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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaagtacctgaacttaagactaattgaaatttcatcttag

Basic information

species Oryza sativa
transcript LOC_Os12g30540.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaagtacctgaacttaagacta---attgaaatttcatcttag
|||||| |||||||| | ||| ||||| ||||||||||| ||||||||||||||||| ||||| || |||||  | ||||||| ||||||||| || |||||  || |||| | | || | ||  |||||||| ||   |||| ||||||| ||   || |   |||||||| |  || |||
GAAAAAAGAAACAGGTTTTGTAGGTCTTAAGAATCAAGGTGCTACCTGTTATATGAATTCTCTCCTTCAAACGTTATACCATACACCATATTTTAGAAAGgt--gaaatcaat-cattgttctgttctacatgtttctctaagcacctgaattttgaaccatttattgaaatgttttcatag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G16170.1 (Glycine max), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaagtacctgaacttaagactaattgaaatttcatcttag---------
 || ||||| || || |||||||| || ||||| ||||||||||| ||||||||||| ||||| || |||||  |||| ||||| || ||||| || |||||  ||     ||   || |  |  | | | |||  | | |  || |   | | || | |||| | || ||  || | |         
AAAGAAGGAGACTGGCTATGTTGGGCTTAAGAACCAAGGAGCTACGTGTTATATGAATTCTCTACTCCAAACCTTGTATCATATTCCTTATTTTAGAAAGgttagaacggtttgtcttattttgttttgcctgaagt-tcacttatcc--attgaaaagtaatgggaagttgttcctggacatttcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 1
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgt---ctgagatcat-tactttttcctagtctacatgatttgttaagtacctgaacttaagactaattgaaatttcatcttag
 ||||||||||| || |||||||| || || |||||||||||||| ||||||||||| ||||| || |||||| ||||||| ||  | |||||| | |||||   |    | ||| ||   |||   ||     ||  |||  |||| |  | | || | |  ||| |    |||    | ||
AAAAAAGGAAACTGGTTATGTTGGACTGAAAAATCAAGGAGCTACATGTTATATGAATTCTCTGCTTCAAACATTGTACCACATTTCTTATTTCCGAAAGgttacccagtagcatataaactttgtaaggtcttatttttttataaggaaat-agctcatgtataaat---ttttttgttcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttt--tcctagtctacatgatttgttaagtacctgaacttaagactaatt--gaaatttcatcttag---------------------
 |||||||| || || |||||||| || ||||| || |||||||| ||||||||||| ||||| || |||||  |||||||||| || |||||  | |||||| |  ||  || || ||  |  |  | | | |     |||   |   |  |||  | | | ||   ||| |||    || |                     
AAAAAAGGAGACTGGCTATGTTGGACTTAAGAACCAGGGAGCTACATGTTATATGAATTCTCTACTTCAAACTTTGTACCATATTCCTTATTTTCGAAAGgtcaggcattgtttctcttattgttgttttccttctgaagttttatttttttactggatagtgatgaggaagtttggatttgggtcctggatgtcatatttcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G11300.1 (Glycine max), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaagtacctgaacttaagactaattgaaatttcatcttag---------------
 || ||||| || || |||||||| || ||||| ||||||||||||||||||||||| ||||| || |||||  |||||||||| || |||||||| |||||  ||  |  ||   || |  |  | | | |||  | | |  |  |   | | || | |||| | || ||  |    |               
CAAGAAGGAGACTGGCTATGTTGGGCTTAAGAACCAAGGAGCTACCTGTTATATGAATTCTCTACTTCAAACCTTGTACCATATTCCTTATTTCAGAAAGgttagaactgtttgtcttattttgttttgcctgaagt-tcacatgtcc--attgaaaagtaatgggaagtttgttcctggatattacatttcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttt--tcctagtctacatgatttgttaagtacctgaacttaagactaatt--gaaatttcatcttag---------------------
 |||||||| || || |||||||| || ||||| || |||||||| ||||||||||| ||||| || |||||  |||||||||| || |||||  | |||||| |  ||  || || ||  |  |  | | | | |   |||   |   |  |||  |   | ||   ||| |||    || |                     
AAAAAAGGAGACTGGCTATGTTGGACTTAAGAACCAGGGAGCTACATGTTATATGAATTCTCTACTCCAAACTTTGTACCATATTCCTTATTTTCGAAAGgtcagccattgtttctcttgttttttttttccttcagaagttttatttttttactggatggtgatgaggaagtttggatttgggtcctggatatcatatttcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaag--tacctgaacttaag-actaa--ttgaaatttc--atcttag
 || ||||| || || |||||||| || ||||| ||||||||||||||||| ||||| || ||||| || ||||| |||||||| || || ||||| |||||  |  |    |  ||||||||  | ||| || ||  || |   ||  || |   ||| ||||   ||| || |    || | ||
AAAGAAGGAGACTGGTTATGTTGGACTGAAGAACCAAGGAGCTACCTGTTACATGAATTCCCTTCTTCAGACACTCTACCATATTCCTTACTTCAGAAAGgttgggaaattctcttttttcctcctttacttgtttcattgatattatttgcaagaaagcactacatttggaactgtgtatttcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaagtacctgaacttaagactaattgaaa----tttcatcttag------------------
 ||||||||||| || |||||||| || ||||| |||||||| || ||||| ||||||||||| || ||||| || || ||||| || || || || |||||     | ||||  | |||     |||||||  | | |     |  |   ||| |   || ||||||    |  ||  ||                    
AAAAAAGGAAACTGGTTATGTTGGACTTAAGAACCAAGGAGCAACTTGTTACATGAACTCTCTCCTCCAAACTCTCTATCATATTCCCTACTTTAGAAAGgttaataaccattgttcttttt---tctacattgtctctgttacatgtcttcttgaagatatttgaaaagggtaacaattttttggatcatgttttttcag

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 5'ss of exon 5
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtc----tgagatcattactttt-tcctagtc-----tacatgatttgttaagtacctgaacttaagactaattgaaatttcatcttag------------
||| ||||||||||||| ||||||  ||||||||||||||||||| || || ||||| ||||| || || ||| |||| ||| | || || ||| |||||||     |    ||| |||     || | ||      || |   ||| || || | || |  || ||     | | | | || | |  |            
GAAGAAGGAAACAGGATTTGTTGGGTTAAAGAATCAAGGAGCTACATGCTACATGAATTCTCTCCTCCAGACATTGTATCATCTGCCTTACTTCCGGAAGgttattttcctgtcaatacagaaatcatggttgtggttagaaccttttttcagcaactcagtttcaggagtctcggattctc-tttcggttcagtacttta

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaagtacctgaacttaagactaattgaaatttcatcttag
 || || || || |||| ||| ||||| || || ||||||||||| ||||| ||||| |||||| |||| |||||||| ||  | |||| |||| | |||||     |||   | ||| |     | |  |   ||  |   ||                                   
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgta-accatctcgattttcttgctttttttacagttattcgtgttggcag-----------------------------

upper sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ18164 (Selaginella moellendorffii), 5'ss of exon 3
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtc-tgagatcattactttttcctagtctaca-tgatttgt-taagtacctgaacttaagactaattgaaatttcatcttag
 || || || || |||| ||| ||||| || || ||||||||||| ||||| ||||| |||||| |||| |||||||| ||  | |||| |||| | |||||    |  ||  |  | || | |  | |||| | ||| || |  | |                                  
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaaccatctcgattttcttgcttgttttacagttattcgtgttggcag---------------------------------

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), 71 (downstream exon)
Score: 35

GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatc ... ttcatcttagGCTGTATATCATATGCCAACTACTGAGAATGACATGCCATCTGGGAGTATTCCTTTAGCCCTGCAGAGCCTTTTTTACAAGCTCCAATACAGCGACAATA




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