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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgtgttatcctattgcgatcatggtactgatatttcattaggtggattctaactgttgtcacacatgtaatgcag

Basic information

species Oryza sativa
transcript LOC_Os12g05900.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G38120.1 (Glycine max), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgtgttatcctattgcgatcatggtactgatatttcattagg---tggattctaactgttgtcacacatgtaatgcag-------------------
 |||||  | || || ||||| |||||||  |||   ||  |  | |||||||||||||| || |||||||| ||||||||||||||||| |||||||| |||       ||| | ||  | |  |     |  |||    ||  |   |     | || | |||| |   |  | || |                     
TTGGGCAATAAACTTAATGGCAGATGTTGCTCAAATGGAAAACTTGAACAAGATGAATGCACGTAATATTGCAATGGTTTTTGCACCAAACATGACTCAAgtaagactaaatcattttttg-ttgtaaatgtagtatacggttctgctcttagccccaatttttgttattgagttcataccagtcaaactcatcttattgg

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G31080.1 (Glycine max), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgt----------agtgtgttatcctattgcgat--catggtactgatatttcattaggtggattctaactgttgtcacacatgtaatgcag----------
||||||  | ||| |||||||||||||||||| | | |||||  | || |||||||||||||| || ||||||||||||||||||||||| |||||||||||          | | | | || ||   | ||   || || |   |   |  |  |      | |||  | || |||    | || |  |           
CTGGGCCATCAATCTGATGGCTGATGTTGTCCTACATGAGCATGTTAATAAGATGAATGCGCGTAACATTGCCATGGTTTTTGCACCAAACATGACTCAGgtgtgtttccatattttttcattctcaagtgactgcaaggaagaaaagatgtaccatacaagtgctatatattttcat-tttctactttactaaattgcat

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA13G39230.1 (Glycine max), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgtgttatcctattgcgatcatg-gtactgatatttcattaggtggattcta-actgttgtcacacatgta-atgcag------------------
||||||  | ||| |||||||||||||||||||| | ||  |  |||| |||||||||||||  ||  |||||||||||||||||||||| |||||||||||    |   ||  | || |  ||    ||  |   |    |  |      | | | ||   ||  | | || |  ||                      
CTGGGCCATCAATCTGATGGCTGATGTTGTCCAACATGAAAATGTAAATAAGATGAATGCGCATAACGTTGCCATGGTTTTTGCACCAAACATGACTCAGgtgtgcttccattttttttcattctcaagtgattgcaaggaagaaaagatgtgccacacaagtgctatatattttcattttctactttactaaattgcat

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA10G08610.1 (Glycine max), 5'ss of exon 5
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTT-GCACCAAATATGACTCAGgtagtgtgttatcctattgcgatcatggtactgat-atttcattaggtggattctaactgttgtcaca----catgtaatgcag----------------
 ||||   | ||  | |||||||||||||  |||   || ||  | |||||||||||||| || ||| |||| ||||||||| |||||||| |||||||| |||       ||| | ||   ||  | ||  |  | |||   |       ||  |   | |||         ||| | || ||                 
-TGGGGGATAAACCTTATGGCTGATGTTGCTCAACTGGAACATTTGAACAAGATGAATGCTCGTAATGTTGCAATGGTTTTTTGCACCAAACATGACTCAAgtaagtcaaaatcttgtttttattgtagtttttgtgattgtctccctcaaatcttggtttttgatttgttaccattttattcaaggcttaattaccaatt

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G18900.1 (Glycine max), 5'ss of exon 6
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgt-------agtgtgttatcctattgcgat----catggtactgatatttcattaggt------ggattctaactgttgtcacacatgtaatgcag----
||||||| ||||||| ||||||||||||| |||||| || ||  | || ||||||||||| || || || ||||||||||||||||||||||||||||| ||       | | | ||||  | ||   ||    ||   |||| | ||     | |        | | || |||||   |   |     | || ||    
CTGGGCTATTAATTTAATGGCTGATGTTGCCCAAGAGGAACACTTGAATAAGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCATgtgagttccaattttttattttttttaaattctccaatttactaaaatgcatgtggacatcttggaaatccaactgaaattttattctgagtgaaggatt

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G35480.1 (Glycine max), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgta---gtgtgttatc--ctattgcgatcatggtactgatatttcattaggtggattctaactgttgtcacacatgtaatgcag-------------------
 |||||  | || || ||||| |||||||  |||   ||  |  | |||||||||||||| ||||||||||| ||||||||||| ||||| |||||||| |||   ||   | ||   ||||||  |   | |||   |  |||  |    |     | || | |||| |   |  |  |  |                    
TTGGGCAATAAACTTAATGGCAGATGTTGCTCAAATGGAAAACTTGAACAAGATGAATGCACGCAATATTGCAATGGTTTTTGCTCCAAACATGACTCAAgtaagagtaaatcattttctattgtaaatgtagtatacagttttgctc---ttagccccaatttttgttattgaattcgtaaaagtcaacctcatcttattgg

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G09560.1 (Glycine max), 5'ss of exon 5
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgt---gttatcctattgcgatca---tggtactgatatttcattaggtggattctaactgttgtcacacatgtaatgcag-----------------
||||||| ||||| | ||||||||||||| |||||| ||  |  | || ||||||||||| || || || ||||||||||||||||||||||||||||| ||    |    ||||  | | | ||  |   |  | || |  |||| || |||| |     ||   | |   | ||  ||   |                  
CTGGGCTATTAATCTAATGGCTGATGTTGCCCAAGAGGAAGACTTGAATAAGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCATgtgagttccaattattttttagtgaagaattttattcttagttttctttgggtgcaagtagaca--tcttggaaatccaactaaaattttactgagtgaaga

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G22400.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgt-agtgtgttatcctattgc-gatcat-ggtactgatatttca-ttaggtggattctaactgttgtcacaca--tgtaatgcag
 |||||  | ||| | ||||| |||||||| ||  | || ||  |||||||||||||| | ||||| || || |||||||| |||||||||||||| ||||| ||| ||  |    |  |  ||| ||   |  | |  |     | || |||  |  ||   |||  | |||  |||| || ||
TTGGGCCATCAATCTAATGGCAGATGTTGTTCAGTATGAACATCTAAACAAGATGAATTCACGCAACATCGCTATGGTTTTCGCACCAAATATGACACAGgtgagtctgcaacaacaaggttgattatcaatgtttaactcggggtcagatgggataaaatgattgagaaacacttgtattgtag

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G11490.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgtgttatcctattgcgatcatggtactgatatttcattaggtgg-attctaactgttgtcacacatgtaat-gcag
 |||||| | ||| | ||||||||||||||  |    || ||| | |||||||||||||| || || ||||| |||||||||||||| || ||||||||||||    ||| |   | ||      |     |  | ||| ||  | | | ||| |      || ||    |  ||| ||||
TTGGGCTATCAATCTAATGGCTGATGTTGTTGAGATGGAACAACTTAACAAGATGAATGCTCGAAACATTGCAATGGTTTTTGCACCTAACATGACTCAGgtaa---gttttttgaatgaatctctaaagat--tgtttgatgtgttcgtattttggtaaatgacatcagtcaaattgcag

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0080g00580.t01 (Vitis vinifera), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgt------gttatcctattgcgatcatggtactgata-----tttcat---taggtggattctaactgttgtcacacatgtaatgcag-------
 |||||  | ||  | ||||| ||||| ||||| || |||||  ||||||| |||||||| ||||| ||||| ||||| ||||||||||| |||||||||||   ||      |||  |   |   ||  || || |   ||     || |||    || || | |  ||    | | ||      | ||||        
TTGGGCCATCAACCTCATGGCAGATGTCGTCCAGGAGGAGCATCTAAACAAAATGAATGCACGCAACATTGCAATGGTCTTTGCACCAAACATGACTCAGgtgaggttgaatggtttacgcttcttgaaaattgtccaagtagggatttgcatgtccagatgaaattgaatgaatatgacgttctcattgcattttaaat

