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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGCCTGCCTGACAAGAGAGGCAGCAGCCATGGCGTTCGACGCCTTCACCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccag

Basic information

species Oryza sativa
transcript LOC_Os03g63710.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 1
GGCTGCCTGCCTGACAAGAGA--GGCAGCAGCCATGGCGTTCGACGCCTTCACCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcctcct-ctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccag
  | | |  |   | ||| ||   ||    ||    || ||||| || | ||||||||||||||||||||||||||| ||||||||||||||||||||||||||   | | |  | | | |  || |      |       | |||     | | | |    | | ||   ||   ||| | | ||            
--CCGGCAACTGCAGAAGCGACCAGCCATGGCGGCAGCCTTCGATGCTTACACCGACAAGAACGCCGTCTTCCGCCGTCTCAAGGCCAAGCCCGAGAACAAGgtgcgtgcgtattgccctgcgctgccatggatctagggcctcctgctccgccggctactgtct-ctcacatca-cgtctccctgcag---------

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G083546_T01 (Zea mays), 5'ss of exon 1
GGCTGCCTGCC-TGACAAGAGAGGCAGCAGCCATGGCGTTCGACGCCTTCACCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccag
 || ||  ||| || |    | ||| || ||   ||| ||||| |||| |||||||||||||||| ||||||||||||||||||||||||||||||||||||||  | | |  |  |    || | |   ||   |||  |||||  |  ||    |  ||   |   |    || | | ||||            
-GCAGCTAGCCATGGCGGCGGCGGCGGCGGCGGCGGCCTTCGATGCCTACACCGACAAGAACGCCATCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtacgtgcttattggcctgcctgcctgccctggatctaggcctcctgcttcg--ccggatcctcagatcacatc-tctccttgcag---------
















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|88739668|gb|CI763176.1|CI763176
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88364273|gb|CI612222.1|CI612222
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGGAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88302091|gb|CI667937.1|CI667937
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88826434|gb|CI776999.1|CI776999
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88361014|gb|CI604581.1|CI604581
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|428827|gb|D24983.1|D24983
EST:     CCGACAAGAACGCCGTNTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58658150|gb|CK046830.1|CK046830
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCCAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58664331|gb|CK053017.1|CK053017
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|66916299|gb|CX103147.1|CX103147
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88721612|gb|CI744911.1|CI744911
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88341494|gb|CI635692.1|CI635692
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29645173|gb|CB650180.1|CB650180
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58680319|gb|CK069006.1|CK069006
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58677850|gb|CK066537.1|CK066537
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|87006728|gb|CI285762.1|CI285762
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCCAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29677839|gb|CB674114.1|CB674114
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29635513|gb|CB640522.1|CB640522
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88288415|gb|CI661620.1|CI661620
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88723709|gb|CI747219.1|CI747219
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88351379|gb|CI627395.1|CI627395
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAT                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|11443001|gb|BF430888.1|BF430888
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29679055|gb|CB675330.1|CB675330
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|33654274|gb|CF276888.1|CF276888
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGCCTGCCTGACAAGAGAGGCAGCAGCCATGGCGTTCGACGCCTTCACCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccag

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