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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttcatcgccatttttactgaggagaccgatttcaattttctattctttatatttggttaagacaaatagatcgctttgttgcatctactcaactaactactatttttgtttgtttgcaaatgttttcccttctattgtgtaactccttttgacttctaatttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATACGTTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g16170.2
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|29677586|gb|CB673861.1|CB673861
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29641025|gb|CB646032.1|CB646032
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29663395|gb|CB659670.1|CB659670
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29678252|gb|CB674527.1|CB674527
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29664316|gb|CB660591.1|CB660591
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29621708|gb|CB626719.1|CB626719
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29681320|gb|CB677595.1|CB677595
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29676459|gb|CB672734.1|CB672734
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29677836|gb|CB674111.1|CB674111
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29664315|gb|CB660590.1|CB660590
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
EST: gi|29639706|gb|CB644715.1|CB644715
EST:     AAATATGAAAAGAGGGAATGCTGAG                         GGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC
genomic: AAATATGAAAAGAGGGAATGCTGAGgcaagttcat ... tttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaatgttttcccttctattgtgtaactccttttgacttctaatttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATACGTTGGAAG
                                       ttctaat  putative branch site (score: 2)
                                             tttcattc  CT-rich tract
                                          taatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttcatcgccatttttactgaggagaccgatttcaattttctattctttatatttggttaagacaaatagatcgctttgttgcatctactcaactaactactatttttgtttgtttgcaaatgttttcccttctattgtgtaactccttttgacttctaatttcattcagGGACTCAATCCACTAATGTTTACTTTTGCATTAGTGGGAAATGTGACATACGTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG