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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcactctacacagcatttacagttagcttaattaaacttgacaatgcagctgaatgtcatctctgttgattgcacaagTGTTGCTTGGGGAGATAGCAAACTTCGTTGCTTATACCTTTGCACCAGCCGTACTTGTGACTCCCCTTGGGGCACTAAGCATAATCGTAAG

Basic information

species Oryza sativa
transcript LOC_Os06g50180.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G461791_T01 (Zea mays), 3'ss of exon 1
gtatgct---cactctacacagcatttacagttagcttaattaaacttgacaatgcagctgaatgtcatctctgttgat-tgcacaagTGTTGCTTGGGGAGATAGCAAACTTCGTTGCTTATACCTTTGCACCAGCCGTACTTGTGACTCCCCTTGGGGCACTAAGCATAATCGTAAG
||||||    | ||| ||| |  || |||  | |  || |  ||  ||| ||   || |||||| |      || || | | |||||||| ||||||||||| | ||||||||| ||||||| |  ||||| || || ||||| |||||||| ||||||||  ||||||||||||||||
gtatgccacgcgctcaacataaaatctactctcaatttta--aactttgccaccccaactgaatttgcctagtgctggtcttcacaagTGCTGCTTGGGGAGGTCGCAAACTTCATTGCTTACATATTTGCGCCGGCTGTACTCGTGACTCCACTTGGGGCGTTAAGCATAATCGTAAG

upper sequence: LOC_Os06g50180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G03390.1 (Glycine max), 3'ss of exon 2
---------------------------gtatgctcactctacacagcatttac--agttagcttaattaaacttgacaatgcagctgaatgtcatctctg-ttgattgcaca-agTGTTGCTTGGGGAGATAGCAAACTTCGTTGCTTATACCTTTGCACCAGCCGTACTTGTGACTCCCCTTGGGGCACTAAGCATAATCGTAAG
                           |    ||| ||||      | ||  |  || | | | | || || ||   |||| | ||   |   ||||     |  ||||  | |||| |  |||||||||| |||||||| |||||||||| || ||| || || || || || ||||||||||| ||||| || || || || ||
gtaagtgtggcaccttgatttcttctcgctctctctctctctctctctttatccaaggttgttgatttgaattttgaaatgaaactattttggatcttgaactatttgcttacagTGATTATTGGGGAGATTGCAAACTTTGTTGCTTATATCTATGCTCCGGCAGTTCTGGTTACTCCCCTTGGTGCACTTAGTATTATTGTCAG
















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: 70 (upstream exon), 68 (downstream exon)
Score: 4

GTGGTGGAGGATACACTTATCTTTTGGAACCTCTATGGTGGGCTGGAATGATGACAAgtatgctcac ... attgcacaagTGTTGCTTGGGGAGATAGCAAACTTCGTTGCTTATACCTTTGCACCAGCCGTACTTGTGACTCCCCTTGGGGCACTAAGCATAATCGTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttaattaaacttgacaatgcagctgaatgtcatctctgttgattgcacaagTGTTGCTTGGGGAGATAGCAAACTTCGTTGCTTATACCTTTGCACCAGCCGTACTTGTGACTCCCCTTGGGGCACTAAGCATAATCGTAAG
                                        tgttgat  putative branch site (score: 4)
     taattaaactt  TA-rich tract