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv08s0007g03140.t01 (Vitis vinifera), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgt-agtgtgttatcctattg-----------cgatcatggtactgatatttcattaggtggattctaactgttgtcacacatgtaatgcag---------
 |||||  | ||||| |||||||||||||  |||   || ||  | |||||||||||||| |||||| | || ||||| ||||||||||| |||||||| || |||| |||||  | |||           || | ||    |   | || | ||  |||   || || | |  |    | ||  | |  |         
TTGGGCAATAAATTTAATGGCTGATGTTGCTCAAATGGAACATTTGAACAAGATGAATGCACGCAATGTGGCTATGGTGTTTGCACCAAACATGACTCAAgtgagtgagttattttcttggccaaaccacacgcttataactcctttgttgcttttagtgatatccaagtttcctgtttcctgacaggtggagagtatat

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 5'ss of exon 4
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtag------tgtgttatcctattgcgatcatggtactgatatttcatt---aggtggattctaactgtt-gtcacacat-gtaatgcag---------------------------------------
||||||||| ||||||||||||||||| |||||||| ||   | | ||||||||||| || ||||||||||| ||||| ||||| || |||||||||||||||       |  |   |||   |  |||  ||| |||   ||  ||||      |   || | ||| ||   | ||  | | || ||                                         
CTGGGCTGTCAATTTGATGGCTGATGTAGTCCAAGACGAAGTAGTCAACAAGATGAACGCTCGCAATATTGCAATGGTCTTTGCTCCTAATATGACTCAGgtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcag

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S1_829V6.2 (Physcomitrella patens), 5'ss of exon 5
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgtgttatcctattgcgatcatggtactgatatttcattaggtggattctaa--ctgttgtcacacatg-taatgcag------------------------------------------------------------------------------------------
||||||  |||| |||||||| ||||| ||  |    |||    | |||||||||||||| ||||||||||| ||||| || || || |||||||| ||||||  | |   | ||   | | ||    |    | |     ||   |||    |    || || |  |||||| |||  ||                                                                                           
CTGGGCCATTAACTTGATGGCCGATGTCGTGGAGCTGGAGTCTTTCAACAAGATGAATGCTCGCAATATTGCAATGGTATTCGCTCCTAATATGACACAGgtatggagcacttctgcagtggtctctatctgtagaagctgttgtatggcgaatggtcctcttttttcacatggtaactcaagattgcttatcctaaaaggtggttttccgttagcatgttatgtgtcaatgaaggttatccctttactgattcatatttactgccctgcag

upper sequence: LOC_Os12g05900.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 5'ss of exon 5
CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgtgttatcctattgcgatca--tggtactgatatttcattagg--tggattc---taac-tgttgtcacacatgtaatgcag----------------------------------------------------------------------------------------------------------
||||||  | ||  | ||||| ||||| ||  |    |||      |||||||||||||| ||||| ||||| ||||||||||| || || ||||| ||||||  | |     ||   | | ||   |  |  ||| | |   ||||   |  |      || | ||||||| | | |||  |                                                                                                              
CTGGGCCATCAACCTCATGGCGGATGTGGTGGAGCTGGAGTCTTACAACAAGATGAATGCTCGCAACATTGCTATGGTTTTTGCTCCGAACATGACACAGgtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcag

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: 57 (upstream exon), 23 (downstream exon)
Score: 3

CTGGGCTGTTAATTTGATGGCTGATGTTGTCCAAGAAGAGCAAATAAACAAGATGAATGCGCGCAATATTGCCATGGTTTTTGCACCAAATATGACTCAGgtagtgtgtt ... tgtaatgcagATGGCAGATCCCTTGACTGCATTGATGTATGCAGTACAAGTGATGAATTTTCTTAAGATGCTAATACAAAAAACCCTCAAGGATAGAGAAGAGTCTGATC




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