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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCACCGACCAGGCCACGGCGCTGCGGCAGGCTGGCGTCCCGGTCATCGGCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgccttttttttttcttcgtctcggtagaaaatttagccccgggtaggggaatatcatcatgatatgtttatccaagttgtgggttataaggatt...

Basic information

species Oryza sativa
transcript LOC_Os01g65090.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G400604_T01 (Zea mays), 5'ss of exon 2
CATCACCGACCAGGCCACGGCGCTGCGGCAGGCTGGCGTCCCGGTCATCGGCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgccttttttttttcttcgtct------cggtagaaaatttagccccgggtaggggaatatcat----catgatatgtttatccaagttgtgggttataaggatt------------------------------------------------------------------------------
||||||||| ||||||| ||||||||||||||| ||||| ||||| ||||| || ||||| |||||||| |||||||||||||||| || ||| || |||||  | |      ||    |   || |      |   ||  |   || | | |  |   |   |   ||    ||| || | | ||    |    | | || ||   |||                                                                              
CATCACCGATCAGGCCATGGCGCTGCGGCAGGCCGGCGTGCCGGTTATCGGTCTAGCCGCGGGGGAGCCAGACTTCGACACGCCGCCCGCGATCGCGGAGgtgaggggtgcaattagcccgcggtataatttcctacagtgagaataacactgaatgcagttgttaaataaaacataatctttctagttgaacacttgatt-tagatattcagcaagaatgtgtcttgttatcaaattgggttatttcaggtaaacattcttgttgcttacctagttaccttatccag

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G400604_T02 (Zea mays), 5'ss of exon 2
CATCACCGACCAGGCCACGGCGCTGCGGCAGGCTGGCGTCCCGGTCATCGGCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgccttttttttttct----tcgtctcggtagaaaatttagccccgg-gtaggggaatatcatcatgatatgt-ttatccaagttgtgggttataaggatt
 | |  |    ||| ||   | | |||||  |     | || ||    ||     || |  | |||| | |   | |||||| |   | | |   |   |||  | ||  |       ||      | |  |  |     ||   |||  || |  | || |   |  | ||     | |    | ||  | |||  |        
-AGCGTCCGGGAGGACAAAACAC-GCGGCGAG-----GACCAGGATGGCGATTGTGCGG--GAGGAGGCAG---TGGACACGTC---CATCAGCCCAAGGgtgagcgcgctgcggccgtccaaaaccatggccatcaccgatcaggccatggcgctgcggcaggccggcgtgccggttatcggtctagccgcgggggagc------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G14720.3 (Glycine max), 5'ss of exon 2
CATCACCGACCAGGCCACGGCGCTGCGGCAGGCTGGCGTCCCGGTCATCGGCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgccttttttttttcttcgtctcggtagaaaattta-gccccgggtaggggaatatcatcatgatatgtttatccaagttgtgggttataaggatt
||||| |||||| ||||| || ||    || || ||||| || |||||  ||||||||||||| |||||||| |||||||||||       || ||||||||   |  |||| |   |||  | | ||  |   || |    |  |    |     | | | ||                                     
CATCAGCGACCACGCCACCGCTCTCTTCCAAGCCGGCGTTCCCGTCATTCGCCTCGCCGCCGGCGAGCCCGATTTCGACACGCCCGCTCCCATAGCTGAGgt---tttctttctgcattccccttttcattcataactacgtgttctttctttaatactgtaattgcag--------------------------------

upper sequence: LOC_Os01g65090.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G31490.1 (Glycine max), 5'ss of exon 1
CATCACCGACCAGGCCACGGCGCTGCGGCAGGCTGGCGTCCCGGTCATCGGCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgccttttttttttcttcgtctcggt-agaaaatttagccccgggtaggggaatatcatcatgatatgtttatccaagttgtgggttataaggatt
||||| |||||| ||||| || ||    || || ||||| || |||||| ||||||||||||| |||||||| |||||||||||       || || |||||   || |||| |   |||  | | ||  | | || |  ||   |    |     ||||   | ||   |                              
CATCAGCGACCACGCCACCGCTCTCGTCCAAGCCGGCGTTCCCGTCATCCGCCTCGCCGCCGGCGAGCCCGATTTCGACACGCCCGCTCCCATAGCCGAGgt---tgtctttctacattccccctttcattcataataactacgtcttctttttttaatagtgtaattgcag-----------------------------

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|88396984|gb|CI578133.1|CI578133
EST:     GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAG                         GCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT
genomic: GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgcct ... tgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT
EST: gi|29645872|gb|CB650879.1|CB650879
EST:     GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAG                         GCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT
genomic: GCCTCGCCGCCGGGGAGCCCGACTTCGACACGCCGCACGTGATTGCTGAGgtaggtgcct ... tgtgatctagGCTGGGATGAATGCAATTAAGGATGGTTATACAAGGTACACTCCTAATGCT