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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_Os03g09140.2
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|33682508|gb|CF310747.1|CF310747
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 54 (upstream exon), 60 (downstream exon)
Score: 5

GCTGGCCAAGTACAAGCTGGTGTTCCTCGGCGACCAGGCGGTGGGGAAGACGGCCATCATCACCCGCTTCATGTACGACAAGTTCGACGCCACCTACCAGgttcgttgat ... cggcgtgcagGCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGAACCGTACGGCTGCAGCTTTG




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