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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtcctaataataaacttatgattttaagtgtggtcgatgcttactgtcatgcacatatgtaatgcag

Basic information

species Oryza sativa
transcript LOC_Os11g05540.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G38120.1 (Glycine max), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtc----ctaataataaactta-----tgattttaagtgtggtc--gatgcttactgtcatgcacatatgtaatgcag-------------
 |||||| | || |||||||| |||||||  |||   ||| |  | |||||||||||||| ||||| ||||| ||||||||||||||||| |||||||| ||||  |    ||     |  |  ||||  ||      | || |     | | |   ||  ||  | |   |  ||||   | |  |              
TTGGGCAATAAACTTAATGGCAGATGTTGCTCAAATGGAAAACTTGAACAAGATGAATGCACGTAATATTGCAATGGTTTTTGCACCAAACATGACTCAAgtaagactaaatcattttttgttgtaaatgtagtatacggttctgctcttagccccaatttttgttattgagttcatac-cagtcaaactcatcttattgg

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G31080.1 (Glycine max), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgt-cctaataataaacttatgattttaagtgtggtcgatgcttactgt-catgcacatatgtaatgcag-----------------------
 |||||  | ||| | |||||||||||||||| | | || ||  | || ||||||||||| ||||||||||| ||||||||||||||||| |||||||||||      |  |   |  | ||   |   ||| |  ||| |  |   |    |||  | || |  | ||| || |                           
CTGGGCCATCAATCTGATGGCTGATGTTGTCCTACATGAGCATGTTAATAAGATGAATGCGCGTAACATTGCCATGGTTTTTGCACCAAACATGACTCAGgtgtgtttccatattttttcattctcaagtgactgcaag-gaagaaaagatgtaccatacaagtgc-tatatattttcattttctactttactaaattgcat

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA13G39230.1 (Glycine max), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtcctaata-ataaacttatgattttaagtgtggtcgatgcttactgt-catgcacatatgtaatgcag-----------------------
 |||||  | ||| | |||||||||||||||||| | ||| |  |||| ||||||||||| | |||| |||| ||||||||||||||||| |||||||||||      |  |  |  |  ||   |   |||||  ||| |  |   |    | |    || |  | ||| || |                           
CTGGGCCATCAATCTGATGGCTGATGTTGTCCAACATGAAAATGTAAATAAGATGAATGCGCATAACGTTGCCATGGTTTTTGCACCAAACATGACTCAGgtgtgcttccattttttttcattctcaagtgattgcaag-gaagaaaagatgtgccacacaagtgc-tatatattttcattttctactttactaaattgcat

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA10G08610.1 (Glycine max), 5'ss of exon 5
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTT-GCACCAAATATGACTCAGgtaatgcactgtcctaataataaacttatgattttaagtgtgg---tcga----tgcttactgtcatgcacatatgtaatgcag----------------
 ||||   | ||  | |||||||||||||  |||   |||||  | ||||||||||||||||||||  |||| ||||||||| |||||||| |||||||| ||||  ||   || |  |  ||   |  |  || | | |||     || |    || ||  ||   ||     || | || ||                 
-TGGGGGATAAACCTTATGGCTGATGTTGCTCAACTGGAACATTTGAACAAGATGAATGCTCGTAATGTTGCAATGGTTTTTTGCACCAAACATGACTCAAgtaagtcaaaatcttgtttttattgtagtttttgtgattgtctccctcaaatcttggtttttgatttgttaccattttattcaaggcttaattaccaatt

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G18900.1 (Glycine max), 5'ss of exon 6
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtcctaataataaacttatgattttaagtgtggtcga-tgcttactgtcatgc-acatatgtaatgcag----------------------
 |||||  ||||||||||||||||||||| |||||| |||||  | || ||||||||||| || ||||| || |||||||||||||||||||||||||| || | |  |     |  || |    |||   | |  | | |  |  | ||| |   | |||     | ||  ||   |                       
CTGGGCTATTAATTTAATGGCTGATGTTGCCCAAGAGGAACACTTGAATAAGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCATgtga-gttccaattttttattttttttaaattctccaatttactaaaatgcatgtggacatcttggaaatccaactgaaattttattctgagtgaaggatt

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G35480.1 (Glycine max), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaa---tgcactgtccta-ataataaacttatgat----tttaagtgtggtcgatgcttactgtcat-gcacatatgtaatgcag--------------
 |||||| | || |||||||| |||||||  |||   ||| |  | |||||||||||||| || || ||||| ||||||||||| ||||| |||||||| ||||   |  |   |  |  ||  ||||  ||  ||    |||   | |   |     ||  ||| || | |    |  ||  ||               
TTGGGCAATAAACTTAATGGCAGATGTTGCTCAAATGGAAAACTTGAACAAGATGAATGCACGCAATATTGCAATGGTTTTTGCTCCAAACATGACTCAAgtaagagtaaatcattttctattgtaaatgtagtatacagttttgctcttagccccaatttttgttattgaattcgtaaaagtcaacctcatcttattgg

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G09560.1 (Glycine max), 5'ss of exon 5
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaa--tgcactgtcctaataataaact-tatgattttaagtgtggtcgatgcttactgtcatgcacatatgtaatgcag----------------------
 |||||  ||||| ||||||||||||||| |||||| ||| |  | || ||||||||||| || ||||| || |||||||||||||||||||||||||| || |  | || |    |  || | ||   | | ||| | ||| |  ||  ||  | |    |  ||  |  | ||| ||                       
CTGGGCTATTAATCTAATGGCTGATGTTGCCCAAGAGGAAGACTTGAATAAGATGAATGCACGGAACATCGCCATGGTTTTTGCACCAAATATGACTCATgtgagttccaattattttttagtgaagaattttattcttagttt--tctttgggtgcaagtagacatcttggaaatccaactaaaattttactgagtgaaga

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G22400.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaa---tgcactgtc----ctaataataaacttatgattttaagtgtggtcgatgcttactgtcatgca-catatgtaatgcag
 |||||  | ||| ||||||| |||||||| ||  | |||||  |||||||||||||| | || ||||| ||||||||||| |||||||||||||| ||||| |   ||||    |     | || || ||  | | | |    ||  | | |      |   |   | | ||  |||| || ||
TTGGGCCATCAATCTAATGGCAGATGTTGTTCAGTATGAACATCTAAACAAGATGAATTCACGCAACATCGCTATGGTTTTCGCACCAAATATGACACAGgtgagtctgcaacaacaaggttgattatcaatgtttaactcggggtcagatgggataaaatgattgagaaacacttgtattgtag

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G11490.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtcctaataataaacttatgatt-ttaagtgtggtcgatgcttactgtcatgcacatatgtaat-gcag
 |||||  | ||| ||||||||||||||||  |    |||||  | ||||||||||||||||| |||||||| |||||||||||||| || |||||||||||||     | |   ||| |    || | |||| ||   |||| |||    ||  |      ||    |  ||| ||||
TTGGGCTATCAATCTAATGGCTGATGTTGTTGAGATGGAACAACTTAACAAGATGAATGCTCGAAACATTGCAATGGTTTTTGCACCTAACATGACTCAGgtaa---gttttttgaatgaatctctaaagattgtttgatgtgttcgtattttggtaaatgacatcagtcaaattgcag

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0080g00580.t01 (Vitis vinifera), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgt-------aatgcactgtcctaataataaact-------tatgattttaagtgt--ggtcgatgcttactgtcatgcacatatgtaatgcag-------
 |||||  | ||  | ||||| ||||| ||||| || || ||  ||||||| |||||||| || |||||||| ||||| ||||||||||| |||||||||||       ||||   |   ||  |   ||| |       || |  |||   |||   |  ||   | | ||      || |    | ||||        
TTGGGCCATCAACCTCATGGCAGATGTCGTCCAGGAGGAGCATCTAAACAAAATGAATGCACGCAACATTGCAATGGTCTTTGCACCAAACATGACTCAGgtgaggttgaatggtttacgcttcttgaaaattgtccaagtagggatttgcatgtccagatgaaattgaatgaatatgacgttctcattgcattttaaat

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv08s0007g03140.t01 (Vitis vinifera), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaa-tgcactgtcctaataataaacttatgatttta-agtgtggtcgatgcttactgtcatgcacatatgtaatgcag---------------------
 |||||| | |||||||||||||||||||  |||   |||||  | |||||||||||||| || ||  | |||||||| ||||||||||| |||||||| || | ||   | |  |  |    ||   |     ||| |      | | |||||   || ||   ||  | |  ||                        
TTGGGCAATAAATTTAATGGCTGATGTTGCTCAAATGGAACATTTGAACAAGATGAATGCACGCAATGTGGCTATGGTGTTTGCACCAAACATGACTCAAgtgagtgagttattttcttggccaaaccacacgcttataactcctttgttgcttttagtgatatccaagtttcctgtttcctgacaggtggagagtatat

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtc---ctaataataaacttatgat-tttaagtgtggtcgatgcttactgtcatgcacat-atgtaatgcag-----------------------------------------------
 ||||| || ||||| ||||||||||| |||||||| |||    | ||||||||||| ||||| || ||||| ||||| ||||| || ||||||||||||||||  ||   ||   ||     |    |  ||    || | |    |  | | ||  | |    | | | |  | ||   |                                               
CTGGGCTGTCAATTTGATGGCTGATGTAGTCCAAGACGAAGTAGTCAACAAGATGAACGCTCGCAATATTGCAATGGTCTTTGCTCCTAATATGACTCAGgtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcag

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S1_829V6.2 (Physcomitrella patens), 5'ss of exon 5
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgta--atgcactgtcctaataat----aaacttatgattttaagtgtggtcgatgcttactgtcatgcacatatgtaatgcag------------------------------------------------------------------------------------------
 |||||  |||| || ||||| ||||| ||  |    ||     | ||||||||||||||||| || ||||| ||||| || || || |||||||| ||||||    |||||     | |  |    |    ||  |  |   || |||   ||| |     |  | |||||  ||||  ||                                                                                           
CTGGGCCATTAACTTGATGGCCGATGTCGTGGAGCTGGAGTCTTTCAACAAGATGAATGCTCGCAATATTGCAATGGTATTCGCTCCTAATATGACACAGgtatggagcacttctgcagtggtctctatctgtagaagctgttgtatggcgaatggtcctcttttttcacatg-gtaactcaagattgcttatcctaaaaggtggttttccgttagcatgttatgtgtcaatgaaggttatccctttactgattcatatttactgccctgcag

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 5'ss of exon 5
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtcctaataataaacttatgattttaagtgtggtcgatgcttactgtcatgca-catatgtaatgcag--------------------------------------------------------------------------------------------------------------------
 |||||  | ||  | ||||| ||||| ||  |    ||       ||||||||||||||||| |||||||||||||||||||| || || ||||| |||||| |  |    |       |   ||  |  |||| |   | ||  |    ||      || | | | |    | | |                                                                                                                    
CTGGGCCATCAACCTCATGGCGGATGTGGTGGAGCTGGAGTCTTACAACAAGATGAATGCTCGCAACATTGCTATGGTTTTTGCTCCGAACATGACACAGgta-tagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcag

upper sequence: LOC_Os11g05540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 5'ss of exon 4
GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcactgtcctaataat----aaacttatgattttaagtgtggtcgatgcttactgtcatgcacatatgtaatgcag------------------------------------------------------------------------------------------------------------------
 ||||| || ||  | ||||||||||| ||  |  | ||   |   || || ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||||  |   |||    |   |    |  |  |  |  | | |     |  | | | |   || |  | || |  | | |||                                                                                                                  
TTGGGCTGTCAACCTGATGGCTGATGTGGTGGAGCACGAGTCGTACAATAAAATGAATGCTCGGAACATCGCTATGGTGTTTGCCCCAAACATGACACAGgtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagattt-cactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|44666927|gb|CR280361.1|CR280361
EST:     AGATGAATGCTCGCAACATTGCTATGGTTTTTGCACCAAATATGACTCAG                         ATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTT
genomic: AGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcact ... tgtaatgcagATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTT




















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: 45 (upstream exon), 71 (downstream exon)
Score: 9

GTGGGCAGTTAATTTAATGGCTGATGTTGTCCAAGAAGAACAGATAAACAAGATGAATGCTCGTAACATTGCTATGGTTTTTGCACCAAATATGACTCAGgtaatgcact ... tgtaatgcagATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTTCTCAAGATGCTAATACAGAAGACCCTCAAGGGTAGACAAGAGTCCAATC




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