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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgatgtcgcgcgcgtccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g09140.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AC166636.1_FGT008 (Zea mays), 5'ss of exon 1
GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgatgtc-gcgcgcg-tccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcga---tgaatttgacg---gtgttcatgttgttgcggcggcggcggcggcgtgcag-------------------
|||||||||||||||||| |||||||| ||| ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||  ||    | | ||   || ||  ||      | ||||  | ||      |   || |||      |  ||  |   | |    | ||   |   ||| | ||||    | || | || || ||| || || || ||    | |                     
GCTGGCCAAGTACAAGCTCGTGTTCCTGGGCAACCAGGCGGTGGGCAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGACACCTACCAGgtcggtctccgcccgccgacgatcttcggct--cccatctccctcgtcccgtatgttttcaggcaggatcattgctactgaacctgtcgtcgaaatctgactctgacctgtgggtccgtgctgctgccgccgccgccgctatatccgctcccccgtgcgtgatgcag

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA08G14390.1 (Glycine max), 5'ss of exon 1
GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgtt--gatgtcgcgcgcgtccccgatcgatcgatcttacgcgctggagagagttcca---gttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcag
 || ||||| |||||||| || ||| | ||||| ||  | || || || ||   ||||||||||||||||||||||||||| || ||| | |||||||||||   |     | ||     | |   |  | ||||  | | |    | |    | |||  |   ||   | |  |||      |  |  |   ||  ||||                                            
TCTCGCCAAATACAAGCTCGTTTTCTTGGGCGATCAATCCGTTGGCAAAACCAGCATCATCACCCGCTTCATGTACGACAAATTTGACACAACCTACCAGgtctatctcattttcattttcatttgccgttgatctctgtcatttac-gacatgcgttttatatgtgcatgtgatttccctcacgtgaatcaatctgtgaa--------------------------------------------

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA05G31200.1 (Glycine max), 5'ss of exon 1
GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgatgtcgcgcgcgtccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcag
 || ||||| |||||||| || ||| | ||||| ||  | || || || ||   ||||||||||||||||||||||||||| |||||| |||||||||||||          | |   | | | | |||  || |||| |    |       | |||   ||  ||| |  ||     |    |||     ||| |||| |   | | |||||  || |                     
TCTCGCCAAATACAAGCTCGTTTTCTTGGGCGATCAATCCGTTGGCAAAACCAGCATCATCACCCGCTTCATGTACGACAAATTCGACACCACCTACCAGgt----------cacattcattctcaatc--tcaatctcattttc------aatttctttttcatttgccgttgatctctctatttacgacatgcattttatt-tatgcatgtgctttc---------------------

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 5'ss of exon 1
GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcg--ttgatgtcgcgc--gcgtccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcag
  | || || || || ||||||||| | || || ||  | || || || ||   ||||||||| || |||||||| || ||||||||| | ||||||||||||     | |   | |      |   | | |     | | || |  | | ||     ||  | || | | || |||||    || |||  || ||| |     ||    ||                                
ATTAGCGAAATATAAACTGGTGTTCTTAGGAGATCAATCTGTCGGCAAAACCAGCATCATCACTCGTTTCATGTATGATAAGTTCGACACAACCTACCAGgttaaatctaaaaccacatcgatgattctgtttctctgtttttgc-tgtttga-----ttttaattctgtctcattttt----aacgtt--tttgatcatcgaaacaacatt--------------------------------

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 5'ss of exon 2
GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgatgtcgcgcgcgtccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcag
                   || ||||| || |||||| | ||||| |||||  ||||||||||||| |||||||| |||||||||||   ||| |||||||| |||         |||| |  ||  |  | |||    ||||     |     || | || |   | |                                                                       
-------------------GTCTTCCTGGGAGACCAGTCTGTGGGCAAGACCTCCATCATCACCCGATTCATGTATGACAAGTTCGATAACACGTACCAGgtgcgt----actctgcgcatttcctttacaacgac--aacgcctgacatgcttttgcggtctccgtgcag---------------------------------------------------------------------

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 1
GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgatgtcgcgcgcgtccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcag
||| || ||||||||||| || || |||||||| ||| | ||||||||||||  ||||||||| || |||||||| || ||||| |||  ||| ||||||||    |||  |  || |  ||  |  ||  ||  | |  |    |||| |   ||| ||                                                                                
GCTTGCAAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgt---atgagattacgagtttcttc--tctctcactttggcaaattgga-aattttcaag--------------------------------------------------------------------------------

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ22994 (Selaginella moellendorffii), 5'ss of exon 1
GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgatgtcgcgcgcgtccccgatcgatcgatcttacgcgctggagagagttccagttttttttcttttttgggcaaggtttgttcgatgaatttgacggtgttcatgttgttgcggcggcggcggcggcgtgcag
||| || ||||||||||| || || |||||||| ||| | ||||||||||||  ||||||||| || |||||||| || ||||| |||  ||| ||||||||    |||  |  || |  ||     ||  ||  | |  |    |||| |   ||| ||                                                                                
GCTTGCGAAGTACAAGCTCGTCTTTCTCGGCGATCAGTCTGTGGGGAAGACGAGCATCATCACGCGATTCATGTATGATAAGTTTGACAACACATACCAGgt---atgagattacgagtttct----tctctcactttggcaaattgga-atttttcaag--------------------------------------------------------------------------------

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|33692708|gb|CF320947.1|CF320947
EST:     CGGCCATCATCACCCGCTTCATGTACGACAAGCTCGACGCCACCTACCAT                         GCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA
genomic: CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgat ... cggcgtgcagGCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA
EST: gi|33684735|gb|CF312974.1|CF312974
EST:     CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAG                         GCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA
genomic: CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgat ... cggcgtgcagGCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA
EST: gi|58692272|gb|CK080959.1|CK080959
EST:     CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAG                         GCGACGATCGGGATCGATTTCCTCTCCAAGACGATGT
genomic: CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgat ... cggcgtgcagGCGACGATCGGGATCGATTTCCTCTCCAAGACGATGT
EST: gi|33688710|gb|CF316949.1|CF316949
EST:     CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAG                         GCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA
genomic: CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgat ... cggcgtgcagGCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA
EST: gi|33682508|gb|CF310747.1|CF310747
EST:     CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAG                         GCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA
genomic: CGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgat ... cggcgtgcagGCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGA