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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGTAGTCCTTAGCACTATAGTCACAAAATGGAGCGAGCTGTCTCATAAGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatgtccctgttgcattacttgttttgtttgactgtttatgatgtttgtttcattcttatgtatatgcaatgtgatgctatcctttgcatagta...

Basic information

species Oryza sativa
transcript LOC_Os01g03760.1
intron # 9
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|88224099|gb|CI223948.1|CI223948
EST:     TGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: TGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|218498275|gb|FG950557.1|FG950557
EST:     AGCTCCGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|27548128|gb|CA766270.2|CA766270
EST:     AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|9055399|gb|AU097597.1|AU097597
EST:     AGCTCAGTGCTGAATCTCTTAA-GTGACTCTGAAGAACTTAAGGACTAAG                         AATGA-NCGCCCCTAGAANCAGCAACGGACTCTGGAAAGCAGNCATCTATC
genomic: AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|86498653|gb|CI141286.1|CI141286
EST:     TAAGGTGACTCTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: TAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|88570918|gb|CI662291.1|CI662291
EST:     AGCTCAGCGCTGAATCTCTTAAGGTGACACTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|88346801|gb|CI657352.1|CI657352
EST:     AGCTCAGTGCTGAATCTCTTAAGGTGACACTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|38477248|gb|CF961381.1|CF961381
EST:     AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
EST: gi|29645236|gb|CB650243.1|CB650243
EST:     AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAG                         AATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC
genomic: AGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatg ... gcaattgcagAATGAGGCGGCCCTAGAAGCAGCAACGGACTCTGGAAAGCAGGCATCTATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGTAGTCCTTAGCACTATAGTCACAAAATGGAGCGAGCTGTCTCATAAGCTCAGTGCTGAATCTCTTAAGGTGACTCTGAAGAACTTAAGGACTAAGgtatgatatgtccctgttgcattacttgttttgtttgactgtttatgatgtttgtttcattcttatgtatatgcaatgtgatgctatcctttgcatagta

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC