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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctattggtttttgctgcgtcattgtcatgttgtagtgctttatttggaatgatgactttgtgtcattcatactttcatgctaactgattatatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATCTTCCCGTGCACTTAATCGTGCTAATCAGATGAATGCTGGCAGTTCCCCG

Basic information

species Oryza sativa
transcript LOC_Os01g36840.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36840.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 14
tctattggtttttgctgcgtcattgtcatgttgtagtgct-ttatttggaatgatgactttgtgtcattcatactttcatgct--aactgattatatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATCTTCCCGTGCACTTAATCGTGCTAATCAGATGAATGCTGGCAGTTCCCCG
        | |     || | |   |||| ||| | || | || ||  ||   |||  ||  || |||  |    ||||| |   |||| ||| | |||| |||||||| |||||||||||| |||| |||||||||||||||||||||||| |  |||||||  |||||||||| ||||| ||||| | |||||||||||| 
--cgccattctccaaagc-ttaacatcatcttgaattgttcttgttatgaggaatgcattaatgccataaacgaattcattcctgaactaattctttttgcagGGACCTTCATTGCCATCGTGTTGGATATGACAACAAAAAATTACCTAAAGCAACCCGTGCTATTAATCGTGCCAATCATATGAACGGTGGCAGTTCCCCA
















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|116874995|gb|EC365503.1|EC365503
EST:     CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTG                         GGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
genomic: CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTGgtaaagtttt ... atatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
EST: gi|11171117|gb|AU163632.1|AU163632
EST:     CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACNG                         GGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
genomic: CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTGgtaaagtttt ... atatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
EST: gi|2443000|gb|C74771.1|C74771
EST:     CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTG                         GGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
genomic: CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTGgtaaagtttt ... atatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
EST: gi|116875003|gb|EC365511.1|EC365511
EST:     CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTG                         GGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
genomic: CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTGgtaaagtttt ... atatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
EST: gi|116875534|gb|EC366042.1|EC366042
EST:     CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTG                         GGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC
genomic: CTTTATCAAAGGCTGGAGAGCCGCTTGAAAGAAATGACATATGAATACTGgtaaagtttt ... atatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaatgatgactttgtgtcattcatactttcatgctaactgattatatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATCTTCCCGTGCACTTAATCGTGCTAATCAGATGAATGCTGGCAGTTCCCCG
                                    taactgattatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctattggtttttgctgcgtcattgtcatgttgtagtgctttatttggaatgatgactttgtgtcattcatactttcatgctaactgattatatttgtagGGACCTGCATTGCCATCGTATTGGTTATGACAACAAAAAATTACCTAAATCTTCCCGTGCACTTAATCGTGCTAATCAGATGAATGCTGGCAGTTCCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - tgctgcg
- - - - - - - - - - - - - catgttg
- - - - - - - - - - - - - - - - -tagtgct
- - - - - - - - - - - - - - - - - - - - - - - - -atgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctaa