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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACATCCTCATCCTCTTCTTCTCCTGGCTGCTCGTCCTCTCCGTCTTCGGCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggacccctccttctcgcttctccctggaattcggattaggatcgagggccagcgttcttggcaagtttagctcgctcgctcgttcgtatcatcagg...

Basic information

species Oryza sativa
transcript LOC_Os04g47970.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g47970.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G05940.1 (Glycine max), 5'ss of exon 1
CTACATCCTCATCCTCTTCTTCTCCTGGCTGCTCGTCCTCTCCGTCTTCGGCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggacccctc----cttctcgcttctccctggaattcggattaggatcgagggccagcgttcttggcaagtttagctcgctcgctcgttcgtatcatcagg
 |||||||||||||| ||||| || ||| | ||||| |||||||||||||| ||| |||||||||| || |||||  |||| || ||||| ||||| || |||     | ||     | | |   || |  |     | |  || |  |    |     | ||||| ||    |||   |   |   | | |  | |  |    
TTACATCCTCATCCTTTTCTTTTCTTGGATCCTCGTTCTCTCCGTCTTCGGTTGCTCCCCCGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgtatctctctctttcttccttttaattatttcctttttacaaataaaaaaattgaaattgagttctgggtgtctttgattttttgatttggtgatttggt----

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G02540.1 (Glycine max), 5'ss of exon 1
CTACATCCTCATCCTCTTCTTCTCCTGGCTGCTCGTCCTCTCCGTCTTCGGCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggacccctccttctcgcttctccctggaattcggattaggatcgagggccagcgttcttggcaagttt-agctcgctcgctcgtt-cgtatcatcagg-----
 |||||||||||||| ||||| || ||| | ||||| |||||||||||||| ||  |||| ||||| || |||||  |||| || ||||| ||||| || ||    | || ||  ||||  | || ||||  |||    |||  || |  | |     | |     ||  || |  | |    || | |   | | ||  |      
ATACATCCTCATCCTTTTCTTTTCTTGGATCCTCGTACTCTCCGTCTTCGGTTGTTCCCCTGGCATCGCTTGGACCATCGTTAATCTCGCACACTTTGCTgt----atccttctatctc-ttgcttcctgtcatttaattta--attgttgccttttttaccaaaaaaaattgaatttgagttctgggtgtcttttatttgttgatt

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G42000.2 (Arabidopsis thaliana), 5'ss of exon 1
CTACATCCTCATCCTCTTCTTCTCCTGGCTGCTCGTCCTCTCCGTCTTCGGCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggacccc--tccttctcgcttctccctggaattcggattaggatcgagggccagcgttcttggcaagtttagctcgctcgctcgttcgtatcatcagg
 || || ||||||||||||||||| ||||| ||||| ||||||||||||   ||  | || ||||| || |||||  | ||  | ||||| || ||| | |||     |||  ||     || | |    | ||| | |   | || |    |    |  || |||     ||| | |  || |                  
TTATATTCTCATCCTCTTCTTCTCTTGGCTCCTCGTTCTCTCCGTCTTCCATTGTTCTCCTGGCATCGCTTGGACCATTGTTCATCTCGCTCATTTCACCgtattattcccgatctcctccgatccaatttcgaaattg---ttggtttctagatttgaatttttgagtttttttgttttctag------------------

upper sequence: LOC_Os04g47970.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 5'ss of exon 1
CTACATCCTCATCCTCTTCTTCTCCTGGCTGCTCGTCCTCTCCGTCTTCGGCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggacccctccttctcgcttctccctggaattcggattaggatcgagggccagcgttcttggcaagtttagctcgctcgctcgttcgtatcatcagg--
|||||||||||| ||||||||| | ||||| || || |||||| ||||||||||| | || ||||||||||||||  ||||||| |||  ||||||   |||| |      | ||| |   ||||| |  || || || ||    |         |  || |||   |||||       |   ||| |  | | || |    
CTACATCCTCATTCTCTTCTTCGCATGGCTCCTTGTTCTCTCCATCTTCGGCTGCTCTCCTGGCATGGCGTGGACAGTCGTCAATCTCTTCCACTTTTTGgtatgttgtttttcttttgatttctctc-agattttgggtttttttttttt-tttgtttttttgttgagttttcaagtgtgtttcggttatttgatgatttt

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|86542403|gb|CI182609.1|CI182609
EST:     CTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCTCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: CTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
EST: gi|86902849|gb|CI312226.1|CI312226
EST:     ATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: ATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
EST: gi|88575156|gb|CI669301.1|CI669301
EST:     GCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: GCTGCACCCCCGGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
EST: gi|88241938|gb|CI241787.1|CI241787
EST:     GGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCG                         ATGACATACCANNNNNNNCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC
genomic: GGCATGGCGTGGACGTTCGTCAACCTCGCCCACTTCGCGgtaaggaccc ... ttaattgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGAC