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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagtttttatccactgaacattcttttggatgtgaacatctgttgtattctagtttttaactcattcaattgtgacacaattaagtaaaaatgtttca...

Basic information

species Oryza sativa
transcript LOC_Os06g45820.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G087598_T01 (Zea mays), 5'ss of exon 2
TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagtttttatccactgaacattcttt-----tggatgtgaacatctgttgtattctagt----ttttaactcattcaattgtgacacaattaagtaaaaatgtttca
|||||| ||||| ||||||||||| ||||||||||||||||| ||| ||||||| ||  ||||||| |||||||| |||||||| |||||||| ||||||||| ||| || | |  || |   | | |     || || |  |  |||||| | |  | ||    || |   |  || | |||  | | | |  |||  ||        
TGGTTTCGAGGGCAACACTGGAATTATTGTTATTGCTGCCACTAACCGGGCTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt-ttcgttggattctatctgtcattgcatttagatttctgttctgtctttgtaatgttgtctattgtttacttgcaa-aaattcgagtctaac-------

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G110408_T01 (Zea mays), 5'ss of exon 2
TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagtttttatccactgaacattcttttggatgtgaacatctgttgtattctagtttttaactcattcaa-ttgtgacacaattaagtaaaaatgtttca-
|||||||||||| ||||| ||||| ||||||||||||||||| ||| | ||||| ||| ||||||| |||||||| |||||||| || ||||||||||||||| ||||| ||    || |   | | |   || || |  |   || | |  |   | |||    | |    ||||       ||   |  |||  ||    
TGGTTTTGAGGGCAACACCGGAATTATTGTTATTGCTGCCACTAACCGAGCTGACATCTTGGATTCCGCTTTACTTAGACCTGGGCGCTTTGACAGACAGgttggtttt-atttgttggattctatctgtcat-tgcatttagattatttgtttaatcttagtaaagttgtcttgtctattgcttgtttgcaaaaattaagt

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G26230.1 (Glycine max), 5'ss of exon 2
TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagtttttatccactgaacattcttttggatgtgaacatctgttgtattctagtttttaactcattcaattgtgacacaattaagtaaaaatgtttca
||| |||||||| |||||||| ||||||||  |||| || || ||||||||||| || || || ||||| ||| | ||||| || || ||||| ||||||||  | || |||      |    || |     ||||||    |    || |  |  |  |  ||  ||||                              
TGGGTTTGAGGGTAACACTGGTATCATTGTCGTTGCAGCAACTAACAGGGCTGACATTCTTGACTCTGCCTTATTGAGACCGGGTCGGTTTGATAGACAGgtatgattatattatgaaatgcctcatgcttttgtgaatgagtaaattactaaacatcattgctttttcag-----------------------------

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 5'ss of exon 2
TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagtttttatccactgaacattcttttggatgtgaacatctgttgtattctagtttttaactcattcaa-ttgtgacacaattaagtaaaaatgtttca
||||||||| || |||||||| || ||||||||||| ||||| |||||||| || || || || ||||| ||| | || |||||||| |||||||||||||| ||     ||  |    | ||| ||||     | | | | | || ||     |   |     | || ||  | ||   ||                   
TGGTTTTGAAGGAAACACTGGTATAATTGTTATTGCAGCCACTAACAGGGCAGACATTCTTGACTCTGCCTTATTGAGGCCTGGACGATTTGACAGACAGgtaagc----atagagaatatattgttttttgccttatcttttattataagtgggaaatacttacgttaaagctttggagcag------------------

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S118_166V6.1 (Physcomitrella patens), 5'ss of exon 1
TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagtttttatccactgaacattcttttggatgtgaacatctgttgtattcta----gtttttaactcattcaattgtgacacaattaagtaaaaatgtttca------
 ||||| || || ||||||||  | ||||| |||||||||||||||||||||||||| || ||  |||| || ||  | |||||| | || ||||||||||| |  |      ||   |||  |  |||  || ||||||    |        |    || | |||||      ||  |       | | ||  | | |           
CGGTTTCGAAGGAAACACTGGTGTGATTGTCATTGCTGCCACCAACAGGGCTGATATTCTCGACGCTGCCTTGCTTCGTCCTGGAAGATTCGACAGACAGgtaatgt------catgaaaccatgatttaaatttgaacaatcttcaatcctcatggtgtatctaacttgcaagatgttagtttcttaatgtggagacgacgtggcacag

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S178_66V6.1 (Physcomitrella patens), 5'ss of exon 3
TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttag-----tttttatccactgaaca---ttcttttggatgtgaacatctgttgtattctagt--ttttaactcattcaattgtgacacaattaagtaaaaatgtttca--------------------------------------
||| |||||||| ||||| ||  | |||||| |||||||||||||||| |||||||| || ||||| ||||| ||  |||| || || || ||  | ||||| |      || | |     |  | |    |||| | | | ||  | ||||||  |   |  |  |||  | |  ||   |  || ||| |  |     || ||  ||                                       
TGGATTTGAGGGTAACACAGGTGTTATTGTTGTTGCTGCCACCAACAGAGCTGATATTCTTGATTCAGCTTTGCTGCGACCAGGTCGATTCGATCGCCAGgtcaagaacattctgactttttacataaacctcttgtagctttgc-cctctgttacagattgatgctttcgaattttttcgtgatgccactagaatcgggaattggatctcctaatttgttggtaacatttacgagtattctgttcag

upper sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S156_30V6.1 (Physcomitrella patens), 5'ss of exon 3
TGGTTTTGAGGGGAACACTGGAATCATTGTTATTGCTGCCACCAACAGGGCTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagtttttatccactgaac---attcttttggatgtgaacatctgttgtattctagtttttaactcat-tcaattgtgacacaattaagtaaaaatgtttca-----------------------------------------------------------------------------------
||| |||||||| ||||| ||  | || ||||||||||| |||||||| ||||||||||| ||| |||||||| |  |||| || || |||||  | |||||||    |||  |  ||| |     ||| | | |  |       | ||||  |    |  | | ||||  ||  ||  ||     || || |    ||||                                                                                      
TGGATTTGAGGGCAACACAGGTGTTATAGTTATTGCTGCTACCAACAGAGCTGATATCCTTGATGCTGCTTTATTGCGACCCGGTCGCTTTGATCGTCAGgttataccttagtctgtgacccgagctctctcgcagct--tttctttttgtggttctctcctcacctcaaatctctttcgatgagcttgag-attggtgttcttgaacttacgttaggcttaagatccagcagcccatcggaatgacactattagttttttctaacgtgaaatcctttcttggtcag

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|29673466|gb|CB669741.1|CB669741
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|58688540|gb|CK077227.1|CK077227
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAG
EST: gi|58692405|gb|CK081092.1|CK081092
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|29662977|gb|CB659252.1|CB659252
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAA                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGACATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|29613926|gb|CB618939.1|CB618939
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTA
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTA
EST: gi|313079833|gb|HO213272.1|HO213272
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGAT
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGAT
EST: gi|58691808|gb|CK080495.1|CK080495
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
EST: gi|25797955|gb|CA753916.1|CA753916
EST:     CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAG                         GTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG
genomic: CTGATATCCTGGATTCTGCTTTACTCAGACCTGGACGTTTTGACAGACAGgttagttttt ... tgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTG