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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctataacacctaatgattgactatgacacggctgtttcgagattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGGCTCCTCCAATGGGAGTGT

Basic information

species Oryza sativa
transcript LOC_Os01g68860.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 6
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctata--acacct-----aatgattgactat---gacacggctgtttcgagattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGGCTCCTCCAATGGGAGTGT
          |    || |||  |  | |  ||| |  |  | | | || | | |   ||||||     |||| |   | ||   ||     ||||     | |||| |||| |||||||| ||||| ||||||||||| ||||||||||||||||||||||| || || |||||||| ||||| || |||||| ||||||||||||| |
----------tacaaataaagcctgtctcacgaataggcactagctagtccttctggtacacctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGGCTGCTCCAATGGGAGTTT

upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 5
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctataacacctaatgattgactatgacacggctgtttcga---gattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGGCTCCTCCAATGGGAGTGT-
    || |   |         ||   |||| || |   | |||| |    |  ||   |     || | | || |||     ||||  | |   | ||||||||| |||||||||||||| ||||||||||| || |||||||||||||||||||| || || ||||| |||||||| ||  ||| | |||||||||   | | 
-aaatagagcctgtctcatcaataggcactagatagtccttttgctgcacctcattgaatggcctg-tcgtct-tgattatcctgtccccaatggtttttcagGGTGAAGAACTGTGCAAATTCTATTCTCGTTACGGCATCTGCAAGTTCGGCGCCAACTGTAAATTCGACCATCCTACAGTGGTTGCTCCAATGGTC-TATG

upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctataacacctaatgattgactatgacacggctgtttcgagattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGG-CTCCTCCAATGGGAGTGT
      ||   || ||  |   || | | |         | || || || |  || |       || |  | | |      |||| || || |    |||||||||  |||||||  |||||||||||| ||||| ||||||||||| ||  | |  || |||||||| || || | |   | || | |  |    |    
-----gtaagctaataaaagacttcagattct-----ttcctttatagt-ctcattatgtggtttggtaaattct--tgttgctggtttgaaa----cagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-

upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctataaca-cctaatgattgactatgacacggctgtttcgagatttt----cagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGG-CTCCTCCAATGGGAGTGT
  ||    |  |  || |     |||      |||| || |  |||| || |  | | |  || || ||    | ||  |      | | |    |||    |||||||||  |||||||  |||||||||||| ||||| ||||||||||| ||  | |  || |||||||| || || | |   | || | |  |    |    
gttggccttcctt-tacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-

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|29684893|gb|CB681168.1|CB681168
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|27334438|gb|CA882889.1|CA882889
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|87006969|gb|CI275277.1|CI275277
EST:     TGCCTACTCCAGATTGTCTCTTGAGTCCAGTGGGTCTTCCACTACGCCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|87007226|gb|CI277301.1|CI277301
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|88959678|gb|CI002288.1|CI002288
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCCTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|18386749|gb|BM419947.1|BM419947
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|88532353|gb|CI461836.1|CI461836
EST:     TCCAGATTGTGTCTTGAGTCCAGTGGTTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|29658444|gb|CB654719.1|CB654719
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|88974704|gb|CI023000.1|CI023000
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
EST: gi|88836402|gb|CI078299.1|CI078299
EST:     TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCG                         GGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: TGCCTACTCCAGATTGTGTCTTGAGTCCAGTGGGTCTTCCACTACGTCCGgtaagttact ... agattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcctataacacctaatgattgactatgacacggctgtttcgagattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGGCTCCTCCAATGGGAGTGT
                    gattgac  putative branch site (score: 3)
                                                ttttc  putative PPT
                taatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctataacacctaatgattgactatgacacggctgtttcgagattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGGCTCCTCCAATGGGAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC