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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattcagttaatttctgctgtttgttggttatgcaaattaacgttttgttttatcttgcccctaacagtattattctaatgtttattttattgtaatatttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g62080.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 6
GGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattcagttaatttctgctgtttgttggttatgcaaattaacgttttgttttatcttgcccctaacagtattattctaatgtttattttattgtaatatttgcag
|| |||||| |||||||||| || ||||||||||| || ||| ||||||| || |||||||| || ||||||||||||||||||||||||||||||||||||| ||| |||||| | |   |||     |   |    | |  ||   |||||    || |||  |  ||||  ||||  ||   | | |  |  |   ||| ||     
GGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgagtactcagtttactctggctacacttaaatgcaaccatctagtcttttga---attttgagc--aacatcattagacttgcgataaagtcttctgaatttt-----

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G33100.1 (Glycine max), 5'ss of exon 6
GGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattcagttaatttctgctgtttgttggttatgcaaattaacgttttgttttatcttgcccctaacagtattattctaatgtttattttattgtaatatttgcag
||||||||||||||||| || ||||| || || || |||||| | ||||| || || ||||||||||| |||| ||||||| | || |||||||| ||||||| ||   || ||    | | |    |      | |  | |||     | | ||| ||  | || ||    | | | ||   ||||  || | ||  |||||  |    
GGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTATCGTTCTTTTCCTATTGATCTTGTTCGGGAGTTTGGCAGACAACTTTTGGAGTCTGTAGCATgtgtgtggacattt--cctgtaccaactaccaaat-tatatattttttgtgtatttgatact-cctctgttgggagt-ttaagatgtgcatat-ataataataagt----

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 5'ss of exon 8
GGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggt---attcagttaatttctgctgtttgttggttatgcaaattaacgttttgttttatcttgcccctaacagtattattctaatgtttattttattgtaatatttgcag
||||||||||||||||| || ||||| || || || || ||| ||||||| || || |||||||||||  ||| ||||||| | || |||||||||||||||| ||   ||    || |    | ||  |   | ||  | ||  |||  |       | || ||   | ||||  | ||  |  ||   |||     |  || |        
GGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTACCGTTCATTTCCCATTGATCTTGTTCGGGAGCTTGGCAGACAACTTTTGGAGTCTGTTGCATgtgtgtggaatattcttgacccattcttctatatagtagtcca--ttagtgccacaaatcatttt--tcttaact-ttttgatacaagacttaggcgttaatagt--------

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|117243444|gb|CT848361.1|CT848361
EST:     GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCAT                         TTATGCATGACCTGCGACTTATTCACACAGATCTGAA-CCTGAGAACATTC
genomic: GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattc ... atatttgcagTTATGCATGACCTGCGACTTATTCACACAGATCTGAAACCTGAGAACATTC
EST: gi|38474798|gb|CF958931.1|CF958931
EST:     GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCAT                         TTATGCATGACCTGCGACTTATTCACACAGATCTGAAACCTGAGAACATTC
genomic: GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattc ... atatttgcagTTATGCATGACCTGCGACTTATTCACACAGATCTGAAACCTGAGAACATTC
EST: gi|29665089|gb|CB661364.1|CB661364
EST:     GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCAT                         TTATGCATGACCTGCGACTTATTCACACAGATCTGA
genomic: GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattc ... atatttgcagTTATGCATGACCTGCGACTTATTCACACAGATCTGA
EST: gi|29679261|gb|CB675536.1|CB675536
EST:     GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCAT                         TTATGCATGACCTGCG
genomic: GATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattc ... atatttgcagTTATGCATGACCTGCG

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: 64 (upstream exon), 49 (downstream exon)
Score: 31

GGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATATTAGAGTCTGTTGCATgtgggtattc ... atatttgcagTTATGCATGACCTGCGACTTATTCACACAGATCTGAAACCTGAGAACATTCTCCTTGTTTCATCAGAATCTATCCGGGTGCCTGATTATAAG




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