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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgcttttccatcctagtttcattttcatgtagtgtcagcataatctgaaagtacatgctgtgctcatcag

Basic information

species Oryza sativa
transcript LOC_Os03g62640.2
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|29665629|gb|CB661904.1|CB661904
EST:     GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|86502553|gb|CI145186.1|CI145186
EST:     GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|18385491|gb|BM418690.1|BM418690
EST:     CAGGAGTAGAGAAGTAAAAGAAGGAAGCCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAGGGACCGCCAATGGTCAGGCATCCAGGGATAGAG
genomic: CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCG-CAATGGTCAGGCATCCAGGGATAGAG
EST: gi|87008593|gb|CI315051.1|CI315051
EST:     AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|88842454|gb|CI081710.1|CI081710
EST:     AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|88223512|gb|CI223361.1|CI223361
EST:     CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|58682879|gb|CK071566.1|CK071566
EST:     GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|454535|gb|D28304.1|D28304
EST:     GAGGAGAGAAGTAAAAGAAGGAAGGCACCTTAAGATGACAGGCG                         ATCAAGAGA-TACAGCAAGGACCGNA-TGGTCAGGCATCCAGGGTTAGAG-
genomic: GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|86499113|gb|CI141746.1|CI141746
EST:     GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|86886570|gb|CI322802.1|CI322802
EST:     CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAACATGACAGGCG                         ATCAATAGAATACAGCAAGGACCGCAAT-GTCAGGCATCCAGGGATAGAGA
genomic: CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29664073|gb|CB660348.1|CB660348
EST:     GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|88841254|gb|CI080708.1|CI080708
EST:     ACAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: ACAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29661288|gb|CB657563.1|CB657563
EST:     GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|86256324|gb|CI012614.1|CI012614
EST:     CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgcttttccatcctagtttcattttcatgtagtgtcagcataatctgaaagtacatgctgtgctcatcag

 AGGAGA
- - - AGAAGT
- - - - - -  AAAGAA
- - - - - - - AAGAAG
- - - - - - - -  AAGGAA
- - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - -  AAGATG