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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtcatgaagtaaacctgatgctgtaatgctcttgtgttaggcccttactcttttctcattgtcaacactaacataacatctgcttttcgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGCGCACCGAATTGCCAGAGGGGCCATTCTGCCTTTTGTACATGCACAGCAC

Basic information

species Oryza sativa
transcript LOC_Os01g71980.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71980.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G129108_T01 (Zea mays), 3'ss of exon 1
actgtcatgaagtaaacctgatgctgtaatgctcttgtgttaggcccttactcttttctcattgtcaacactaacataacatctgcttttcgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGCGCACCGAATTGCCAGAGGGGCCATTCTGCCTTTTGTACATGCACAGCAC
|   || ||   |    || | |   || || | ||| ||      |||    |  | ||| |||  |||      | || || |  ||| |  |||||||||| |  || |  ||||| |||||||| ||||||||  |  |||| || |||||||||||||| | ||| ||||||||| | |||||||||||||| ||
atcctcgtgctttgttgctaaaggcttagtgttattgcgtcccagacttctcttggtgtcagtgtttacatggcatttacttcggaattttggtttccagCTCCAGCAATTGACGGTGAACGTCTGAAAAAGTATGTGTTCTACAAACTCCGCACCGAATTGCCTGTGGGTCCATTCTGCATCTTGTACATGCACAGTAC

upper sequence: LOC_Os01g71980.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G369652_T01 (Zea mays), 3'ss of exon 1
actgtcatgaagtaaacctgatgctgtaatgctcttgtgttaggcccttactcttttctcattgtcaacactaacataacatctgcttttcgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGCGCACCGAATTGCCAGAGGGGCCATTCTGCCTTTTGTACATGCACAGCAC
|   || ||    |   ||       || |  | |||  |  |   ||     |  | ||| |||  |||      |||| |  |  ||| |  |||||||||| || || | |||||| |||||||||||||||||  |  |||| ||||||||||||||||| | ||| ||||||||| |||||||||| ||||||||
atcctcgtgcttcattgctacaagcttagtcttattgcttccgagactattcttggtgtcaatgtttacatgttattaactttggaatttgggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGCGCACCGAATTGCCTGTGGGTCCATTCTGCATTTTGTACATCCACAGCAC
















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|58672220|gb|CK060906.1|CK060906
EST:     CGACAGGGCCGGGAGGCGCATCGTCCGCGTCGTCGGCAGGTTCTTCCCTG                         CTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGC
genomic: CGACAGGGCCGGGAGGCGCATCGTCCGCGTCGTCGGCAGGTTCTTCCCTGgtgcgccaaa ... cgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGC
EST: gi|568004|gb|D38839.1|D38839
EST:     CGACAGGGCCGGGAGN-GCATCGTCCGCGTCGTCGGCAGGTTCTTCCCTG                         CTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGC
genomic: CGACAGGGCCGGGAGGCGCATCGTCCGCGTCGTCGGCAGGTTCTTCCCTGgtgcgccaaa ... cgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGC
EST: gi|8857437|gb|AU094755.1|AU094755
EST:     CGACAGGGCCGGGAGGCGCATCGTCCGCGTCGTCGGCAGGTTCTTCCCTG                         CTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTTCACAAGCTG
genomic: CGACAGGGCCGGGAGGCGCATCGTCCGCGTCGTCGGCAGGTTCTTCCCTGgtgcgccaaa ... cgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTT-CACAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttactcttttctcattgtcaacactaacataacatctgcttttcgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGCGCACCGAATTGCCAGAGGGGCCATTCTGCCTTTTGTACATGCACAGCAC
                                    tctgcttttc  CT-rich tract
                          taacataa  TA-rich tract