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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgatgttggctcactatatagttctgtagtcccacttatataaagtcttgaggaacaaagttttatttttgttacacttgatatgcattgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAAGGAATAACGAAAAACCATCTCTTCATGGGAATAATTGCTATAACTACTG

Basic information

species Oryza sativa
transcript LOC_Os08g40530.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G309782_T01 (Zea mays), 3'ss of exon 3
cttgatgttggctcactatatagttctgtagtcccacttatataaagtct-tgaggaacaaagttttatttttg--ttacacttgatatgcattgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAAGGAATAACGAAAAACCATCTCTTCATGGGAATAATTGCTATAACTACTG
    ||        ||  |||  |  ||   |    ||  | | || ||  ||  || |        |  ||||  |||   | | | ||  ||  ||||||||||||||| |||||||||||||| || |||||||| | |||||||||||||||  | ||||| || || || |||||||||||||| | |||||| || |
---tataaaaatatacattattttgatgatttatggctcgtgttaactccatgtagatctggaacgaaggtttgagttaacttgggtgtgttttttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AC214484.3_FGT001 (Zea mays), 3'ss of exon 4
---cttgatgttggctcactatatagttctgtagtcccactta----tataaagtcttgaggaacaaagttttatttttgttacacttgatatgcattgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAAGGAATAACGAAAAACCATCTCTTCATGGGAATAATTGCTATAACTACTG
       || |||  |   |  ||  || | | | ||   |||     ||  ||   |  ||||  ||| |||      ||||   | | | ||  ||      ||||||||||| |||||||||||||| || |||||||| | |||||||||||||||    ||||| || || || |||||||||||||| | |||||| || |
tatgaaaatattgattattttgatgatt-tatggcccgtgttaactccatgtagatct--ggaatgaaggtttga----gttaacttgggtgtgtttttttatgcagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGCCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G132712_T01 (Zea mays), 3'ss of exon 30
cttgatgt-tggctcactatatagttctgtagtcccactta----tataaagtcttgaggaacaaagttttatttttgttacacttgatatgcattgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAAGGAATAACGAAAAACCATCTCTTCATGGGAATAATTGCTATAACTACTG
 |  |  | | | | | | |   | | | | | ||   |||     ||  ||   |  ||||| ||| |||   ||   |    |   | |   ||  ||||||||||||||| |||||||||||||| || |||||||| | |||||||||||||||  | ||||| || || || |||||||||||||| | |||||| || |
-tgaaaatatagattattttgatgatttatggcccgtgttaactccatgtagatct--ggaacgaaggtttgagttaacttgggt--gtgttttttttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG

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|29665351|gb|CB661626.1|CB661626
EST:     CTGAGAAAACACAAAACACCTTTATCTTCAACACCTTTGTCTTTTGCCAG                         ATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAA
genomic: CTGAGAAAACACAAAACACCTTTATCTTCAACACCTTTGTCTTTTGCCAGgtgggttggc ... tgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAA
EST: gi|58690194|gb|CK078881.1|CK078881
EST:     CTGAGAAAACACAAAACACCTTTATCTTCAACACCTTTGTCTTTTGCCAG                         ATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAA
genomic: CTGAGAAAACACAAAACACCTTTATCTTCAACACCTTTGTCTTTTGCCAGgtgggttggc ... tgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAA
EST: gi|23322134|gb|BU572379.1|BU572379
EST:     CTGAGAAAACACAAAACACCTTTATCTTCAACACCTTTGTCTTTTGCCAG                         ATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAA
genomic: CTGAGAAAACACAAAACACCTTTATCTTCAACACCTTTGTCTTTTGCCAGgtgggttggc ... tgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcttgaggaacaaagttttatttttgttacacttgatatgcattgcatgccagATCTTCAACGAGTTCAATGCACGCAAGCCCGAGGAGAGGAATGTCTTCAAAGGAATAACGAAAAACCATCTCTTCATGGGAATAATTGCTATAACTACTG
                                acttgat  putative branch site (score: 5)
          aacaaagttttatttt  TA-rich tract