Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc...

Basic information

species Oryza sativa
transcript LOC_Os08g12840.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G024482_T01 (Zea mays), 5'ss of exon 2
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatg----attccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc-
|||||||||||| |||||||||||||| || ||||||||||| |||||||| || ||||| || ||||| ||||||||||| ||||| |||||||| ||||||||    | | || | | |||     |||||   | |     ||   ||| ||   |     |   |  ||   ||   ||  |||| |     |  || || 
AGAATATGCAGTGGGGATCAAGAATGTTACAATAAATGATAATTTCTTCCCAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcaccaattcattgtgttgctgatcatgtttagggtctggatc--ttacta---acaattttgatatttaattgtccttacatcaccagaggtgatgatcc

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G07870.1 (Glycine max), 5'ss of exon 3
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgat-caaattgtttagtatatatggcctctgttgtttc-ctgaggtttgatcatctct-cattgtggtc-
||  | |||||| |  || |||||||| || |||||||| ||||| || ||||||||||| || ||| |||| || ||||||||||||||| |||||||||||      ||||||  || |     | |  |    | |   || | | || |   || |      | |||   || |      | |  |||    | |  |  
AGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTTTTTCCTGGGCATTTTCCTGAAAGACCAATCATGCCTGGTGTTCTCCTGGTTGAGgtaaa----cactatgctgacccttttatattccctttccttttctcttgtcttcttgcctgaaactatttgattgtgaaagtgtaagttctgtgctttaatta

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G05800.1 (Glycine max), 5'ss of exon 3
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtt-tagtatatatggcc--tctgttgtttcctgaggtttgatcatctctcattgtggtc
||  | |||||| |  || |||||||| || |||||||| |||||||| ||||| ||||| || ||| | || || |||||||||||||| ||||| ||||||  |  | | || | ||   | | ||     ||  |  |   || |  ||| | |      | |||  ||| ||    | | | ||| |     |      
AGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTCTTTCCTGGACATTTTCCAGAAAGGCCAATCATGCCTGGTGTTCTAATGGTCGAGgtactaaacta-tacactgtgctgcttgctgcctgcccctacctttattatatctctaattattttgtccttttcttgtctctaaacatgttatggtaaaa--

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G24650.1 (Glycine max), 5'ss of exon 3
------AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatg-tgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc
      ||  | |||||| |  || |||||||| || |||||||| ||||| || ||||||||||| || ||| |||| || ||||||||||||||||||||| |||||  |  | | |||      | | |   |  | |  |    || | |  | |  ||| |  |  || |||  | | || | |  |||| |  ||      
TCCTGGAGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTTTTTCCTGGGCATTTTCCAGAAAGACCAATCATGCCTGGTGTTCTCATGgtttaggta-aacactaatatgagtctagctacccttttatatttcctttatattctcttcatgcctgcaatttttttatcaagtgtaaaaatctgtgctt------

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G19200.1 (Glycine max), 5'ss of exon 2
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc------
||  | |||||| |  || |||||||| || |||||||| |||||||| ||||| ||||| || ||| | ||||| |||||||||||||| ||||||||||||  |    | |  | |    |||   | |  |  |   ||   ||| | ||| | | |  ||   | ||   |    || ||||     | ||   ||      
AGTTTCTGCAGTGGCTATAAAGAATGTGACAATAAATGACAACTTCTTTCCTGGACATTTTCCAGAAAGGCCCATCATGCCTGGTGTTCTAATGGTTGAGgtactaaaata-tgcactatgctcc---tacctttgttgtatctcttatt-tattttgtccttgccttgtctctaaacatg-tcatgataaaatggaatcaatttg

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc-
 |  |  || || |  || ||||||||||| || ||||| || ||||||||||| |||||||| |||||||| || |||||||||||||||||| ||||||||  | |   |  |    |   | |  |  |||  ||||   | | |  |||| | |    || | | |     | | |  || | ||  | ||   |  
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaa-atattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G10160.1 (Arabidopsis thaliana), 5'ss of exon 3
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc-----
 | || ||| || |  || || || || || || ||||| || ||||| |||||||||||||| ||  |||| ||||||||||| ||||||||||||||||||  |||    | |       ||  | | || |  || ||  ||| | | | | || | | | ||  |   | |      | | | | | |   | | |     
TGTATCTGCGGTAGCTATTAAAAACGTTACCATTAATGACAATTTCTTTCCTGGGCATTTCCCTGAGAGACCTATAATGCCTGGAGTTCTCATGGTTGAGgta--atttgcatttgccctattctctcttct-tactccaaaagttcaatctgtttg-catatatttatagttaaaagagaagc-tttttgagcctagacattta

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 5'ss of exon 3
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctga--ggtttgatcatctctcattgtggtc---
||  | ||| ||||  || |||||||| || ||||||||||||||||| ||||||||||| |||||  | || || |||||||||||||||||||||||||||   |     |    |  | |  |  |  | |  |    || |||||| |  ||    | |   ||| | ||   |   | |   | ||   || || |    
AGTTTCTGCTGTTGCCATAAAGAATGTAACAATAAATGATAACTTCTTTCCTGGGCATTTTCCCGAGAGGCCAATTATGCCTGGTGTTCTCATGGTTGAGgtaatttcttgttcccgtaccttttaaatattttttt----ttctttagt-tgcattatttttaaagttacatgtatgaggtaaatgtttccatttttgctacaa

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv00s0357g00070.t01 (Vitis vinifera), 5'ss of exon 3
AGAATAT--GCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctct-cattgtggtc
 | || |  ||| | |  || |||||||| || ||||   |||||||||| |||||||| ||||| ||  | || || ||||||||||| |||||||||||||||   || |    |       |  |||| ||    |  ||||   |    || |        |    |   |||    | |  | |||  |||  | || 
-GGATCTCAGCAATAGCAATTAAGAATGTGACTATAA-CAATAACTTCTTTCCTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgta-atttgcttattgccaaactttatgttcttcatttgaattcaatttactagaaaataaaagaaaatgtttgaaaaataaagaactcgacatatttgtg

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 5'ss of exon 3
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctct-cattgtggtc
    |  ||||| |  || |||||||| || ||||| ||||||||||| |||||||| ||||| ||  | || || ||||||||||| |||||||||||||||   || |    |       | ||||| ||    |  ||||   |    || |      | |    |   |||    | |  | |||  |||  | || 
GATCTCAGCAGTAGCAATTAAGAATGTGACTATAAACGATAACTTCTTTCCTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgta-atttgcttattgccaaacttcatgttcttcatttgaattcaatttactagaaaataacagaaaatgtttgaaaaataaagaactcaacatatttgtg

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S196_99V6.1 (Physcomitrella patens), 5'ss of exon 1
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggc---atccatgtgctgtgatcaaattgtt-tagtatatatggcctctgttgtt--tcctgaggtttgatcatctctcattgtggtc
 || |  || ||||  || || ||||| || || ||||| |||||||||||||| || |||||| | || ||||| |||||||| || |||||||| |||||| ||   || |  |  |     |||    || | |||    |   ||  |||    ||||  |  ||   |  |      || ||  ||| |||  ||      
GGAGTCGGCTGTTGCCATAAAAAATGTGACTATCAATGACAACTTCTTCCCTGGTCACTTCCCCCAGCGGCCCATCATGCCTGGGGTGCTCATGGTAGAGgtaagacgtcatttcagggatttgatcatcttgatatgaatgtaacattgcagtgcgcatggtttaggtcaataatgtaatagtgtgggcatttctattt------

upper sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggc--atccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc-
 || |  |  || |  || ||||| || || || ||||| || ||||||||||| || |||||| | ||||| || ||||||||||| |||||| |||||||  ||   || | | |  ||  |||    ||    | | |||||    | |  |  |  | |||   |  |  || | |   || | |  |  |  ||||  
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgctaatctcaatgtgaaggtgaaatta--gactgcaatttacttctagggcatattgcgatagcatga-cagttttattggttg

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|38477393|gb|CF961526.1|CF961526
EST:     CTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCGTGGTTGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGA
genomic: CTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattcc ... ttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGA