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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtataattggatgatatattaagtgtcttaagaagattaatcttgaacaatattaaaatgtcttgtatattgaagttgaactacaaaactctaattatgcttattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA

Basic information

species Oryza sativa
transcript LOC_Os01g46700.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 13
gtagtataattggatgatatattaagtgtcttaagaagattaatcttgaacaat-------attaaaatgtcttgtatattgaagttgaactacaaaactctaattatgct-tattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA
         |||  |    |    ||| || ||  |  ||| || |||  |||        |  || | ||  |  || |    | |||| ||    | ||    |||||| ||| |||||| ||  || ||||||||||| ||||||| ||||||||||||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| | |
--------gttgtttatctttcgtagtttcgtactataatttatgttgctcaagtggattgaccaacaagtaatacatttctgtgctgaagtatggcagtc----tatgctctatgctcatctatctctgcagATGTGTGTGATTTGTAAGCAAATACATGGTTCATGTACTCAATGCTACAGGTGCTCTACTTACTACCATGCCATTTGTGCATCAAGGGCAGGCTATCGAA

upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 14
gtagtataattggatgatatattaagtgtcttaagaagat-taatcttgaacaatattaaaatgtcttgtatattgaagttgaactacaaaactctaattatgcttattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA
                      |   | |  |  ||   | |    |||       ||   ||||||  |    |  | |  ||  |  | | |||||   |    |||   |        | ||||| ||||| ||||||| |||||| ||||||||||||||||| || | || ||| || ||||||| ||||||||| ||||| |||||||| || ||| | |
---------------------ctccatttggtgggagcttcttgcattgggtttccttttgatgtctcttgg--tccactctaatgaatacaatctaaaagtctgcatt---acttgaattttcagATTTGTGTTATTTGTAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCCGGTTATCGAA

upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 5
gtagtataattggatgatatattaagtgtcttaagaagattaatcttgaacaatattaaaatgtcttgtatattgaagttgaactacaaaactctaattatgcttattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA
     | |  ||     ||| |    | |     ||  |||  ||| |   ||| | |    |  ||||| ||   | |  || |            | | |  |  | | ||  |    | ||||| ||||| ||||||| | |||| ||||||||||| ||||| || | || ||| || ||||||| |||||| || |||||||||||||| || ||| |||
-----aaagctgataagtatttctgattt-----gataatttctctcggtgaatctcagtccgg-ttgtacatgccaatgtaatt------------taaagtctgctataattga--atttcagATTTGTGTTATTTGTAAGGAAATTCATGGTTCGTGCACACAATGTTGCAAGTGTTCCACTTATTTCCATGCTATGTGTGCATCAAGGGCTGGTTATCGGA

upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 14
gtagtataattggatgatatattaagtgtcttaagaagattaatcttgaacaatattaaaatgtcttgtatattgaagttgaactacaaaactctaattatgcttattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA
        ||| | ||        ||  | ||     |  |   |||        || |  | |||||       |   | ||| |  | | |||||  ||    |||   |        | ||||| ||||| ||||| | |||||| ||||||||||||||||| || | || ||| || ||||||| ||||||||| ||||| |||||||| || ||| | |
--------atttggtgg------gagctttttgcattgggttgcctt--------ttgatgtctcttggtccactactcttaacaaatacaatctaaaaatctgcatt---acttgaattttcagATTTGTGTTATTTGCAAGCAAATTCATGGTTCGTGTACACAATGTTGCAAGTGTTCTACTTATTTCCATGCCATGTGTGCTTCAAGGGCTGGTTATCGAA

upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 14
gtagtataattggatgatatattaagtgtcttaagaagattaatct--tgaacaatattaaaatg----tcttgtatattgaagttgaactacaaaactctaattatgc-ttattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA
                              || | ||  |||   |  ||   |||||| |  ||    ||||| | ||  |  || | ||       ||| | | ||| || || ||||  |    | ||||| || || || |||| ||||||||||||||| || |||||||| | || ||| || ||||| |||||||| || |||||||||||||| || ||| | |
-----------------------------tttgaaaatgttagcatgatgtttaatattgagttggttttcttgcacatgaatcttcagctgatgtgatctgagtttgccttgttttcatgaa---attcagATTTGCGTAATCTGTAAGCAAATACATGGTTCATGCACACAGTGTTGCAAGTGTTCTACTTACTACCATGCAATGTGTGCATCAAGGGCGGGGTATCGTA

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: 73 (upstream exon), 73 (downstream exon)
Score: 9

CCACAAGTTGCTTTTGCTAGTGATGAGCTGATGGAACCTGCTATTGGGATATTGAATATTACGCCTTTGCTATTCATGAAGgtagtataat ... attgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaagttgaactacaaaactctaattatgcttattctcatccattgctccagATGTGTGTCATTTGTAGGCAAATACATGGTTCGTGTACACAGTGCTACAGGTGCTCAACTTATTACCATGCCATCTGTGCATCAAGGGCAGGCTATAGGA
                     ctctaat  putative branch site (score: 9)
                                              ttgctcc  putative PPT
                 aaaactctaattat  TA-rich tract