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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctctagaacttcgtctgcattgttgccaatctcagcgctggaattcagaagagttctttgttaaaagttgttgcaatggcggatatattggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAAGTACGAGGGGACGAGCCCGGCGGGGTCGCACAAGCCGAACACGGCGGTG

Basic information

species Oryza sativa
transcript LOC_Os06g42560.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g42560.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G054465_T01 (Zea mays), 3'ss of exon 3
--cctctagaacttcgtctgcattgttgccaatctcagc-gctggaattcagaagagttctttgttaaaagttgttgcaatggcggata-----tattggtgatg--cagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAAGTACGAGGGGACGAGCCCGGCGGGGTCGCACAAGCCGAACACGGCGGTG
   | |||  || || |  |   ||  | ||||  | || ||||    |   |  |   ||  |  | |   || ||  |  |   | |     |  ||   | |  |||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || |||
gtaccctacgacctctttcgtgctg--gtcaatagctgctgctgctgctgctagcaacgctcgggcagagtatggtgtgagtgaacacaaccaatgctgccaacgttcagGGCCAGGAGGCTGGAGAAGCTGCTCGGCACGCCGGCGAAGATCTACTACAAGTACGAGGGGACCAGCCCGGCGGGGTCGCACAAGCCCAACACCGCCGTG

upper sequence: LOC_Os06g42560.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24275 (Selaginella moellendorffii), 3'ss of exon 1
cctctagaacttcgtctgcattgttgccaatctcagcgctggaattcagaagagttctttgttaaaagttgttgcaatggcggatatattggtgatgc-agGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAAGTACGAGGGGACGAGCCCGGCGGGGTCGCACAAGCCGAACACGGCGGTG
                                     | | || ||     ||   ||||  |     |  | ||  | |  |   | ||    |||| ||||| | | | || ||   | |||| |  || || || | ||| |||||||||||||||||   ||| || ||||| || ||||||||||||||||| || 
-------------------------------------gtttgagttttttcgaagcctttcct-----tcatcgct-tagttgtactgttatgcatgccagGGCCAAGCGACTAGAACGGTTGCTAGAAACTCCTGCAAGGATTTACTACAAGTACGAGGGTGTGAGTCCAGCGGGATCACACAAGCCGAACACGGCCGTC

upper sequence: LOC_Os06g42560.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35538 (Selaginella moellendorffii), 3'ss of exon 1
cctctagaacttcgtctgcattgttgccaatctcagcgctggaattcagaagagttctttgttaaaagttgttgcaatggcggatatattggtgatgc-agGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAAGTACGAGGGGACGAGCCCGGCGGGGTCGCACAAGCCGAACACGGCGGTG
                                     | | || ||     ||   ||||  |     |  | ||  | |  |   | ||    |||| ||||| | | | || ||   | |||| |  || || || | ||| |||||||||||||||||   ||| || ||||| || ||||||||||||||||| || 
-------------------------------------gtttgagtttttttgaagccttttct-----tcatcgct-tagttgtactgttatgcatgccagGGCCAAGCGACTAGAACGGTTGCTAGAAACTCCTGCAAGGATATACTACAAGTACGAGGGTGTGAGTCCAGCGGGATCACACAAGCCGAACACGGCCGTC

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|218501383|gb|FG961875.1|FG961875
EST:     GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAG                         GGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
genomic: GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAGgtagaacact ... ggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
EST: gi|8857394|gb|AU094712.1|AU094712
EST:     GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAG                         GGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
genomic: GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAGgtagaacact ... ggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
EST: gi|58692587|gb|CK081274.1|CK081274
EST:     GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAG                         GGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
genomic: GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAGgtagaacact ... ggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
EST: gi|29643117|gb|CB648124.1|CB648124
EST:     GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAG                         GGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
genomic: GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAGgtagaacact ... ggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
EST: gi|7274060|gb|AU032635.2|AU032635
EST:     GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAG                         GGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
genomic: GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAGgtagaacact ... ggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
EST: gi|58692853|gb|CK081540.1|CK081540
EST:     GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAG                         GGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
genomic: GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAGgtagaacact ... ggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
EST: gi|58691998|gb|CK080685.1|CK080685
EST:     GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAG                         GGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA
genomic: GAGGAGGTCGCCGAGGTTTACAAGCTCTGGCGCCCGACGCCGCTGATCAGgtagaacact ... ggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagaagagttctttgttaaaagttgttgcaatggcggatatattggtgatgcagGGCGAGGAGGCTGGAGAAGCTGCTGGGCACGCCGGCGAAGATCTACTACAAGTACGAGGGGACGAGCCCGGCGGGGTCGCACAAGCCGAACACGGCGGTG
            tttgttaaaa  TA-rich tract