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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaatctccatgcattccattcaatttcatgaaacatatattttgcaaaagatactaaatgcattcccttctttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os11g04030.1
intron # 2
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|29680054|gb|CB676329.1|CB676329
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88359862|gb|CI617773.1|CI617773
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88356270|gb|CI613552.1|CI613552
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGAT-CTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|29674310|gb|CB670585.1|CB670585
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|29644401|gb|CB649408.1|CB649408
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88576396|gb|CI670541.1|CI670541
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTG
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTG
EST: gi|33677870|gb|CF306109.1|CF306109
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88334950|gb|CI648725.1|CI648725
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88330064|gb|CI652455.1|CI652455
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|33677492|gb|CF305731.1|CF305731
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88347612|gb|CI634297.1|CI634297
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|87008869|gb|CI304812.1|CI304812
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTG
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTG
EST: gi|88301079|gb|CI594605.1|CI594605
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGA
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGA
EST: gi|29682083|gb|CB678358.1|CB678358
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|29679865|gb|CB676140.1|CB676140
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88332574|gb|CI651734.1|CI651734
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88353644|gb|CI633035.1|CI633035
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|33678908|gb|CF307147.1|CF307147
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88330118|gb|CI650794.1|CI650794
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAA
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAA
EST: gi|29678070|gb|CB674345.1|CB674345
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88303400|gb|CI669048.1|CI669048
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG                         ATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATGgtaagtttaa ... tttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgaaacatatattttgcaaaagatactaaatgcattcccttctttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG
                          tactaaa  putative branch site (score: 1)
                                 tgcattcccttcttt  CT-rich tract
         atatattttgcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttaatctccatgcattccattcaatttcatgaaacatatattttgcaaaagatactaaatgcattcccttctttacaacagATAAGGGAATTGCATATTTCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA