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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttctcacatagctatgcattcattataacatcctattggcttcctttccgtcctagtttgataatttgctaatgccttgctgttactaaccgtc...

Basic information

species Oryza sativa
transcript LOC_Os01g48990.1
intron # 11
splice site 5'
intron type U2

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|88282514|gb|CI403910.1|CI403910
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTTTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88464777|gb|CI512082.1|CI512082
EST:     GAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTNCCC
genomic: GAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88563944|gb|CI494661.1|CI494661
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88437594|gb|CI511495.1|CI511495
EST:     AACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: AACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|29687191|gb|CB683466.1|CB683466
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|89181456|gb|CI112962.1|CI112962
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88224956|gb|CI224872.1|CI224872
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88379134|gb|CI508652.1|CI508652
EST:     ATAGCTATGAGAGCANATGGGAAACCAGGAATGTCTNATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: ATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|86524944|gb|CI165150.1|CI165150
EST:     CAGAGATAGCCATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88285389|gb|CI507259.1|CI507259
EST:     ATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: ATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88254825|gb|CI351453.1|CI351453
EST:     CAGAGATAGCTATGAGACCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCCCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88462332|gb|CI511997.1|CI511997
EST:     AATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: AATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88419202|gb|CI511354.1|CI511354
EST:     CAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88454733|gb|CI511705.1|CI511705
EST:     ATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTTTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: ATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88437587|gb|CI511488.1|CI511488
EST:     ACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: ACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|86425592|gb|CI070689.1|CI070689
EST:     CAGAGANAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88449163|gb|CI560624.1|CI560624
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88228493|gb|CI227973.1|CI227973
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88285431|gb|CI507301.1|CI507301
EST:     ACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: ACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88484705|gb|CI421976.1|CI421976
EST:     ATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: ATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|86853793|gb|CI329239.1|CI329239
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88318826|gb|CI508422.1|CI508422
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTNTTTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|86872693|gb|CI341903.1|CI341903
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         TTCATGGATTTTGTGTCCCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88565200|gb|CI495917.1|CI495917
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|86865914|gb|CI335530.1|CI335530
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         CTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88462165|gb|CI511830.1|CI511830
EST:     AGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: AGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88378562|gb|CI506266.1|CI506266
EST:     GGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: GGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88539149|gb|CI468237.1|CI468237
EST:     CAGANATAGCTATTAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         TTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTNCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88462016|gb|CI504514.1|CI504514
EST:     GGAAACCAGGAATTTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: GGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88995282|gb|CI036857.1|CI036857
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|29626889|gb|CB631900.1|CB631900
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88564728|gb|CI495445.1|CI495445
EST:     AGAGATAGCTATGAGAGGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         TTCATGGATTTTGTTTCNCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: AGAGATAGCTATGAGA-GCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|86496003|gb|CI138636.1|CI138636
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88467773|gb|CI507198.1|CI507198
EST:     CAGATGGGAAACCAGGAATGTCTGATGAGGGAG                         TTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCC
genomic: CAGATGGGAAACCAGGAATGTCTGATGA-GGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCC
EST: gi|88549854|gb|CI479780.1|CI479780
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTNTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88437529|gb|CI511430.1|CI511430
EST:     GAAACCAGGAATGTCTGATGAGGAG                         TTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: GAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|109712615|gb|CI105223.1|CI105223
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88975066|gb|CI023317.1|CI023317
EST:     CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
EST: gi|88661613|gb|CI457222.1|CI457222
EST:     CAGAGATAGCTATGAGAGCANATGGGAAACCAGGAATGTCTGATGAGGAG                         GTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC
genomic: CAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttct ... attcttgcagGTCATGGATTTTGTGTCGCGCTACCTACCAGCATACCACGCATATTTGCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAGgtttgtttctcacatagctatgcattcattataacatcctattggcttcctttccgtcctagtttgataatttgctaatgccttgctgttactaaccgtc

- - - - - - -  AGAGCA
- - - - - - - - GAGCAG
- - - - - - - - - GCAGAT
- - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - -  GAGGAG