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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAGgtatttggactagtagtgaattactctcttggttattgtgacatctccaagttcaatggtcttatttagccatgtaaatttgtacgcttcag

Basic information

species Oryza sativa
transcript LOC_Os11g10420.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g10420.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G176698_T01 (Zea mays), 5'ss of exon 13
GTGATGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAGgtatttggactagtagtgaattactctcttggttattgtgacatctccaagttcaatggtcttatttagccatgtaaatttgtacgcttcag
|||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||    | ||   | || |  ||   ||||||  || ||| | ||     |  |    || || ||   || |   ||||| |       
GTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTTAAGgtat----attaaatgagactcccttggttggttgctgggacttttcatttctttacaagct-atatattaatttgtgtttgttcag-----

upper sequence: LOC_Os11g10420.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S263_81V6.1 (Physcomitrella patens), 5'ss of exon 13
GTGATGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAGgtatttg--gactagtagtgaattactctcttggttattgtgacatct--ccaagttcaatggtcttatttagccatgtaaatttgtacgcttcag------------------------
|| |||||||||||||| ||||| ||  | ||||| |||| |||||||||||||||||        |  | |  || || | |  ||||        | | |  |   || |  || |    | |  |   |  || |  |||  |   |                        
GTAATGGATTCTGATGCGGAGGGTACTGCAAGTGAATTCTATGACTACTTCAAGgtatccaccagtttcttgcaaaatattttggtggtagccaattcttttatctttgtcctttgattccttctttctgagctaactgatactttattgaactgggctactttgtttgttcag
















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|29682738|gb|CB679013.1|CB679013
EST:     TGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAG                         GTTCTATGCATTCAAGGGTTCCTTACTTGCCGGAAGCATGCAGAGCGTATT
genomic: TGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAGgtatttggac ... tacgcttcagGTTCTATGCATTCAAGGGTTCCTTACTTGCCGGAAGCATGCAGAGCGTATT
EST: gi|428172|gb|D24320.1|D24320
EST:     TGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAG                         GTTCTATGCATTCAAGGGTTCCTTACTTGCCGGAAGCATGCAGAGCGTATT
genomic: TGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAGgtatttggac ... tacgcttcagGTTCTATGCATTCAAGGGTTCCTTACTTGCCGGAAGCATGCAGAGCGTATT

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: 74 (upstream exon), 49 (downstream exon)
Score: 13

GTGATGGATTCTGATGCAGAGGGAACACCCAGTGAGTTCTTTGACTACTTCAAGgtatttggac ... tacgcttcagGTTCTATGCATTCAAGGGTTCCTTACTTGCCGGAAGCATGCAGAGCGTATTATACTACTAGTAGAAATGTTGCAG




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