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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct...

Basic information

species Oryza sativa
transcript LOC_Os06g05180.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 6
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaaca---atgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| ||||||||||||||||||||||||||| ||| ||   |  |  |||| ||||||| |   ||    || || | || |  |   | | |   |||  |||  ||  ||   |||  |   |     |||   
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttcttttctaatttatctctgcttttagacccatt--ttctattttgtggaagacaggtta--

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaacaatgagtttcttttattttggtacctgtttct--ctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||| |||||||||||||||| ||| ||   |  |  |||| ||||||| |   | |  ||||| ||||   |  | | |||   |||  |||  ||  ||   |||  |   |     |||   
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaaaatatatattgactttttttttctaatttatctctgcttttagacccatt--ttctattttgtggaagacaggttat-

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 2
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgact-tttgatccaaaaca---atgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| ||||||||||||||||||||||||||| ||| ||   |  |  |||| | ||||| |   ||    || || | || |  |   | | |   |||  |||  ||  ||   |||  |   |     |||   
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcggtttgtttcaaaatatatattgactttttcttttctaatttatctctgcttttagacccatt--ttctattttgttgaagacaggtta--

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 16
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttt----tgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||||||| | |||| ||||||||| |||||| |||||||||||||||| ||||| |||| ||| ||| |  | | |    ||||      | | |   || | |   | |  |   | |||   |||  | | |||  ||   |||| |||        |    
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCAAAGGCACAATACAATAGgtttgttccaaaatgtaaactgatttttttctacgctcttttctctctctaatttatctttgcttttagatccgtt--ttctatttcgtaacggcagattat--

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctct-ttgaacctgttgatttggtttcttaataattttgttcct-----
| ||| | || |||||||||||||||||||||||||||||||| ||| | ||| | || ||||| ||| ||||||| || || || | |||  |||| | ||  |   || || || | | ||| ||||||| ||  |||| |||   ||  |     | |  |  |  |||   |     ||   |||  ||||| |        
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgtagg--acttacctt-gttgcaagacaatga-ttgattttctttcaatatgtagaaatatgcttgatatgt--gtagaaattaaaaatgtttttggtaacagaat

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgt--tagttgctgacttttgatccaaaac--aatgagtttcttttattttggtacctgtttctctttga-acctgttgattt-ggtttcttaataattttgttcct
||||| | ||||||||||| |||||||||||||| |||||||| ||| | ||| | || ||||| ||| ||||||| || || || | |||  |||| | ||  |||||  |  || ||        ||  |||||   |   ||  |||  |      || | ||||| |  | ||||    || || ||  |||   |      
TACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGCATCATAACAGgtagtagttattttctgttatgttgttacggaatgacccttactttctttatttagaaattatgtttgatatgttttgagaaaggcttttttgtaagggt------

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATA------Agttagttgc--tgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
| ||| | || |||||||||||||||||||||||||||||||| ||| | ||| | || ||||||||| | ||||| || || || | |||  |||| |      |||||||| |  ||  ||  | | ||| | ||||| ||  |||| |||   ||  ||||    | ||  | || |   |       |||| |||  | ||   
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagttagttaccttgtgttacgttgcaagataatga-ttaattttctttcaata--tgttgaaatatg--cttgatatgtgtagaaattaaaaatgctttt---

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct-----------------------------------------------------------
||||| | |||||||||||||||||||| |||||||||||||| ||| | ||||  || |||||  | ||||| || || || |||| |||  |||||| ||  |    ||   |||    |  |  |  |       |  ||| ||||    ||     | |   |  | | |  |  |   ||||  ||| | |||||                                                           
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaa--attgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgt-tagttgctgacttttgatccaaaacaatgagtttcttttattttg-----gtacctgtttctctttgaacctgt-tgatttggtttcttaataattttgttcct
||||||| | |||||||||||||||||||||||| |||||||| ||  || ||||||||| ||| |||||||| |  || ||  | | ||| || |||| ||   |    | |   |  |   | | ||| |   || | | | ||||     |||  ||| ||     |     || ||||||| |  |||  ||  ||       
TACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCTCAAGAGCACTACAATAGgtactgaaattcatagtatactgacagcaaagtaattgtgtgaatttgatggtgtagatgtgtcctcaggttgtagtctgatttgatagcttgctagatt-------

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagtt------gctgacttttgatccaaaacaatgagtttcttt-tattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct
||||||| |||||||||||||||||||| |||||||||||||| ||  | ||||| || |||||  ||||||| || || || || |  ||  |||||| || | ||      | || || ||| |  | |||| | |  |       |      |||    |  | |||| | ||       || ||| |    ||||||||    
TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttctactgttggctgttggtaaacaacagtaaaataagaggcaaacacttacaatgtagtatttggatcttc----atgttttgtggggaattttgta---

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|58690875|gb|CK079562.1|CK079562
EST:     GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAA                         TGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
genomic: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
EST: gi|2443004|gb|C74775.1|C74775
EST:     GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAA                         TGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
genomic: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT