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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcattaccagatttatctaagtaactaatggtgtcagaaaatgcacaaccatgaattgcaattttcttatgttatttggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g48990.1
intron # 10
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|88563944|gb|CI494661.1|CI494661
EST:     CTAGTTGCGTNTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: CTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|29687191|gb|CB683466.1|CB683466
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|89181456|gb|CI112962.1|CI112962
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88224956|gb|CI224872.1|CI224872
EST:     AAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: AAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|86524944|gb|CI165150.1|CI165150
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCCATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88254825|gb|CI351453.1|CI351453
EST:     TGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGACCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|86425592|gb|CI070689.1|CI070689
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGANAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88228493|gb|CI227973.1|CI227973
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|86853793|gb|CI329239.1|CI329239
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88318826|gb|CI508422.1|CI508422
EST:     GCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: GCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|86872693|gb|CI341903.1|CI341903
EST:     TAAA-GAACCTAGTTGCGTGTACCAGTGGAGACTCCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|86865914|gb|CI335530.1|CI335530
EST:     GTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAATGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: GTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88539149|gb|CI468237.1|CI468237
EST:     TACCAGTGGAGACTGCAG                         GCAGANATAGCTATTAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88995282|gb|CI036857.1|CI036857
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|29626889|gb|CB631900.1|CB631900
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88564728|gb|CI495445.1|CI495445
EST:     CCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGGCAGATGGGAAACCAGGAATGTCTGATGAGGA
genomic: CCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGA-GCAGATGGGAAACCAGGAATGTCTGATGAGGA
EST: gi|86496003|gb|CI138636.1|CI138636
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGAGTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88549854|gb|CI479780.1|CI479780
EST:     TTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|109712615|gb|CI105223.1|CI105223
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
EST: gi|88975066|gb|CI023317.1|CI023317
EST:     TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAG                         GCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
genomic: TGGTCATAAAAATAAAGGAACCTAGTTGCGTGTACCAGTGGAGACTGCAGgtcattacca ... ggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagaaaatgcacaaccatgaattgcaattttcttatgttatttggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG
                           aattttcttatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattaccagatttatctaagtaactaatggtgtcagaaaatgcacaaccatgaattgcaattttcttatgttatttggatttacagGCAGAGATAGCTATGAGAGCAGATGGGAAACCAGGAATGTCTGATGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG