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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatattgcatttagtagaccatgatccattttgctactcttttgcttaagtagacagttgtacccatttccttatgctactatgtttttacctttgcagGAGGAAATCCAGAAGAAAACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTG

Basic information

species Oryza sativa
transcript LOC_Os03g39640.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G153928_T03 (Zea mays), 3'ss of exon 4
---acatattgcatttagtagaccatgatccattttgctactcttttgcttaagtagacagttgtacccatttccttatgctactatgttttt-acctttgcagGAGGAAATCCAGAAGAAAACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTG
    |   || | |||   |    |  | | | ||  ||| | | | | ||   ||||||||    | || ||||||  |||||| ||||||| ||| || |||||||||||||||||||||||||| |||||||| | || ||  || ||||||||||| ||||||||||| ||||| ||||| |||||||||||||| ||||
caagctggttactttttccatgttacaagctagtt-acta-tttgtcgtttgcttagacagtc--tctcaattccttccgctactctgtttttcaccctttcagGAGGAAATCCAGAAGAAAACAGGCTATATAGTAAGGCGGGGGGATGGAACATTTGATGTTGATGCAAACACATCGATAGATCACCTATCTGAAGAGCTTG

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------acatattgcatttagtagaccatgatccattttgctactcttt-tgcttaagtagacagttgtacccatttccttatgctactatgtttttacctttgcagGAGGAAATCCAGAAGAAAACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTG
                                      |  |||  || | |||     ||| ||       ||   || |   | ||   | ||  |   | | || || |   | |  ||||||   ||    |||||||||| ||||||||||| |||||||| ||||||   |  || || | || ||| |||||||| || || || || |||||  |||||||||||||  
gtaagctcatcctagtttcagcttgttgccattcttcaaggttgggttgaatagtaggagattcagaacaaaacgggttatatctgagagcagaggagattcaaatttctcac-ttccattgttttgggctcaatagGAGGAAATTCAGAAGAAAACGGGTTATATCGTGATGAGAGCAGAGGGGATATATGATGTTGATGCCAACACTTCGATTGACCAGTTATCTGAAGAACTCA

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 11
--------------------------------------------acatattgcatttagtagaccatgatccatttt----gctactcttttgcttaagtagacagttgtacccatttccttatg-ctactatgtttttacctttgcagGAGGAAATCCAGAAGAAAACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTG
                                            || ||     | |||   |   | | | || |        |||  |||||  |     |  | | ||  |  || |||||| |  | ||| ||||  ||    ||||||| || |||||||||||||| ||||| || |||   ||||| || | || ||| |||||||| ||||||||||| ||||| ||||||||||||||  
gtaagtgccctagtttcaactctttaagaaaatcgtcattctagacctac-atttctagagaatattaacctatatcttacataacttatttgcccattagtaaggctctattccattgcttatggcctccatgattttggctcaatagGAGGAGATTCAGAAGAAAACAGGATATATTGTCATGAGAGATGAGGGCATATATGATGTTGATGCTAATACATCAATTGACCAGCTATCTGAAGAACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaagtagacagttgtacccatttccttatgctactatgtttttacctttgcagGAGGAAATCCAGAAGAAAACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTG
                                        tttttaccttt  CT-rich tract
                                    tatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatattgcatttagtagaccatgatccattttgctactcttttgcttaagtagacagttgtacccatttccttatgctactatgtttttacctttgcagGAGGAAATCCAGAAGAAAACAGGTTATATAGTGATGCTGGATGACGGAACATTTGACGTTGATGCAAATACATCAATAGACCACCTATCTGAAGAACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC