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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttggttagacccttaattttcaggggtagtataactattcgatgtattacag

Basic information

species Oryza sativa
transcript LOC_Os02g11840.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgatgtattacag
||||||||||||||||||  |||| ||||| ||||||||||| ||||||||||||||||||||||||||||  |||||||||||||| ||||||||||||||  || ||||  | |  | ||||| ||||  | | ||||  ||   |||||| | || | |   || |        |   ||||| |||  |||| ||||||
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggt-tttttgtcac-ttaaaaagacatc-ttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 15
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgatgtattacag--------
|||||||||||| |||||  |||| ||||| ||||||||||| |||||||| |||||||| |||||||| |  || |||||||||||||||||||||||||| ||| ||||||| |  | ||||| ||||  | | ||||  ||   |||||| | || ||    || |        |   ||||| |||  || | ||   |        
TCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAGAGgtgagttttttcatcac-ttaaaaagacatcct-atatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttacag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G141587_T05 (Zea mays), 5'ss of exon 15
---TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgatgtattacag-----
   |||||||||||| |||||  |||| ||||| ||||||||||| |||||||| |||||||| |||||||| |  || |||||||||||||||||||||||||| ||| ||||||| |  | ||||| ||||  | | ||||  ||   |||||| | || ||    || |        |   ||||| |||  || | ||   |     
GCTTCATGAGATCAACGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagttttttcatcac-ttaaaaagacatcct-atatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgtta

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttggttagaccctt--aatt----ttcaggggtagtataactattcgatgtattacag------------
 ||||| || ||||||||  || |||| ||| | |||||||| ||||| ||||||||||||||||| || |   | |||||||||||||| || || ||||||   | | |  |    || | | | |    | | | | || |||   |  |  ||  ||||    | || || |  |   ||   | |||| || |               
ACATGAAATGAATGAACGTGTCAGAACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATTCCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatgcataatgattatgaatttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaat--acattgtcacatatgatttggttagacccttaattttcaggggtagtata-actattcgatgtattacag--------------------------------------------------------------
|||||| || ||||||||  || | || ||  | |||||||| |||||||||||||||||||||||||| |   ||||||| || ||||| || || ||||||  || | |  |    |  | | |  | |  |   |||||   ||  ||  || |||  || |||    |  | |    |  |  || | ||| |                                                               
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAACAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 4
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtat----tttcattata---tcaaaaatacattgt---cacatatga---tttggttagac------ccttaattttcaggggta----gtataactattcgatgtattacag------------------------------------------
|||||| || ||||||||  || | || ||  | |||||||| |||||||||||||||| ||||||||| |   ||||||| || ||||| || || ||||||  |||    || | || ||   ||||||   |  |||    |  |||     | | | ||  |       |||  | |||| |  |      |||   ||||   || | ||||                                           
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAGCAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttag

upper sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 19
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaag---tattttcattatatcaaaaatacattgtcacatatgatttggttagacccttaattttcaggggtagtataactattcgatgtattacag
  |||| | |||||||||  | || |||||| |||||||||| |||||||||||||| | ||| ||||| |   |||||||||||||||| || || ||||||||    ||||  |   | |   ||| | |  ||   || |  |||  || |    ||    || ||    ||||   || ||     ||||||||
CAATGAAACCAATGAACGTGTTCGGACTGGCTTATGGGTTGGGGATTGTTTTATCTATACCAACTCTTCTTGGAGGCTTAATTACTGTGTTGGTGGTGAGgtaaggctcatttctaggtttttggaaagaaac-gttttatgttttttattttg----ttgtaattgagattcagtactcctctt----atattacag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttggttagacccttaattttcaggggtagtataactattcgatgtattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA