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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcaagcaaatgaattgtatgagccagtgattgtgatgtactaatacgattcttctggaatgtcctaacactaacgagttctttccttgtcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGGTATGCCTCGAGC

Basic information

species Oryza sativa
transcript LOC_Os09g28570.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 15
tgtcaagcaaatgaattgtatgagccagtgattgtgatgtacta-atacgattcttctggaatgtcctaacactaac---gagttctttccttgtcaactt-cagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGGTATGCCTCGAGC
    |   |    || | | ||||| |   ||||  |  |  |  ||   ||  | |   |   | ||        |   ||    ||||| | |||| || |||||||| ||||||||  | |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||             
--gtatataggacaactat-tgagctac--attggtagatgttggatctaatattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG-------------

upper sequence: LOC_Os09g28570.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G479068_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------------tgtcaagcaaat---gaattgtatgagccagtgattgtgatgta-ctaatacgattcttctggaatgtcctaacactaacgagttctttccttgtcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGGTATGCCTCGAGC
                                                                                            |  | | || |    ||| |  |  |   |||| || | |   | | | | | |        |||   ||||| | ||  ||| | |   |||   || |||||||||| ||||||||  |||| ||||| ||| |||||||||| |||||||| ||||| ||| |||||||| |||||||||||||||||             
gtatgttcgtgctgaataacaccaaatctaaaaggacgcttttacacagatcgtagttatcacacactgaatctaaaaggacgcttctcgcttaactaccacaaccagaactagaaaaagaagtgcttttaaaagagccactgcaaggacaaatgaag--cctaaaatta-tgagatatcatctttctaatttcagGCTGGCTTTTTCCTGGTCCAATATGCGCACCTGTGGCAAGACCATCTTGAAAAACTGTTTAACCTGTATTCCTCTGGAAAGCTAAAG-------------

upper sequence: LOC_Os09g28570.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 15
tgtcaagcaaatgaattgtatgagccagtgattgtgatgtactaatacgattctt-ctggaatgtcctaacactaac--gagttctttccttgtc----aacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGGTATGCCTCGAGC
     ||  ||    ||  ||   |||   ||||  || | |    |  |||     |  | | | |||  | | ||    |||| ||| |  |     || ||||| |||| ||||||||  | || |||| ||||||||||||||| |||||||||| ||| ||| | || ||  | || ||||||||||||             
-----agtgaactcttttcat--tccaagcattgcaatctcccgtgaaaatttccgttttatttttctatgatttacttatgttcgttcataattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG-------------

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|3766964|gb|AU031074.1|AU031074
EST:     GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGGCTCACTTGTGGCAAGATCATCTTGG
genomic: GGAACTACACTGGACTATGTGATAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATG-CTCACTTGTGGCAAGATCATCTTG-
EST: gi|88969673|gb|CI383176.1|CI383176
EST:     TAAGATTCTTGCTAAAAGTCAAACTGTG                         GCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGCCAAGATCATCTTGAC
genomic: TAAGATTCTTGCTAAAAGTCAAACTGTGgtatgtgtga ... tcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgattcttctggaatgtcctaacactaacgagttctttccttgtcaacttcagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGGTATGCCTCGAGC
                        cactaac  putative branch site (score: 1)
                                  ttctttccttgtc  putative PPT