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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttcaaaactaacttttctatattatagtttcaactaacttgtctatattatagtttcaactccttacataaacatgtctggtgtatgtacttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCAGGTAACAACCTCATTCAGGGAGCCTATGCGCGGGATAAATAGAGATAGC

Basic information

species Oryza sativa
transcript LOC_Os02g53210.4
intron # 9
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|29674942|gb|CB671217.1|CB671217
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|22306999|gb|BQ908221.1|BQ908221
EST:     TTGTGAAGGCACACCGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACACGTGGGCCTGGCAACTTGACTTGCC
genomic: TTGTGAAGGCACA-CGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACA-GTGGGCCTGGCAACTTGACTTGCC
EST: gi|87031749|gb|CI272450.1|CI272450
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|38482043|gb|CF966104.1|CF966104
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|86862924|gb|CI331739.1|CI331739
EST:     ATACCACCTCTTGTGAAGGCACACGGA-GTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|89189355|gb|CI048894.1|CI048894
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|33692951|gb|CF321190.1|CF321190
EST:     GTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: GTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|88836029|gb|CI371134.1|CI371134
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|58693404|gb|CK082091.1|CK082091
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|86827594|gb|CI272900.1|CI272900
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACTGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|29631130|gb|CB636139.1|CB636139
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|89192271|gb|CI049732.1|CI049732
EST:     ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: ATACCACCTCTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|86862439|gb|CI345531.1|CI345531
EST:     CTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: CTTGTGAAGGCACACGGAGGTATTCTAGTCAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
EST: gi|88258867|gb|CI359257.1|CI359257
EST:     CAAAATCATCCT                         CAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA
genomic: CAAAATCATCCTgtaagtcctt ... acttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattatagtttcaactccttacataaacatgtctggtgtatgtacttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCAGGTAACAACCTCATTCAGGGAGCCTATGCGCGGGATAAATAGAGATAGC
                 tccttac  putative branch site (score: 2)
                                            tacttct  putative PPT
                    ttacataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttcaaaactaacttttctatattatagtttcaactaacttgtctatattatagtttcaactccttacataaacatgtctggtgtatgtacttctgtagCAAAGGAAAACTCACACGAGATAACAGTGGGCCTGGCAACTTGACTTGCCAGGTAACAACCTCATTCAGGGAGCCTATGCGCGGGATAAATAGAGATAGC

- - - aaactaa
- - - - - - - - - - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtatg