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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctgtttcttttctttgctagtcaatatgatcaccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT

Basic information

species Oryza sativa
transcript LOC_Os12g09610.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G098815_T03 (Zea mays), 3'ss of exon 9
gtatgtctgtttcttttctttgctagtcaatatgatcaccaacact-tttttttaatatattttaattg--tgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT
|| ||||| |    ||  ||   |  ||  ||| ||||   |  |    || ||  |    |||| |||   ||   |  | ||||  |||||||| |||||||||||||| ||||| |||||| ||||||||||||||||||| ||||| || |||||||| || || || || ||||| |||||||||
gtgtgtctctgctcttggttccatgttc--tattatcatatatgcagccttcttcctgccctttatttgatcgatgatccttttttgtagTTACTTTGATGTTCTTGTGCACATGGAAATGAGCTTGCATTCTATGGAAGTTGTGAACAGACTCACTACTGCCGTTGACCTTCCAACAGAATTTGTCCAT

upper sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G00610.3 (Glycine max), 3'ss of exon 9
---------gtatgtctgtt-tcttttctttgct--agtcaatatgat-caccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT
          |   ||| || | || ||| ||||  |||  |||   | | | | | || || |||  | |||||  ||| ||    |||     | ||| |||||    || |||||  ||||||| ||||| || ||||| ||||||||||| ||||||||||| || || || ||||| ||| |  | ||  | || 
gtatgcatttttcctctattatattatctgtgctttagtacatacattgccctatcgctattattttctttatttctatt-tgcttatttatggatacagATACTTCACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTTACAACAGCAGTTGAACTACCGTCTCAATTCATTCAC

upper sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
---------gtatgtctgtt-tcttttctttgct--agtcaatatgat-caccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT
          |   ||| || | || ||| ||||  |||  |||   | | | | | || || |||  | |||||  ||| ||    |||     | ||| |||||    || |||||  ||||||| ||||| || ||||| ||||||||||| |||||||| || || ||||| ||||| ||  |  | ||  | || 
gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctttatttctatt-tgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC

upper sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgtctgtttcttttctttgctagtcaatatgatcaccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT
||| |||     ||| |   | | |     ||   ||  | | | || |   |  || | |   | | | |   |   ||| ||||| || |  || | ||| |   ||||||| ||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || |  || ||  | |  
gtaagtcatcaccttattggttccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatg--cttcttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG

upper sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 9
-------------------gtatgtctgtttcttttctttgct-agtcaatatgatcaccaacacttt--------------tttttaatatattttaattgtgacccttttctttt----tcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT
                    | |  || | |   ||  || || |    ||| |    ||| ||||||              |||||  | ||||||   | |      ||| || |    | || |||||    ||||||||   |||||| |||||||| ||||| |||||||| || |||||||||||||| || || ||||| || || || ||||| || 
gtatgtttttgtcatgttgatttacctttcttgctttattactgaaatgataagcatcccagcactttaatctttttcttttttttttctgtatttttgctttcctttcttttttgtcaatttagGTACTTCAGAGTTCTTGTCAGTATGGACATGAGCCTACATTCAATGGAAGTCGTTAACAGGCTTACTACAGCGGTTGAACTTCCCACCGAATTTGTACAC

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: 68 (upstream exon), 75 (downstream exon)
Score: 17

GACCTTGTTGAACACAATCCACTCATTGCTGTTGAAATTCTTTCGAAATTGATGAACTCTCCTGACATTGATGGgtatgtctgt ... tctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcaccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT
                           ttttaat  putative branch site (score: 17)
                                    tgacccttttcttttt  putative PPT
        aacacttttttttaat  TA-rich tract