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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGTTCTCCATATGTAGCATCTGTTGCACCTGGAAGCATCCCAACAAGCTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctgattttcctttcaacttatgacccttctatataagcaaattgagactctagatttttattatttgtgatggcaatttctgtagaggaaatt...

Basic information

species Oryza sativa
transcript LOC_Os09g38790.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 4
GTAAGTTCTCCATATGTAGCATCTGTTGCACCTGGAAGCATCCCAACAAGCTCTCCATCAG---TTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaag---agctgattttcctttcaacttatgacccttctatataagcaaattgagactctagatttttattatttgtgatggcaatttctgtagaggaaatt
   | ||| |||| | ||||||||||||||||||||| ||| ||| ||||||||||| |||   | | |  ||||||| | ||||||| | | | ||||||||||| |   | || |     ||| | |  |     |  |  |  |  | | |||    |   ||    |      |  || |      ||| |   || |    
---AATTCCCCATTTTTAGCATCTGTTGCACCTGGAACCATTCCAGCAAGCTCTCCAGCAGCAGTCGGTGTTGCAGGAATTGGATATGGAACCAATAACCAAGgtatgttgatcttaaagctcttcctatgtcaatgcactgcaatttggtatattttcgcgaaagggcctctagcgtaatggttaaggcttccgagtagcac---
















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|88589372|gb|CI707242.1|CI707242
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCCTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|29680885|gb|CB677160.1|CB677160
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|29655595|gb|CB651870.1|CB651870
EST:     CTCTCCATCACTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGATGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|38475380|gb|CF959513.1|CF959513
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATACGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAAGAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|88588125|gb|CI705920.1|CI705920
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|88436645|gb|CI691377.1|CI691377
EST:     CTCTCCATCAGCTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|25797175|gb|CA753136.1|CA753136
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|95100848|gb|CI692566.1|CI692566
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|33679167|gb|CF307406.1|CF307406
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|88584106|gb|CI701634.1|CI701634
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTCCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|88586844|gb|CI704565.1|CI704565
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|95101217|gb|CI692956.1|CI692956
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|29624560|gb|CB629571.1|CB629571
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|88386761|gb|CI682916.1|CI682916
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTANTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|88584300|gb|CI701845.1|CI701845
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|88590829|gb|CI707721.1|CI707721
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
EST: gi|29680924|gb|CB677199.1|CB677199
EST:     CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAG                         GTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC
genomic: CTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctg ... tctgttccagGTACAGGAGGTCCAGCGGCTGTACCTCCACCCGCTTCTAATAATAAAGCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGTTCTCCATATGTAGCATCTGTTGCACCTGGAAGCATCCCAACAAGCTCTCCATCAGTTGCTCCTGCAGGAGTAGGATATGCAGCTACTAACCAAGgtaagagctgattttcctttcaacttatgacccttctatataagcaaattgagactctagatttttattatttgtgatggcaatttctgtagaggaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT