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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacatttcatgtcatcataaccctgccgatctcaaagacaagcacaacatgatttaaattgcacaagcaatattaatcagtatgcctcatttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAGCAGCGATGCAAGGCTTGAGCTTCTGTGAAGATAATGACCTAAAGGCTAG

Basic information

species Oryza sativa
transcript LOC_Os03g06120.3
intron # 7
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|25806375|gb|CA762336.1|CA762336
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|87021652|gb|CI276051.1|CI276051
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88961682|gb|CI096900.1|CI096900
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88269959|gb|CI381257.1|CI381257
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88413197|gb|CI523758.1|CI523758
EST:     ATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: ATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|86542310|gb|CI182516.1|CI182516
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|16753523|gb|BM037902.1|BM037902
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88961463|gb|CI096770.1|CI096770
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|44674180|gb|CR287614.1|CR287614
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88273954|gb|CI394360.1|CI394360
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|29637808|gb|CB642817.1|CB642817
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|33803496|gb|CF327623.1|CF327623
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88459853|gb|CI524312.1|CI524312
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGAGTAAGATTAGCCCACCCTCATTTCAGTACATGGAACAGTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88474728|gb|CI411999.1|CI411999
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|86845185|gb|CI340315.1|CI340315
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGGTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|89169017|gb|CI020557.1|CI020557
EST:     CTGTGCGCTTGTTCAAGAATGGCGGAAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|86865997|gb|CI336768.1|CI336768
EST:     CTTTGCGCTTGTTCAAGAAT-GCCGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88374950|gb|CI521016.1|CI521016
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88960115|gb|CI381993.1|CI381993
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|89178286|gb|CI391465.1|CI391465
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAG-TGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAA
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACT-AA
EST: gi|88851118|gb|CI373876.1|CI373876
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88962482|gb|CI097634.1|CI097634
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88846689|gb|CI373457.1|CI373457
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|58596859|gb|CK007387.1|CK007387
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88286952|gb|CI520262.1|CI520262
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|87034567|gb|CI189191.1|CI189191
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGAGTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|86886085|gb|CI321121.1|CI321121
EST:     CTGTGCGCTTTTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88906222|gb|CI375294.1|CI375294
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTTGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
EST: gi|88250929|gb|CI248780.1|CI248780
EST:     CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG                         GAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG
genomic: CTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATGgtgagtttcc ... tttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacatgatttaaattgcacaagcaatattaatcagtatgcctcatttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAGCAGCGATGCAAGGCTTGAGCTTCTGTGAAGATAATGACCTAAAGGCTAG
                          tattaat  putative branch site (score: 2)
                                        cctcatttcct  putative PPT
                        aatattaatcagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacatttcatgtcatcataaccctgccgatctcaaagacaagcacaacatgatttaaattgcacaagcaatattaatcagtatgcctcatttcctgcagGAGAGAGGACTAAGATTAGCCCACCCTCATTTCAGTACATGGAACACTAAGCAGCGATGCAAGGCTTGAGCTTCTGTGAAGATAATGACCTAAAGGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA