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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtatgctctaatgtgatttgagcagctattatccttttcatatttgccaattcagttcagttccttctcttattgctctgttcctttcttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG

Basic information

species Oryza sativa
transcript LOC_Os01g71300.2
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|88667209|gb|CI715367.1|CI715367
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|89171382|gb|CI720441.1|CI720441
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88973956|gb|CI718364.1|CI718364
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88672977|gb|CI727092.1|CI727092
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88675003|gb|CI729116.1|CI729116
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88594517|gb|CI714475.1|CI714475
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88674163|gb|CI728276.1|CI728276
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88676307|gb|CI730420.1|CI730420
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88905121|gb|CI712420.1|CI712420
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|89172489|gb|CI721548.1|CI721548
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|89172386|gb|CI721445.1|CI721445
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88669850|gb|CI723966.1|CI723966
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88594817|gb|CI714775.1|CI714775
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88676329|gb|CI730442.1|CI730442
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88674672|gb|CI728785.1|CI728785
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88667436|gb|CI722175.1|CI722175
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88595192|gb|CI715348.1|CI715348
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88673403|gb|CI727516.1|CI727516
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88594033|gb|CI713987.1|CI713987
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAN                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88673631|gb|CI727744.1|CI727744
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88593847|gb|CI713801.1|CI713801
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88670559|gb|CI724675.1|CI724675
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88954490|gb|CI718469.1|CI718469
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88675254|gb|CI727369.1|CI727369
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88672556|gb|CI726672.1|CI726672
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88675704|gb|CI729817.1|CI729817
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88675991|gb|CI730104.1|CI730104
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|33793279|gb|CF322520.1|CF322520
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|29670940|gb|CB667215.1|CB667215
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccaattcagttcagttccttctcttattgctctgttcctttcttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
             ttcagttccttctctt  CT-rich tract
                         tcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtatgctctaatgtgatttgagcagctattatccttttcatatttgccaattcagttcagttccttctcttattgctctgttcctttcttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG