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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTACGTAGGTTGTGTATTTGTTGGCTTTGAATCAAACAACATCATTGCTTGTGGTCCAGgtacccaatatatggtggtatgcaagactggaactatatacatggaggctgctttgagttaactctggagattagtgacacaaagtggccaaaagcagat...

Basic information

species Zea mays
transcript GRMZM2G127941_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127941_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g05240.1 (Oryza sativa), 5'ss of exon 11
GTACTACGTAGGTTGTGTATTTGTTGGCTTTGAATCAAACAACATCATTGCTTGTGGTCCAGgtacccaatatatggtggtatgcaagactggaactatatacatggaggctgctttgagttaactctggagattagtgacacaaagtggccaaaagcagat-----------------------------------------------------------------------------------------------------
                                                                  ||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||| |||||||||  ||| |||||||| |||| |                                                                                                     
-----------------------------------------------------------------TCCAATCTATGGTGGGATGCAAGACTGGAACTATATACATGGAGGTTGCTTTGAGTTAACCCTGGAAATTAGTGACGTAAAATGGCCAAAGGCAGCTGAGgtatttttctttttttttgcatctagttatctgcctatcaatttccagataacttgataatcactttgttgtgttatttcttccaaattcttctatag

upper sequence: GRMZM2G127941_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G31000.2 (Glycine max), 5'ss of exon 4
------------------GTACTACGTAGGTTGTGTATTTGTTGGCT---TTGAATCAAACAACATCATTGCTTGTGGTCCAGgtacccaatatatggtggtatgcaagactggaactatatacatggaggctgc----tttgagttaactctggagattagtgacacaaagtggccaaaagcagat----------------
                  | |  |       | | ||  || |||||   |||| |  | |      |||  |  |  |  | |  |||| |   || ||   |  |   || |      |     | || ||      ||  |  ||  ||||||   |||  | | ||   || |||       |                
CCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTTGTGATAATAAATG-GCCCAGTGC-TGCTGAGgt-tagttctagcttctaaactgagcagtctttaaaattacaagtatatctggaatatagcaaaataattaggacaatttttttttttttgaacggccaaa

upper sequence: GRMZM2G127941_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G36590.1 (Glycine max), 5'ss of exon 11
------------------GTACTACGTAGGTTGTGTATTTGTTGGCT---TTGAATCAAACAACATCATTGCTTGTGGTCCAGgtacccaatatatggtggtatgcaagactggaactatatacatggaggctgctttgagttaactctggagattag--tgacacaaagtggccaaaagcagat----------------------
                  | |  |       | | ||  || |||||   |||| |  | |      |||  |  |  |  |  |  || |   ||| || |  |      |  | || | || |  |||    |||| | || ||         | |  | |  |||| |    | || || ||                      
CCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTAGTGATAAT--AAATGGCCTA---ATGCTGCTGAGgttagttctagct-tctaaaccgagcagtctttaaatttacaagtatatctggaataaagcaaaataattagaa-caaattacactcacatcccaagtttta

upper sequence: GRMZM2G127941_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G71696.1 (Arabidopsis thaliana), 5'ss of exon 10
GTACTACGTAGGTTGTGTATTTGTTGGCTTTGAATCAAACAACATCATTGCTTGTGGTCCAGgtacccaatatatggtggtatgcaagactggaactatatacatggaggctgctttgagttaactctggagattagtgacacaaagtggccaaaagc---agat--------------------------------------------------------------------------------------
                                                                 |||||| |||||||| |||||||||||||| || ||| |||| || |||||||| || |||||||| || || ||||  |||||||| |||||   |||                                                                                       
-----------------------------------------------------------------CCCAATTTATGGTGGCATGCAAGACTGGAATTACATATATGGGGGATGCTTTGAATTGACTCTGGAAATAAGCGACAACAAGTGGCCTAAAGCCTCAGAGgtcaaatcttatattcctatgtgataactgtttctccttcgcaaggtagttagctgatactaatagagttcacacatgttacacag

upper sequence: GRMZM2G127941_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv18s0157g00050.t01 (Vitis vinifera), 5'ss of exon 11
GTACTACGTAGGTTGTGTATTTGTTGGCTTTGAATCAAACAACATCATTGCTTGTGGTCCAGgtacccaatatatggtggtatgcaagactggaactatatacatggaggctgctttgagttaactctggagattagtgacacaaagtggccaaaagcagat-------------------------------------------------------------------------------------------------------
                                                                 ||| ||||||||||| |||||||| ||||||||||||||||| ||||| ||||| || || |||||||| |||||||  |||||||| ||  |   |                                                                                                       
-----------------------------------------------------------------CCCCATATATGGTGGCATGCAAGATTGGAACTATATACATGGTGGCTGTTTTGAATTGACACTGGAGATCAGTGACAACAAGTGGCCTAACACTATTGAGgtttgatctcagttgagttgtctttgcttcaatactcagtactattccatgtggaccaagacttgaatggtattgtgaattggttatttcctaaacaatc

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTACGTAGGTTGTGTATTTGTTGGCTTTGAATCAAACAACATCATTGCTTGTGGTCCAGgtacccaatatatggtggtatgcaagactggaactatatacatggaggctgctttgagttaactctggagattagtgacacaaagtggccaaaagcagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagcag