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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctcttgttcttttcccagtccttttccatcaagattggtcccaattcaaattcatcatgattttcctgaaacaatatttgtactgatgtatgtg...

Basic information

species Oryza sativa
transcript LOC_Os06g33710.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G047867_T01 (Zea mays), 5'ss of exon 3
GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctcttgttcttttcccagtccttttccatcaagattggtcccaattcaaattcatcatgattttcctgaaacaatatttgtactgatgtatgtg------
|||||||||||||||||||||||||||| || || |||||||||||||||||||||||  || |   |  |  |    ||  | ||| | |    ||    |    ||  || |||  |   ||   | | |  |||| ||          
GTAAAACAAGCAAAGTGCAGTACTTCAATAACCCGATGTGGCCTGgtatttctcttgt--ttctgaaaaacaata---atagaaatttgccatgttttttttcttccaacatcttca-ggttcacattgtatgatgatataaaacttggtc
















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|29677612|gb|CB673887.1|CB673887
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29678039|gb|CB674314.1|CB674314
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29661773|gb|CB658048.1|CB658048
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29660327|gb|CB656602.1|CB656602
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29657057|gb|CB653332.1|CB653332
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29681267|gb|CB677542.1|CB677542
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|88431166|gb|CI574337.1|CI574337
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29681920|gb|CB678195.1|CB678195
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29674257|gb|CB670532.1|CB670532
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29657894|gb|CB654169.1|CB654169
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|58690531|gb|CK079218.1|CK079218
EST:     CTCTGGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: CTCTGGTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
EST: gi|29639074|gb|CB644083.1|CB644083
EST:     GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTG                         GAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC
genomic: GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctct ... ttatacacagGAGAAGCTCATTCTCTGAAAGTAGAGAATATTCTGTATCAAGGGAAATCAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAAACAAGCAAAGTGCAGTACTTCAACAATCCAATGTGGCCTGgtatttctcttgttcttttcccagtccttttccatcaagattggtcccaattcaaattcatcatgattttcctgaaacaatatttgtactgatgtatgtg

- - -  AAGCAA
- - - -  GCAAAG