ||||||||  |  |  | |    | ||||    ||||||||||||||||||| ||||||||| ||||||||||||||||| ||||||||||| ||||| || || ||||| ||||||||||| ||||||||||| |
------------------------------------------------------------aca-tctagcaatgacact----tatgtatgaaactgaactgaatacgaca-aggacaacctgcggtgcctaaatcctgctacttctctttgttgtatgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCAC

upper sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G030280_T01 (Zea mays), 3'ss of exon 8
gtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtac-taaatcctctttatcttttccactatatg----aagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACCACTAGGCAGTCTGCCCGTGCGCTTCTTGTGATAAGCGATTACTCTTCGC---------------------
                                                                                      |||  |  | ||   || ||    | ||  |||  |   || | ||||||||  |  |  | |    | ||||    ||||||||||||||||||| ||||||||| ||||||||||||||||| ||||||||||| ||||| || || ||||| ||||||||||| ||||||||||| |                     
--------------------------------------------------------------------------------------gtatgaaactgaactgaatacgaca-aggacaacctgcggtgcctaaatcctgctacttctctttgttgtatgtatcaaggctgacaacctgcggctgcagACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCACGTCTCCGTGCCCTAAGCTCTC
















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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACCACTAGGCAGTCTGCCCGTGCGCTTCTTGTGATAAGCGATTACTCTTCGC
                    tactaaa  putative branch site (score: 1)
                           tcctctttatcttttc  CT-rich tract
                                tttatctttt  TA-rich tract