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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtcaagatgctcatgctctttctcaagttttcctaacacatgagcatattattcagaggggaaaaaaatctgtgtggactaacttttcctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAAGAAGCAAACGTGTGCTTTTTATGTGAGGTCAAGCAAGATAATTTTTCGA

Basic information

species Oryza sativa
transcript LOC_Os12g13130.2
intron # 10
splice site 3'
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|88690274|gb|CI734353.1|CI734353
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCC
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCC
EST: gi|86841250|gb|CI342973.1|CI342973
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88374442|gb|CI515926.1|CI515926
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88849353|gb|CI087875.1|CI087875
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88482726|gb|CI419997.1|CI419997
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88304334|gb|CI515607.1|CI515607
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88303968|gb|CI513042.1|CI513042
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88382508|gb|CI535716.1|CI535716
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88688437|gb|CI732013.1|CI732013
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATG
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATG
EST: gi|29645805|gb|CB650812.1|CB650812
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTTTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|29645769|gb|CB650776.1|CB650776
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88260579|gb|CI362872.1|CI362872
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
EST: gi|88222581|gb|CI222537.1|CI222537
EST:     ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT                         CCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA
genomic: ACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATTgtaagttgcc ... ctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatattattcagaggggaaaaaaatctgtgtggactaacttttcctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAAGAAGCAAACGTGTGCTTTTTATGTGAGGTCAAGCAAGATAATTTTTCGA
                                 gactaac  putative branch site (score: 1)
                                       cttttcctattttc  CT-rich tract
                  aaaaaaatct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtcaagatgctcatgctctttctcaagttttcctaacacatgagcatattattcagaggggaaaaaaatctgtgtggactaacttttcctattttcagCCATGCCCTGCTTCTTCCCTATGCAGCCCCTCATGCAGATGCAATCGTCAAGAAGCAAACGTGTGCTTTTTATGTGAGGTCAAGCAAGATAATTTTTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA