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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g17120.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044237_T02 (Zea mays), 5'ss of exon 12
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
||||||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| || ||         ||  ||    ||||    |          |||| |  ||  || |       | |  ||| ||| |||| |||  |||||||  || |     | |  | | |  |  ||||  |  | | |    || |||| |   | ||||| ||   | ||| |||||  |   || || ||
GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgcataa--------tcctttgatgccattttga---------acattataattgggctt------ctaagttttaataaacaatttggcttatctgaaaagt-taaaactttagtctgtactatat--agctccttcctatattttcatgaatatgacataa-tgtttaatgtgcct-tcttctgtgcag

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G05090.1 (Glycine max), 5'ss of exon 12
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgact-tgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
||||||||||||||||| ||||| ||||| |||||||| || ||||||||||| ||  |||||||            ||||  ||    ||  |  || || ||| | |||  |||     || |      ||| | ||   ||| |||  | |||     |      ||  |  ||                                                                                    
GTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAGgt------------atttt-tttgtgtca-aggataaggatatt-tgcatcatgactgttgatttatgtgattgtgttcttttataatccaatattaatcctccacagttcttgt-----------------------------------------------------------------------------------

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA13G19450.1 (Glycine max), 5'ss of exon 13
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
||||||||||||||||| ||||| ||||| |||||||| || || |||||||| ||  |||||||            ||||  ||    ||  |  || || ||| | |||  |||     || |      ||||| |  |||| |||| | |||     |      ||     ||                                                                                    
GTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAGgt------------atttt-tttgtgtca-aggataaggatatt-tgcatcatgactgttgatttatgtgact-gttgttttatattccaatattaatcctccacagtccttgtgc---------------------------------------------------------------------------------

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT2G37500.2 (Arabidopsis thaliana), 5'ss of exon 13
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
|| |||||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || |||||| |     ||  | |    | | | |  ||| |  |  |   |       ||  |   || ||  |  | |  ||                                                                                                                        
GTGATGCAAGGACTTGCTAAATCAATAGCTTGGGATGGTGAAGGTGCTACATGTCTCATCGAGgttcacaaaataaaacta---ttattcccaaccctttgattgaaaacaaatcttaaccaataacacaaata-tcaacag----------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 5'ss of exon 13
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
|||||||| |||||||||||||| |||||||||||||| || || |||||||| ||||||||||| | | |  |  ||||  |  ||    |||   | |    ||  |    || | | |   |   |||  | ||  |       || ||||   | | |     ||| |                                                                                        
GTAATGCAGGGTCTTGCAAAATCAATAGCATGGGATGGAGAAGGAGCAACATGCCTAATTGAGgt-atgagtcttacattaaaagcat---gcatacttaatg-agcctaacccaatat-tgcaaatttgaccatttttc--caatcatgcaaaccaaat-agtgaacaaat----------------------------------------------------------------------------------------

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|86259939|gb|CI065812.1|CI065812
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG                         GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT




















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: 45 (upstream exon), 39 (downstream exon)
Score: 24

GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAGTATGATACTGTTTAGCAGCAA




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