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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatccacatcccctttctgatgaatcattcatctctctcccacctggagtagttttttttttgtctggaattcgctcgcgttcgttaaccctagctttctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTCCCCCAAAAAGTTTGCTTCCTGGGATTACTACGAGGAGGAGGAGAGGGGA

Basic information

species Oryza sativa
transcript LOC_Os02g15870.1
intron # 1
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|88742626|gb|CI766134.1|CI766134
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|29675363|gb|CB671638.1|CB671638
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88424077|gb|CI689779.1|CI689779
EST:     GAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|29631823|gb|CB636832.1|CB636832
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88736013|gb|CI759521.1|CI759521
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88765983|gb|CI775073.1|CI775073
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88734603|gb|CI758111.1|CI758111
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88403375|gb|CI573098.1|CI573098
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88740170|gb|CI763678.1|CI763678
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88762354|gb|CI771910.1|CI771910
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAANAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|33654216|gb|CF276830.1|CF276830
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|29631793|gb|CB636802.1|CB636802
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
EST: gi|88732838|gb|CI756015.1|CI756015
EST:     GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAG                         ATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC
genomic: GTCGAGGCGAGCAGAGCAGGGGAGCCGGGAGGGGAGGGCATCCTGGTGAGgtgagcatcc ... tctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttgtctggaattcgctcgcgttcgttaaccctagctttctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTCCCCCAAAAAGTTTGCTTCCTGGGATTACTACGAGGAGGAGGAGAGGGGA
                              cgttaac  putative branch site (score: 3)
                                    ccctagctttctctt  CT-rich tract
     tttttgt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatccacatcccctttctgatgaatcattcatctctctcccacctggagtagttttttttttgtctggaattcgctcgcgttcgttaaccctagctttctcttgtagATCTGGAAGAAGCTCTCCTCTTAATTAACCTGTGTAAAAGTTTGTTTGTTCCCCCAAAAAGTTTGCTTCCTGGGATTACTACGAGGAGGAGGAGAGGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG