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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtttttctcggcctttgtcatgtttctcttataattaatatcgcgttacctcttaaaattctcttagaaccatataaaacagaaggttgaaac...

Basic information

species Oryza sativa
transcript LOC_Os11g08300.1
intron # 8
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|38468735|gb|CF952866.1|CF952866
EST:     ACACTCATGGCAGANGGAAATTTTTGGTCCNCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: ACACTCATGGCAGA-GGAAATTTTTGGTCC-CTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29639823|gb|CB644832.1|CB644832
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29659085|gb|CB655360.1|CB655360
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|58587745|gb|CF986053.1|CF986053
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29660180|gb|CB656455.1|CB656455
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29643719|gb|CB648726.1|CB648726
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29665741|gb|CB662016.1|CB662016
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|58687760|gb|CK076447.1|CK076447
EST:     ACACTCATGGCAGAGGAAA-TTTTGGTCCCTTACTTCCCA-TGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: ACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29680880|gb|CB677155.1|CB677155
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29670820|gb|CB667095.1|CB667095
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29666336|gb|CB662611.1|CB662611
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29665740|gb|CB662015.1|CB662015
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29660176|gb|CB656451.1|CB656451
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|58588762|gb|CF987070.1|CF987070
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGGCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29660181|gb|CB656456.1|CB656456
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29645893|gb|CB650900.1|CB650900
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29658062|gb|CB654337.1|CB654337
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29677331|gb|CB673606.1|CB673606
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|29683211|gb|CB679486.1|CB679486
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|33675797|gb|CF304036.1|CF304036
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|58588330|gb|CF986638.1|CF986638
EST:     AACACTCAGTGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: AACACTCA-TGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
EST: gi|86831182|gb|CI297451.1|CI297451
EST:     CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACA                         GTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA
genomic: CAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtt ... tggttcctagGTTGACAAGATTGAAGATAGCATCCAGTTCATCAACTCAAGGACCAAGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAATAGCTCCTACTGTGTTGTTAGATGTTCCTCTTGATACAACACTCATGGCAGAGGAAATTTTTGGTCCCTTACTTCCCATTGTAACAgtaagtggtttttctcggcctttgtcatgtttctcttataattaatatcgcgttacctcttaaaattctcttagaaccatataaaacagaaggttgaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA