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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtactgtggttaactggttatcatttgtctgagtagtgcatactagcaacattattttccgtatatgataatttcagcttaatgaggtctgacaagatattcctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAAGTCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g19150.5
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G075992_T01 (Zea mays), 3'ss of exon 2
gtatgtactgtggttaactggttatcatttgtctgagtagtgcatactagcaacattattttccgtatatgataatttcagcttaatgaggtctgacaagatattcctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAAGTCCTG
            ||   |  ||  | |  | ||| |  | ||  || ||| ||| ||   ||   |   || |||||              | |  | |   | |  ||| | ||||||| |||||||  |||||| |||| ||||||||||| |||||||| |||||| ||
------------gtatccgtgtggttagatttcttaa-aatgttta-tagaaacgtttggtttgattattggtaattat------------tttatcgaataactattgtgacagGTGAACCCACATACCCATCAGCTGAAGTTGTGTGACTTCGGCAGTGCCAAAGTCTTG
















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|29628248|gb|CB633259.1|CB633259
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
EST: gi|33683226|gb|CF311465.1|CF311465
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
EST: gi|29668828|gb|CB665103.1|CB665103
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
EST: gi|29628183|gb|CB633194.1|CB633194
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
EST: gi|29637277|gb|CB642286.1|CB642286
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
EST: gi|29666642|gb|CB662917.1|CB662917
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
EST: gi|218502361|gb|FG956952.1|FG956952
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
EST: gi|29668963|gb|CB665238.1|CB665238
EST:     ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTG                         GTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA
genomic: ATAACTGTGTGGGAGTATGCCACAGAGATATAAAGCCACAGAATATATTGgtatgtactg ... cctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccgtatatgataatttcagcttaatgaggtctgacaagatattcctgtcatagGTGAATCCACATAATCATCAGTTGAAATTGTGTGACTTTGGCAGTGCAAAAGTCCTG
                              gtctgac  putative branch site (score: 3)
                                           ttcctgtc  putative PPT
     tatatgataatttca  TA-rich tract