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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag

Basic information

species Oryza sativa
transcript LOC_Os04g51610.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G391042_T02 (Zea mays), 5'ss of exon 17
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgactt----attccctatttcttg-tcaattttaag
|| |||||||| |||||||| ||||| |||||||| ||||||||||| ||||| |||||||| || ||  |||| || ||||||||    || ||||    |||||   |  || | |||       | | || | ||   |  |  ||    |||| || |  |||  || ||    |||| ||  ||| || |  ||||||||
GTGAGGAGGCTTTCTGCATGCGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTGACGTTAAATCAGgtgcaatggtgtt----tattc---actttatacac-------gcttcagatatttccgtttgtt----aaatctgattggccctgattttaaaattctcttcttcctgattgattttaag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G140328_T02 (Zea mays), 5'ss of exon 17
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgactt----attccctatttcttg-tcaattttaag
||||||||||| |||||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||  | ||||| ||||||||    || ||||     | | |  |  |  || || |   ||  |    |||| || | || ||   ||| | || |  |||  || ||    |||| ||  ||| || |  ||||||||
GTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAGgtgcaatggtgtttattcactttatacatactg-acatacatgtttc---agataattc-tgtttgttgaa-tctgattggccctgatttttaaattctcttcttcctggttgattttaag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 18
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag
||  | ||||| || ||||| ||||||||||| || || |||||||||||||| || ||||| |||||  |||| || |||||||| |||| |||| | || |        ||||   | | |    ||  | | |     |||| |||    | ||||   ||          |   || |    || || | || |  
GTGCGAAGGCTGTCAGCATGCGAAACTATGGGATCTGCTACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAATCAGgt-gggttctgtggccaga------gggttggatagtccaagagaagctatgg----ccataattt---acatttatgcatatgaataaaagctcccaagagttatctaattga--

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 18
----------------GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag
                || || ||||| || ||||| ||||||||||| || || |||||||||||||| || |||||||||||  |||| || |||||||| |||| |||| | || |        ||||   | | |    |   | | |     |||| |||    | ||||   ||          |   || |    || || | || |  
TCTAACTTTTGTGCAGGTGAGAAGGCTGTCCGCATGCGAAACTATGGGATCTGCTACAACAATTTGCAGTGATAAGACAGGAACTTTGACCTTAAATCAGgt-gggttctgtggccaga------gggttggatagtccaagaggagctatgg----ccataattt---acatttatgcatatgaataaaagctcccaagagttatctaattga--

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 19
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtgga---tacaaagatgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag
||  || |||| || || |||||||||||||| || ||||||||||||||||| || |||||||||||  |||| || |||||||   | |       ||||  ||| |   |||  || |   | ||    ||     |  ||  || ||     | | | |   || ||      || ||| |||| || || |       
GTACGGCGGCTATCAGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAGgcgagtt-------tcattatctaaggcttggacaatctagagggagttatggctacaatttataatctataacactagtaaaggca------ataccccattttttatctac------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 16
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag
|| |||||||| ||||| ||||| || ||||| ||||||||||| |||||||| || ||||| |||||  ||||| ||||||||||| | | ||| |    ||||   |   |  | |   |   |       | | | |                                                            
GTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAGGTTAg-ttctgattcagtattgaaaccctattccctatttataatatttatggtaag-----------------------------------------------------------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA17G06520.1 (Glycine max), 5'ss of exon 19
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag
|| |||||||| ||||| ||||| || ||||| ||||||||||| |||||||| || ||||| |||||  ||||| ||||||||||| | | ||| |    ||||   ||   | |  | |    |  ||   ||| | |  |||  ||   | |     ||  |   | | | |||     | | ||||          
GTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAGgttag-ttctgattcagtattga-aaccctattta-taatatttatggtaagct-acacatacttgttggagagcactt-gttgcaaat-attttaattctattgt----------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA07G00630.1 (Glycine max), 5'ss of exon 19
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaag---atgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag
||  || |||| || || |||||||||||||| || ||||||||||||||||| || |||||||||||  |||| || |||||||   | |       ||||  ||| |   |||  || |   | ||  |  | |   || ||  || ||     | ||| |   || ||      || |||  ||| |  || |       
GTACGGCGGCTATCGGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAGgcgagtt-------tcattatcttaggcttggacaatctagagggaattatggctataatttataatctataacattagtaaaggca------ataccccgtttttgatctac------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 16
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatc-catgattccagaaatttg--ctcagccacgacttattccctatttcttgtcaattttaag
|| || ||||| || || |||||||| ||||| ||||| |||||||| ||||| ||||| || |||||  | ||||||||||||||| |            ||| |   |   ||||  ||||  | || |  || |  |||  |   ||| ||| |  |    | | ||   ||  |    |                    
GTTAGAAGGCTTTCAGCTTGTGAAACCATGGGATCAGCAACAACAATCTGCAGTGACAAAACTGGAACTTTAACTTTGAATCAGgttag------------tatccagtaaaatgtgagcttc--ttgacatgaaaaccatcatacccttctagatagctaactttacccctcacaaaaatacag------------------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 19
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgacttattccctatttcttgtcaattttaag
||  ||||||| ||||| ||||| || ||||| ||  |||| || |||||||| || ||||||||||| || ||||||||||||||||  |  | | |  ||    | | |          ||  || |  |    ||    | | |||     ||||||   ||     | |||||   |||||   ||          
GTACGGAGGCTTTCTGCTTGTGAGACCATGGGCTCTTCCACGACTATTTGCAGTGATAAGACAGGAACTCTAACTTTGAATCAGgttgatta-tatggcaattactttattacatattttgtcactgaagtcctgaatctggcttaattatttgaatttg--aaggttaaatttatt---tattttgagt----------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 18
GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgctgttgtcatattctcaatgttgtgcacttcggtggatacaaagatgatccatgattccagaaatttgctcagccacgacttat-tccctatttcttgtcaattttaag
||  | ||||| || || |||||||||||||| || || |||||||||||||| || ||||| |||||  | || |||||| ||||      ||||||| |  || |  |  ||   |  || | || |            | ||  | | | ||  ||   |    | || ||   |||  | |   | | |        
GTGCGTAGGCTTTCAGCCTGTGAAACTATGGGCTCTGCAACAACAATTTGCAGTGATAAGACTGGAACATTAACCTTGAATAAGgt------ctgttgtaaatttttggaccttt--ctttttgctgaact----accttccaattttcctaaaagcttaagcttttaagatttgggtccacaatgtatatgatgc-----

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|29667907|gb|CB664182.1|CB664182
EST:     CAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG                         ATGACTGTTGTGGAGGCTTACTTTGGTGGAAAGAAAATGGATCCTCCAGAT
genomic: CAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgct ... caattttaagATGACTGTTGTGGAGGCTTACTTTGGTGGAAAGAAAATGGATCCTCCAGAT




















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: 61 (upstream exon), 69 (downstream exon)
Score: 41

GTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAGgttgggtgct ... caattttaagATGACTGTTGTGGAGGCTTACTTTGGTGGAAAGAAAATGGATCCTCCAGATAATGTTCAGGTGTTATCTGCTTCAATCTCATCATTGATTGTCGAAGGAA




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