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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag

Basic information

species Oryza sativa
transcript LOC_Os05g44922.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgata--tagctcttctgattggtca--ttgtctcatgtgcttatgtacattacccag
|||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||| || ||||||||   | |||     |   || | | |  || |||||||||||||  |  ||| || || | ||   |  | ||| ||||
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G36050.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctat-gtgatatagctcttctgattggtcattgtctcat--gtgcttatgtacattacccag-------------
||| || || ||| | || || ||  | |||||  ||||||||||||| ||||| || |  ||||| |||||||  ||||| ||||| ||||||||||||||   |||  |   ||  |  |||    | |||   ||||   |||    | ||  |||  ||  |    || ||||| ||              
TGATATACATAAGCGTGGGGGAACTATCCTTGGTTCATCACGAGGTGGACATGACACCACTAAGATAGTTGACAGTATTCAAGATCGGGGAATTAATCAGgtc--tgcattgcattctatttattacaacatataacttcattttgtatgtagtaacatcagtagtctaataaattactcaatcaattccaccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G15170.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtg-atatagctct-tctgattggtcattgtctcatgtgcttatgtacatta--cccag
||| || || ||| | || || || || ||||| |||||||||||||| ||||| || |||||||| |||||||  ||||| ||||| ||||| ||||||||   |||  || |||  |  ||   | |||||  | | | ||    || | |   |||  |   ||| |   | |    |||
TGATATACATAAGCGTGGGGGAACTGTCCTTGGAACATCACGAGGTGGACATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtc--tgcacttctttcaatgtagcagtatatatttttgtgtgccgtgtaagtacatcagattaatatctctctgaatttcag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G03570.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctat---gtgatatagctc--ttctgattg-------gtcattgtctcatgtgcttatgtacattacccag
|||||| || ||| | || || ||  | |||||  ||||||||||||| |||||||| |  ||||| |||||||  ||||| ||||| ||||||||||||||   |||  ||  ||  |  |||      || || ||   || ||  ||        |||       |    || ||  |  |   ||||
TGACATACATAAGCGTGGGGGAACTATCCTTGGTTCATCACGAGGTGGACATGATACCACTAAGATAGTTGACAGTATTCAAGATCGGGGAATTAATCAGgtc--tgcatttcattctatttattacaacatgtaacttcattttgtatgtataaaaatcagcagtctaataactcattcaattccaccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G01710.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGG-GGTGGGA--CAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgc--ggttgtttgcacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag
  || |  |  |  |  | | | |  |||     || |  | |  ||||   |||  |    |  |||| |    ||  |    || |  ||  |||  | |||||| ||      || | | |   | |  |  |   | || |      | |  || |  | |  ||    |||        
-TACGTTAAAGATTGTTGATAGCATCCAGGATCGGGGAATTAATCAGGTTTACATACT-TGGAGGAGATGGAACTCAG-AGAGGGGCTTCTGTGATTTTTGAGgtaattgttaaaatgctggtatgca-gaaagttgatttttttaggcaattaaggttttgt-tatttgcacacag-------

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G09320.1 (Glycine max), 5'ss of exon 5
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtc----tcatgtgcttatgt---acattacccag-----------------------------------------------------------------
||| ||||| ||| | || || ||  ||||||| ||||||||||| || ||||||||    ||||| ||||||| ||| |||||||| ||||||||||||||  |  |   |||  ||     | | ||  || |  |     || | | ||      ||||    |   ||       || |||                                                                  
TGATATCCATAAGCGTGGGGGTACGATTCTTGGGACATCACGAGGGGGGCATGATACTGGCAAGATAGTTGACAGCATCCAGGATCGAGGAATTAATCAGgtttac-catgtgtcagctgtattataatgaagtttctgatgatgatgaatgcgggaatcataaattagagttttgttatatccatgtacttaaaacctaagtaggttattgtcatcgcatgggttttcattgcttgggttatggttacag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G00870.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtctca-tgtgcttatgtacattacccag
||| || || ||| | || || || || || || |||||||||||||| ||||| || |||||||| |||||||  ||||| ||||| ||||| ||||||||   |||  || |||  |  || |   ||  |    |      | | |   ||||  ||   ||  |            
TGATATACATAAGCGTGGGGGAACTGTCCTCGGAACATCACGAGGTGGACATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtc--tgcatttctttctattta-gcagtagtgtatgtacatcagattaacatctctctgaatttcag------------

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G02400.2 (Glycine max), 5'ss of exon 7
------------------TGACATCCACAA--GAGGGGTGGGACAGTT-------CTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCG---TGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgat-tggtcattgtctcatgtgcttatg-tacattacccag-------------------------------------------------------------------
                  |  ||| ||  |  | ||  |    ||| |       |||||   ||   ||  |    ||||  ||   | |||| ||||    ||| |  |      | |  || |      | || | |||   |  | || |||  |   | | |  |||| |  | |    || |  || | ||   | ||   | |                                                                    
CACCTCAAAGATTGTTGATAGCATTCAGGACCGGGGAATTAATCAGGTTTATATACTTGGAGGATATGGAACTCAGTATGAAGCAGCTATGATTTTTGAGgtaattaataaatagactaggtttgagtgctgatattcagtttgctataactttgtatt--tgttttaatgatctactgacaaactaacttgatgataacatatgctctaaaagtttggtagatataataattttcactatttaaatttgtactcacaagattaagttatttatgcag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G09180.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtc-tcatgtgctta----tgtacattacccag-----------------------------------------------------------------
||||||||| ||| | || || ||| ||||||| ||||| ||||| || ||||||||    ||||| ||||||| ||| |||||||| ||||||||||||||  |  |   |||   |     | | ||  || |  |     || | | ||   ||||    |||    | |    || |||                                                                  
TGACATCCATAAGCGTGGGGGTACAATTCTTGGGACATCCCGAGGGGGGCATGATACGGGCAAGATAGTTGACAGCATCCAGGATCGAGGAATTAATCAGgtttac-catgtgtcaactgtattataatgaagtttctaatgatgatgaatgcaatcataaatttagagttttgttatatccatgtacttaaaacctaagtaggttattgtcatcgcatgggttttcattgtttgggttatggttacag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgta--aatg-----cggttgtttgcaccta--tgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag
||| ||||| ||| | || |||||  | ||||| || ||||||||||| || ||||| | |||||| ||||||| |||||| ||||| ||||| ||||||||    ||      |   | ||| ||||    | || |  |    | |  |        |   | ||||  || | | |||    |||
TGATATCCATAAGCGTGGAGGGACTATCCTTGGGACCTCACGAGGTGGTCACGATACCACAAAGATAGTTGACAGCATTCAAGATCGAGGAATCAATCAGgttttgataaccatcacctctttacaccgtgttctgttccaagagtacatacaaactcgttcttgatgtagtttttttcatcgttcag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgta---aatgcggttgtttgcacctatgt------gat-atagctcttctgatt-----ggtcattgtctcatgtgcttatgtacattacccag--------------------------------------------------
||||||||| ||  | ||||| || || |||||||||||| |||| |||||||||||   |||||| ||||||| ||||||||||||||| |||||||||||    || |   |  |||     | |||       || || | | || |||||       |     |   ||||||   |||| | | ||  |                                                  
TGACATCCATAAACGTGGTGGTACTGTCCTTGGCACATCAAGAGGAGGCCATGATACCTCAAAGATAGTTGACAGCATTCAGGATCGTGGGATTAATCAGgtgcctaaaggattaatttttcattgtgttccttaaatgatggttattatgatttctgaaattggaattctatgtgcagctgta-actgccagggcatgcaatttccatgcatgatgttgattcattttcttttgatgttccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgta-------aatgcggttgtttgcac---ctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag--------------------------------------
||| || || ||  | || || ||  | ||||| |||||||||||||||||||||||   |||||| |||||||  ||||||||||||||||| ||||||||        ||| |  ||  |||  |    ||| |||   |    ||| || |  |   | | |  |   | |  | |||   |                                          
TGATATTCATAAACGTGGGGGAACCATACTTGGGACATCACGAGGTGGCCATGATACCTCAAAGATAGTTGACAGTATTCAGGATCGTGGAATCAATCAGgtctgtagacaatactatttcttgtccaagttatctgagtcacactttcggagttttgtgtatttgctacacctgggcacacctcttcaatgcatggacgttagatttatagctttgttgatctcag

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|569752|gb|D40601.1|D40601
EST:     ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAG                         GTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTC
genomic: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcgg ... cattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTC
EST: gi|571842|gb|D41353.1|D41353
EST:     ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAG                         GTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATTGAGATCTT
genomic: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcgg ... cattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATAT-GAGATCTT