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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACCGTCGCCATGACCGCGACCGGGATAGGGATTATGACCGCTCCCGCGGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctgaataataggcacacttttttatttgaaacccttgtgcctcacatcgttgactgacccaggtatttgtttatgatttcag

Basic information

species Zea mays
transcript GRMZM2G118014_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118014_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g62640.5 (Oryza sativa), 5'ss of exon 11
---GGGACCGTCGCCATGACCGCGACCGGGATAGGGATTATGACCGCTCCCGCGGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctgaataataggcacacttttttatttgaaacccttgtgcctcacatcgttgactgacc-caggtatttgtt--tatgatttcag----------------------------------------------------------------------------------
   ||||||| |||||||| ||||| |||||||| ||||||||||| || || ||  |||| ||||||||||| || ||||| || ||||||||||||||   |||| | | |||  |       ||   || | |    |  |  ||  |  |    |   | ||||  |    ||||    ||| ||  ||                                                                                   
ATAGGGACCGCCGCCATGATCGCGATCGGGATAGAGATTATGACCGTTCGCGTGGCCATGATTCAAGGAGAAGGGAACGTTCTCGATCCAGGGAGCGCAG-
















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|76286405|gb|DV025973.1|DV025973
EST:     GAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|83279326|gb|DV943334.1|DV943334
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|14243774|gb|BG841437.2|BG841437
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|211519312|gb|FL433830.1|FL433830
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|211148420|gb|FL475620.1|FL475620
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|76286406|gb|DV025974.1|DV025974
EST:     GAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|161588478|gb|EY959060.1|EY959060
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAG
EST: gi|149086754|gb|EE176294.2|EE176294
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|24767722|gb|CA402862.1|CA402862
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|60349927|gb|DN216900.1|DN216900
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
EST: gi|211168469|gb|FK981061.1|FK981061
EST:     GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAG                         GCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG
genomic: GGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctga ... atgatttcagGCGCCATGAGAGATACTAAATGTTACTCCATGGCTGACAGATTTTGGATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACCGTCGCCATGACCGCGACCGGGATAGGGATTATGACCGCTCCCGCGGATATGACTCAAGGAGAAGAGAGCGTTCACGCTCCAGGGAGCGCAGCAGgtattgctgaataataggcacacttttttatttgaaacccttgtgcctcacatcgttgactgacccaggtatttgtttatgatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA