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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaacttcatctacacccttttctctctgctgttgtaactagaaagaatttgtgatcctttgccctccagtgctcttgtaaactacagtgctttt...

Basic information

species Oryza sativa
transcript LOC_Os03g09140.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AC166636.1_FGT008 (Zea mays), 5'ss of exon 3
GGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaacttcatctacacccttttctctctgctgttgtaactagaaagaatttgtgatcctttgccctccagtgctcttgtaa-actacagtgctttt--------
||| ||||||||||||||||||||||| ||| ||||||| || |||||||| || || || || || || || |||||||||||||| || ||||| ||    || | |   |   |     ||    |||   ||   |    | ||   ||||   | | | |||   ||||| ||  || | ||  |        
GGACACAGCTGGGCAGGAGAGGTTCCGCAGCCTGATCCCGAGCTACATCAGAGACTCCTCCGTAGCCGTCATCGTTTACGATGTGACCGgtaagttgaccgtctccaaaagatagacc----gccagcgta--cagtctgtgcctttg---ctttctacactaatgcagctgtaacacgccaattctgatttcttgga

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 5'ss of exon 3
GGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaacttcatctacacccttttctctctgctgttgtaactagaaagaatttgtgatcctttgccctccagtgctcttgtaaactacagtgctttt
|||||| ||||| || || || ||| ||||  | ||||||||||||||||| ||||||||||| ||  |  |||| ||||||||  |  | ||||  || |    | | | ||||  |      | ||              |||||| || | ||   || |    |  | |    | |||       
GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCAgtaagtccacctttgtttctctctttgattcaccttctt-------------ttttgtgttcttatgtgttcaatcaatactttgtgttgcag-------

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S39_147V6.1 (Physcomitrella patens), 5'ss of exon 5
GGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaacttcatctacacccttttctctctgctgt-tgtaactagaaagaatttgtgatcctttgccctccagtgctcttgtaaactacagtgctttt-
||| || ||||| |||||||||||  |||| ||||| || || |||||| ||||||| || ||||||||| |||| || |||||  |  | ||||  | ||  |  |    |||  |     ||  | |||   || |    | ||||               ||     | |         |||  |   
GGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCAgtaagt--atttgtttgattttcttacccaagagcactgtgtctttacacttgagttgttgcgtaagatttgttagaaggatggcctctactggtgtatcaa

upper sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaacttcatctacaccc------ttttctctctgctgttgtaactagaaagaatttgtgatcctttgccctccagtgctcttgtaaactacagtgctttt
|||||| ||||| |||||||||||| |||| || || || ||||||||  ||||||| || ||||||||| |||| ||||||||  |  | ||||  | ||     |||         |||| |  ||      ||     |   |  |  ||  |  |           | | ||  |  |  || |       
GGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAAgtaagtacatttttgtgacaaaagaggaattttgttcctcacacagttgtacggttggctcagtattagtacattaattgtttcactgatgtaacacggg------

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|33682509|gb|CF310748.1|CF310748
EST:     GTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: GTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
EST: gi|16577976|gb|BI812071.1|BI812071
EST:     GCAGTGATTGTTTACGATGTGACTG                         ACA-GCACGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACA
genomic: GCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCA-GTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACA
EST: gi|33684735|gb|CF312974.1|CF312974
EST:     AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
EST: gi|33688710|gb|CF316949.1|CF316949
EST:     AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGT-TATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
EST: gi|33682508|gb|CF310747.1|CF310747
EST:     AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG                         ACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC
genomic: AAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTGgcaagttaac ... ttgttttcagACAGGCAGTCCTTTTTGAGTATATCGAAGTGGATTGAAGAGGTAAATACAC