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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag

Basic information

species Oryza sativa
transcript LOC_Os05g44560.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G173700_T03 (Zea mays), 5'ss of exon 11
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
||| || ||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || |||||||| || ||||||||||| |||||||||    | |   | ||  || |     |  |||||  | |   || | |  |  | ||  |   |||  ||   |||  |  || |  | |  |  |||  |||                                     
TTTTTCTGACATACAACCACTGATCCGATCAGTTCTGGATGGATTCAACGTTTGTATTTTTGCATATGGCCAGACTGGTTCTGGCAAAACTTACACTATGgtacta----taaaataaatcataataa---aaaattgtcatca--ctacaatagtaatattactgattatgatatctgttttgt-tgtt--attatt--taatctttag-----------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA05G35130.1 (Glycine max), 5'ss of exon 12
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaactttt-------accgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 | ||| ||||||||| |  | ||  |||||||||| ||||| |  ||||| ||||| ||||||||||| |||||||||||||| |||||||| |||||||||  |||  |        |  ||| |||  ||    || ||| ||| || |   | |||  || || |    | |      ||   ||||                                                             
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACAATGgtatgaaccctctgaataaattgatttttatctcatacatcat-gttattgaagga-attcttcattctataagatgccaacctttctcag-------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA08G01800.1 (Glycine max), 5'ss of exon 14
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 |||  ||||| ||||||  |||||||||| ||||||||||| | |||||||||||| |||||||||||||||||||| || ||||| || || || |||||| |   || || |  | |  | ||   |  |    ||   || | ||  ||   |||    | || | || |||| |                                                                  
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATATACGATGgta-tgcattatatccgtttaatgctttttatgttgcgtatctagcctaattta--cttagcaactgcttttctactag------------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 14
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatctttt--ttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 |||  ||||| ||||||  |||||||||| ||||||||||| | |||||||||||| ||||||||||||||||| || || ||||| || || || ||||||   | | |   ||    |||| ||  |    ||  |   || ||| | |   |   ||    |||| | || |||| |                                                                  
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATATACGATGgtatgcattatattcg----tttaatgcttttttatgttgcgtatcttgtctaatttacttagcaattgcttttctactag------------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA13G33390.1 (Glycine max), 5'ss of exon 10
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 |   | ||||| ||| |  | || |||||||| |||||||| || ||||| ||||| ||||||||||| || ||||||||||| ||||||||||||||||||   |  ||||   |||| |  |    ||| |||| | | |||   | |||  || || |    | | |  |  |   | ||                                                             
GTATGCTGACATACAAGCCTTTATACGATCAGTACTTGATGGGTTTAATGTATGTATATTTGCTTATGGCCAGACTGGTTCAGGGAAAACTTACACAATGgtaagcaactttatatatatatatc--attcatcattttagataaagga-attactcattctataagatgtcattatttcttag-------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA07G10190.1 (Glycine max), 5'ss of exon 13
---TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctca-gcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
   | | | | | || |||    | || |||||||| |||||||| || ||||| ||||| ||||||||||| || ||||||| ||||||||||||||||||||||         | | |  || || |  | ||   |||| | |||| ||| |||   | | ||                                                                                   
GTGTATGTTGAA-ATACAAGATTTTATACGATCAGTGCTTGATGGCTTTAATGTATGTATATTTGCTTATGGCCAGACTGgtttaggaaaaacttacacaatggta---------agcaactttatattcacacatatattgattttaattta-attcgccgtcttag---------------------------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA08G04580.1 (Glycine max), 5'ss of exon 6
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 | ||| ||||||||| |  | ||  |||||||||| |||||||  ||||| ||||| ||||||||||| |||||||||||||| |||||||| || ||||||  |||  |     |||| ||               || ||| || |||   ||| |       | ||||| |    |||  |||  |  |  | | | |||||||  |||                                
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACGATGgtatgaaccctc-tgaatatattg-------------atttttatctcatac--atcat-------gctattgaaggaattcttcattctataa-gatgccaacttttc-tcag-------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 5'ss of exon 13
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattg----atcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 || || || ||  |||| || ||||||||||||||||| || | |||||| ||||| ||||| |||||||| || || ||||| |||||||||||||||||||| |  || ||   ||| | || |  | ||       |  || | ||        ||   |   |||   |||||  | || |||                                                             
ATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTACACAATGgtactca--ttcactagtatatcac-gattaagtggc-cagacaaatgatgccactacattcataccattatcattgtttttgtccag-------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 5'ss of exon 13
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgat-cttttttattggtattgtactggtt-cagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 || || |||||   ||||||| || | ||||| |||||||| | |||||||||||| ||||| ||||| || || || ||||| |||||||| |||||||||      || || | | |||    |  | ||  ||  |   || | |   |||| |  |||||      ||    |  || |||                                                             
CTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTATACAATGgtat--gtattcactgttgtttctgagagtaagatttcataggaa-taacgctgatgcgcttttaccttcgttccctttctttcag-------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 5'ss of exon 12
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
|||||  || | || |||  ||||||||||  |||||||||| | |||||| ||||| ||||||||||| || || ||||| ||||| ||||| || ||||||  ||                ||  |   ||  ||||| || |  ||| |     |  |   |    | | |     | |   |  |   |  |   | || || | | || ||                             
TTTCTTAGATACTCGACCTATGATTCGATCCATTCTTGATGGCTACAATGTATGTATATTTGCTTATGGCCAGACGGGTTCTGGAAAGACTTATACGATGgtaagaa----------------acatgtctagttttgttctttatatatttatgcatcatgagtctccaatttctctttgccaaaaaaaaaagagtctcgaatttctaaccattt-----------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 14
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
|||||  || | || |||  | ||||||||  |||||||||| |  ||||||||||| ||||| |||||||| |||||||| ||||||||||| |||||||||  || |   | |   |||||  |  |       | |    ||    |||   | ||| | |  | |  | |  ||    | ||                                                           
TTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTATACAATGgta--aattacaagcttgattttgttaacgatatgctttaaccaatgattataagtttttctaacagtttctattttg--caaacacag--------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 5'ss of exon 13
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 || || |||| ||||||  || | ||||| ||||||||||| |  ||||| ||||| ||||||||||||||||||||||| || || || ||||||||||||  ||||| ||   || |||||     ||  ||| |      |  | | ||||| ||||  ||    |     || ||  |   |  ||   | |  |||                                           
GTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATACACAATGgtatgaacttgtat--atgttttag----tctacatggc-----atatgtgttgatattttcaataaaaa-----cttgtgtaatgtattgtctttcctctag------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 5'ss of exon 15
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaactta-tattgatcttttttattggta-ttgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 || |  |||| ||||||  | |||||||| || |||||||||| |||||| ||||| ||||| |||||||||||||| || |||||||| || || ||||||   ||        || ||| |       |  ||  |    |  ||| ||||  |  ||   | || |  || |  |  | |||                                                             
ATTTTTAGACACTCAACCATTAATTCGATCTGTACTTGATGGATACAATGTCTGTATATTTGCCTATGGTCAAACTGGCTCTGGAAAAACCTATACTATGgtatgtacccac-tttatttttcatccaaaaaatatgttaaagagattactatttgtacttcacactgttccttttgtttctccag-------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ12333 (Selaginella moellendorffii), 5'ss of exon 9
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 |||  ||| | ||| ||  |||| || |||||||||||||| | ||| || ||||||||||| ||||||||||| || || |||||||| ||||| |||||| | |   | ||  ||||| |||     || |||| ||   ||||       || |  | ||  |                                                                              
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtattta---tgac--atattatacaa---caacattatttgcaact-------atttgctgtacag------------------------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ19920 (Selaginella moellendorffii), 5'ss of exon 9
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
 |||  ||| | ||| ||  |||| || |||||||||||||| | ||| || ||||||||||| ||||||||||| || || |||||||| ||||| |||||    | || |  |   ||| |||     || |||| ||   ||||       || |  | ||  |                                                                              
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgt----atttatgacataattatacaa---caacattatttgcaact-------atttgctgtacag------------------------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ28715 (Selaginella moellendorffii), 5'ss of exon 10
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
|||   |||    || ||  |||||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||| |||||||| || || ||||||  | || | | |  |   |||     |  | |||   ||  | | ||   |                                                                                           
TTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATATACTATGgta--agctgtgagc--tccgttaggatttgtgtattaacgtctattgatgcag-------------------------------------------------------------------------------------------

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ30678 (Selaginella moellendorffii), 5'ss of exon 10
TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaacttttaccgatattttactggctcagcattgttgttaacttatattgatcttttttattggtattgtactggttcagcatgatgcactgctactaacttttgatcacttatgttctattccaataattttgttcttag
|||   |||    || ||  |||||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||| |||||||| || || ||||||  |  | | | |  |   |||     |  | |||   ||  | | ||   |                                                                                           
TTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATATACTATGgta--aggtgtgagc--tccgttaagatttgtgtattaacgtctattgatgcag-------------------------------------------------------------------------------------------

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|58599286|gb|CK009814.1|CK009814
EST:     TTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATG                         AGTGGACCCAGCACATCAAAACAAGATTGGGGTGTCAATTACAGGGCTTTA
genomic: TTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaactt ... ttgttcttagAGTGGACCCAGCACATCAAAACAAGATTGGGGTGTCAATTACAGGGCTTTA
EST: gi|86901422|gb|CI308403.1|CI308403
EST:     TTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATG                         AGTGGACCCAGCACATCAAAACAAGATTGGGGT
genomic: TTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaactt ... ttgttcttagAGTGGACCCAGCACATCAAAACAAGATTGGGGT

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), 47 (downstream exon)
Score: 7

TTTCTCGGACATTCAACCGCTGATTCGATCAGTTCTTGATGGATTCAATGTTTGTATTTTTGCTTATGGTCAAACTGGTTCAGGAAAAACTTACACAATGgtactaactt ... ttgttcttagAGTGGACCCAGCACATCAAAACAAGATTGGGGTGTCAATTACAGGGCTTTAAATGATTTATTTGATATCTCACTAAGTAGGAGAAATGCTTTCTCTTATG




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