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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgcttctgtttctatttccggaacatccttactgagttactgactgattcgggggttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g42320.4
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 10
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgc-ttctgttt--ctatttccggaacatccttactgagttactgactgattcgggggttgcag-------
|||||||||||| ||||||||||||||||||||||| ||||| ||||||||| ||||||||||||||  || | |      || |  ||   || ||  | || ||||| | | ||||| | | || ||| ||   |           
ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatcgctcgcatccctgttgtacttgcttagtttagaaatatcctaaat-agttaataattggttccggatcttggacttgcag

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgcttct-gtttctatttccggaacatccttactgagttactgactgattcgg-------gggttgcag
||||||||| || ||||||||||||||||||||||| ||||| ||||||||| ||||||||||||||  |    |    ||| | ||| ||   |    |||||||| | | ||||||| | || ||| |       |  ||||||
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgc---aacccacttgtagttgcttagtttaaaacatcctaaat-agttactaattggttctgcatcttggacttgcag

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G850355_T04 (Zea mays), 5'ss of exon 9
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgcttct-gtttctatttccggaacatccttactgagttactgactgattcgg-------gggttgcag---------------------
||||||||| || ||||| ||||||||||||||||| ||||| ||||||||| ||||||||||||||  |    |    ||| | ||| ||   |    |||||||| | | ||||||| | || ||| |       |  ||||||                     
ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgc---aacccacttgtagttgcttagtttaaaacatcctaaat-agttactaattggttctgcatcttggacttgcagatatgaggggcaaatttcctc

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 10
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgcttct-gtttctatttccggaacatccttactgagttactgactgattcgg-------gggttgcag
||||||||| || ||||| ||||||||||||||||| ||||| ||||||||| ||||||||||||||  |    |    ||| | ||| ||   |    |||||||| | | ||||||| | || ||| |       |  ||||||
ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgc---aacccacttgtagttgcttagtttaaaacatcctaaat-agttactaattggttctgcatcttggacttgcag

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
-------------------------------------ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtag-gtgcttctgtttctatttccggaacatccttactgagttac--------tgactgattcgggggttgcag----------------
                                      |||||||| || |||||||||||||||||  |||| || || || ||||||||||| |||||||| | || | ||  |||   |     | | | |   | ||  |||   |  ||         ||||   ||      || | |                
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttcaagtttatgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G41330.1 (Glycine max), 5'ss of exon 10
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggt-----gcttctgtttctatttccggaacatccttactgagttactgactgattcgggggttgcag----------------------
 |||||||| || |||||||||||||||||  |||| || || || ||||||||||| |||||||| |      |  |     | || ||     | |      | | ||||| |||   | ||||   ||      || | |                      
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATGTTGACTCTGAAGGAAGGgtaggagcatgacattccaagtttatgcactaaataattataaaaccttaatgaa--aatgacatgtttaactattactgtccattaggaggcccaaacatt

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G16660.1 (Glycine max), 5'ss of exon 10
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgcttctgtttctatttccggaacatccttactgagttactgactgattcgggggttgcag-----------------------------
 |||||||| || ||||||||||||||| |  |||| || || || ||||||||||| |||||||| |    | | |   ||     | |||   | ||| ||   |  |   ||| |   | |||      |||                                
GTACACAGATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtagga---gcatgctatttcaagtttatgcactgaa-atttattttatattatttggttattttcatcttgacatttgacctatggcacatccctccaaacca

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G17810.3 (Glycine max), 5'ss of exon 10
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtag-gtgcttctgtttctatttccggaacatccttactgagttac--------tgactgattcgggggttgcag----------------
 |||||||| || |||||||||||||||||  |||| || || || ||||||||||| |||||||| | || | ||  |||   |     | | | |   | ||  |||   |  ||         ||||   ||      || | |                
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttcaagtttatgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca

upper sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgt-cttgtaggtgcttctgtttctatttccggaacatccttact-gagttactgactgattcgggggttgcag-----------------------
 ||||||||||||||||| ||||| |||||||| || || || ||  ||||  ||||||||||||| || |   |      |  | ||   |  |      | |  | |   |||||     |  ||||   | |  ||                        
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgcttctgtttctatttccggaacatccttactgagttactgactgattcgggggttgcag

- - - - - - -  GGAGCT
- - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG