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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattataatctaatcccaattcccagatccagtccaagtcccactaatagaagcagtgatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTACCAGGAGGATGATAATAATCTGGTCGGCTGGTCTGCTACATGCCTGCTAT

Basic information

species Oryza sativa
transcript LOC_Os01g35160.1
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|88367457|gb|CI566423.1|CI566423
EST:     GTCACAGAGTCAAACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88379034|gb|CI681864.1|CI681864
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88458178|gb|CI695136.1|CI695136
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88851664|gb|CI674866.1|CI674866
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTACCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88358780|gb|CI649329.1|CI649329
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88313503|gb|CI671623.1|CI671623
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88592315|gb|CI710413.1|CI710413
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88579828|gb|CI691814.1|CI691814
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88590201|gb|CI709034.1|CI709034
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|58652619|gb|CK041299.1|CK041299
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
EST: gi|88371985|gb|CI681502.1|CI681502
EST:     GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAG                         GTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC
genomic: GTCACAGAGTCACACACACCCTGTCGAGCGAATATGCATGTCTTCTCAAGgtattataat ... gatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccaattcccagatccagtccaagtcccactaatagaagcagtgatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTACCAGGAGGATGATAATAATCTGGTCGGCTGGTCTGCTACATGCCTGCTAT
                             cactaat  putative branch site (score: 2)
                                               tttttc  putative PPT
                                taatagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattataatctaatcccaattcccagatccagtccaagtcccactaatagaagcagtgatttttcagGTCTAGCTAGCCATCCACTCGAACTCTCTTGTTCTTGTTACCCAGATCTACCAGGAGGATGATAATAATCTGGTCGGCTGGTCTGCTACATGCCTGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG