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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGTTTCATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataattgcgtgtcatcctactattgagtatgtattttttttcctatctgtggttggttactaatcaagcatactcagctctatcctaattgccatc...

Basic information

species Oryza sativa
transcript LOC_Os01g10150.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 12
TTCAGTTTCATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataattgcgtgtcatcctactattgagtatgtattttttttcctatctgtggttggttactaatcaagcatactcagctctatcctaattgccatc--------
||||||| | ||| | ||| | ||||||||||||||||||||||||||||||||||||||  | |||||| | ||||| ||   |||||||||||||||||||| | ||      |  |  |    |  |  || | |     ||| | ||| |  ||  ||| ||   ||  ||| ||||||||  |||  |||   |         
TTCAGTTGCCTCCAGCTCAAACCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACATCTCAAGTATACGAACTTTCTAGTTACTTTCTTCACAAGgtaagtgatca---attttgttgacttcaaagatctgtaagggttctt-tcttttttttcttaata--taatgatattcagctct--cctgcttgttttagagaaaaa

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 12
TTCAGTTT--CATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataa--ttgcgtgtcatcc-tactattgagtatgtattttttttcctatct--gtggttggttactaatca--agcatactcagctctatcctaatt-gccatc--------------------------------------------------
  |||| |  | || |||||  |||| |||||  | ||||||||||||||||||||||| || || |||||  |||||||||| |  | ||| |||||||||||     |  ||  || | | |  |   |||  |  |||  | ||  |  ||||   ||     |||  |||  |  | |||  | | || |||  || ||  | |                                                    
--CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACAGCACAAGTTTATGAACTCTCTCCCTTCTTCCTTCACAAGgttggctagtttatgttttagctgtggcattatgcgtgtgatgttggtgatatcatagtatcatgtttgtaactattatcat-tttatctgtatagtattttactaattttgttttgaacttaatgtagtctaacaaactcatgtttctttttaatag

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA04G09070.2 (Glycine max), 5'ss of exon 12
TTCAGTTT--CATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataa--ttgcgtgtcatcc-tactattgagtatgtattttttttcctatc-tgtggttggttactaatcaagcatactcagctctatcctaattgccatc-----------------------------------------------------
  |||| |  | || |||||  |||| |||||  | ||||||||||||||||||||||| ||||| |||||  |||||||||| |   |||| |||||||||||     |  ||  || | | |  |   |||  |  |||  | ||  |  |||| | |  |    |    | | |  ||  |    ||| | ||   |   |                                                       
--CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTCTCTCCCCACTTCCTTCACAAGgttggctagtttatgttttagcggtggcattatgcgtgtggtgttggtgatatcctattatcatctttgtaactattatcgttttatctgtactgtattttactaattttgtttttaacttaacgtaggctaacaaactcacgtttctgtttaatag

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 12
TTCAGTTT--CATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataattgcgtgtcatcctact---attgagtatgtattttttttcctatc-tgtggttggttactaatcaagcatactcagctctatcctaattgccatc-----------------------------------------------------
  |||| |  | || |||||  |||| |||||  | ||||||||||||||||||||||| ||||| |||||  ||||||| || |   |||| |||||||||||     | |   |||  |  |  |   |||  | ||||  | ||  |  |||| | |  |    |    | | |  ||  |    ||| | ||   |   |                                                       
--CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTGTCTCCCCACTTCCTTCACAAGgtttgctagtttatgttttagtggtggcattatgcatgtggtgttggtgatatcatattatcatctttggaactattatcgttttatctgtactgtattttactaattttgtttttaacttaacgtaggctaacaaactcacgtttctgtttaatag

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
TTCAGTTT--CATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaata--attgcgtgtcatcctactattgagtatgtattttttttcctatctgtggt-tggttactaatca--agcatactc-agctctatcctaattgccatc----------------------------------------------------------------------
  |||| |  | || |||  | || |||||||  ||||||||||||| |||||||||||||| || |||||  |||| || || |  || ||||||||||||||   |   ||| | | |  |    | || |  ||  ||||| | ||   || |||  |    |||    |||  || ||  || ||   |||   ||  || |                                                                        
--CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctcatttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgaggcatattacaag-gctacttctttcagcttactgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag

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|29688779|gb|CB685054.1|CB685054
EST:     CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
genomic: CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
EST: gi|29670786|gb|CB667061.1|CB667061
EST:     CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
genomic: CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
EST: gi|29645032|gb|CB650039.1|CB650039
EST:     CTGGTTTTTCCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATCGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
genomic: CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
EST: gi|89195193|gb|CI051306.1|CI051306
EST:     CAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
genomic: CAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
EST: gi|58611769|gb|CK039481.1|CK039481
EST:     CTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCGTTGGGC
genomic: CTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTC-TTTGGC
EST: gi|29670785|gb|CB667060.1|CB667060
EST:     CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
genomic: CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
EST: gi|87040610|gb|CI195232.1|CI195232
EST:     CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
genomic: CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
EST: gi|3766584|gb|AU030694.1|AU030694
EST:     CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGCAATTACTATATTACTTCTTTGGCT
genomic: CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
EST: gi|27546382|gb|CA764550.2|CA764550
EST:     CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAG                         GAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT
genomic: CTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCT

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: 56 (upstream exon), 70 (downstream exon)
Score: 20

TTCAGTTTCATCCTGTTCAGATCTGTGGGCTTTAATTATGGATGCTGGCACTGGTTTTACCGCCCAAGTACATGAACTCTCCCATTACTTTCTTCACAAGgtaaataatt ... gctttgatagGAATGGATAATGGAGCAGTGGGAGAGAAATTACTATATTACTTCTTTGGCTGGTTCAAATAATGGAAGCTCGGTGGTGATCATGTCAACAG




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