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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactatacaggctgaatttttcaatagctgaatatttgcagcttggcttgatatatattcatctatagtaaaattgaagttctatgccactgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGA

Basic information

species Oryza sativa
transcript LOC_Os12g06810.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 1
aactatacaggctgaa--tttttcaatagctgaatatttgcagcttggcttgatatatattcatctatagtaaaattg-aagttctatgccactgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGA---------
    ||||  ||||||   | ||   |       |||      |    || | ||| |  | || | |||     ||  ||  | | |  ||||| |||| ||| | |  || ||||  |||| |||||| ||      | |||||||||||||||||| |||||||||||||| || || || | |||||||||||| ||||         
--agatacttgctgaaagctatttcttcttgcgctatgatggaccatactagctattttgtgat-tctagcgcccttacaaaatatttatcactgctttgcagGTTTT--GCCGCTCGAGTTT-AGATAAGTT------CCTTCAATGCATCGTGTTGGGAGTGCTGGTAACACAGCTGGCTCGACTCGACCGAGAAAAGAGAAGCGCTTCA
















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|88357841|gb|CI625092.1|CI625092
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88423157|gb|CI613458.1|CI613458
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88398573|gb|CI598538.1|CI598538
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88299650|gb|CI574763.1|CI574763
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88731171|gb|CI754784.1|CI754784
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88392717|gb|CI623948.1|CI623948
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88333238|gb|CI641081.1|CI641081
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88427243|gb|CI586791.1|CI586791
EST:     CTCCGCCT-CCTGCCTCGCCGCCGCGCG-CACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGG-TTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88720333|gb|CI743632.1|CI743632
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88299299|gb|CI572251.1|CI572251
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88385685|gb|CI566547.1|CI566547
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88575849|gb|CI669994.1|CI669994
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|58659315|gb|CK047995.1|CK047995
EST:     CTCCGCCTCCCTGCCTCGCCGCCGGG-GCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88357189|gb|CI616076.1|CI616076
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88360459|gb|CI608461.1|CI608461
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88350674|gb|CI617529.1|CI617529
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88730866|gb|CI754479.1|CI754479
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88352046|gb|CI626046.1|CI626046
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88372748|gb|CI612676.1|CI612676
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88725276|gb|CI748535.1|CI748535
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88392951|gb|CI614833.1|CI614833
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGGTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88351371|gb|CI627387.1|CI627387
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88581848|gb|CI699062.1|CI699062
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88411008|gb|CI606227.1|CI606227
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCAACTCGCCGTCGAATCGAAG                         GCTATAAGCTGCT-CGGTTTTAGAT-AATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88315130|gb|CI611794.1|CI611794
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88356655|gb|CI617738.1|CI617738
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88405503|gb|CI588709.1|CI588709
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|117217320|gb|CT852008.1|CT852008
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88311817|gb|CI577423.1|CI577423
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCAACTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|29666968|gb|CB663243.1|CB663243
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88729484|gb|CI752994.1|CI752994
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88351353|gb|CI627369.1|CI627369
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88431514|gb|CI579631.1|CI579631
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
EST: gi|88299553|gb|CI574666.1|CI574666
EST:     CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAG                         GCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT
genomic: CTCCGCCTCCCTGCCTCGCCGCCGCGCGCCACCTCGCCGTCGAATCGAAGgtacggtact ... tgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgatatatattcatctatagtaaaattgaagttctatgccactgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGA
                                          cactgat  putative branch site (score: 3)
     atatatattcatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactatacaggctgaatttttcaatagctgaatatttgcagcttggcttgatatatattcatctatagtaaaattgaagttctatgccactgatttgtagGCTATAAGCTGCTCCGGTTTTAGATAAATTAGGCATCTTTCAATGCATCGTGTTGGAAGTGCTGGTAACACGGCAGGTTCAAGTCGACCGAGAAAGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - -caggctg
- - - - - gctgaat
- - - - - - - - - - - - - - - - - -ttgcagc
- - - - - - - - - - - - - - - - - - - - - -tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgcc