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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgcatttcatgtatggacaattaagcgactgttgcagttaacatatatagatttttggacatgcacacagctcatgcatggttttttgtgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAGTGCGCTAAGATCCTATATCTCGTACGCTCTGAGCTGAAGTTCATGAAAT

Basic information

species Oryza sativa
transcript LOC_Os04g14654.1
intron # 4
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|88453003|gb|CI574550.1|CI574550
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAG                         GAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAA
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAA
EST: gi|88301457|gb|CI597150.1|CI597150
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGAC-TCACTGCTAAAG                         GAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
EST: gi|33677575|gb|CF305814.1|CF305814
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAG                         GAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
EST: gi|88350673|gb|CI617528.1|CI617528
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAG                         GAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTG
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTG
EST: gi|88723438|gb|CI746948.1|CI746948
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAG                         GAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAAC
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAAC
EST: gi|29635893|gb|CB640902.1|CB640902
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAG                         GAATATGGTGCANAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
EST: gi|117229564|gb|CT859877.1|CT859877
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAG                         GAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
EST: gi|29641506|gb|CB646513.1|CB646513
EST:     CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAG                         GAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG
genomic: CCAAGCTCGCGGGTACCCTGTCTCTGATTCTGCAGACCTCACTGCTAAAGgtgcgatgag ... tgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatagatttttggacatgcacacagctcatgcatggttttttgtgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAGTGCGCTAAGATCCTATATCTCGTACGCTCTGAGCTGAAGTTCATGAAAT
                                      ttttttgt  CT-rich tract
     agattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgcatttcatgtatggacaattaagcgactgttgcagttaacatatatagatttttggacatgcacacagctcatgcatggttttttgtgcttgtcagGAATATGGTGCAGAGTTGCGGCTTCTCTCTGCTGAACCCCTCCAAACTGAGTGCGCTAAGATCCTATATCTCGTACGCTCTGAGCTGAAGTTCATGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG