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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatgcctttgccattttatttccatcgcatgtcacctagaaactacacttttcttatgcctctttttgaatcctgcag

Basic information

species Zea mays
transcript GRMZM2G110185_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 4
GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatgcctttgccattttat------ttccatcgcatgtcacc--tagaaactacacttttcttatgcctctt-tttgaatcctgcag-------------------------------------------------------------------------------------------------------
|||||||| || |||||||| ||||  || ||| | || ||||||||||||||||| ||||| || || ||||||||||||    ||   ||   || | |        | |||     |  ||    |    || ||| || || |||     |  ||||||      ||                                                                                                       
GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATATGTTATCAATGTGAAGCAGATTGCAAAGgtaatctatattttcaacaatgtgaagaagatgccaaactgtcccattgtttctcaccacatttatcctatattcttggtttgaagatgttagacttcacttactgttatgaaattgtcaatgggttggcaaagctgttgattcttttctttatgctgtcaggactaataatccttctgcgttctttttatgacag

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 4
GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatg-acatgcctttgccattttatttccatcgcatgtcacctagaaactacacttttcttatgcctctttttgaatcctgcag---------------
|| ||||| || ||||||||||||| ||| ||| | || |||||||| |||||||| ||||| || || |||||||||||    | ||   | |   ||   | |    ||  || || |  |   |  | |   || ||        | | | |||                     
GTGGCAAGGTGCACAAAGATTATAAACCCAAATTCTGAAGATGCCAAGTATGTTATCAATGTGAAGCAGATTGCAAAGgtgcctatatttttgtttaataacaatcttttcatatttccctgatctatcagatagttgtttgaatatatctggcatcacttgttaatcaagatatttc

upper sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 4
GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatgcctttgccattttatttccatcgcatgtcacctagaaactac--acttttcttatgc-ctctttttgaatcctgcag-------------
|| |||||||| |||||||| || ||||| ||| | || |||||||||||||| |||||||| |||||||||||||||||| |       |||   | | | ||||   |    |  || |  |||  |   |||||  || |    || |||||  |  | ||              
GTGGCAAGATGCACAAAGATAATTAGCCCCAATTCTGAGGATGCCAAATATGTGATAAATGTTAAACAAATTGCAAAGgtaagcttcaattttaagactctgtttcttcctatagaaacttgtaaagcatggactttctttttctgttccttttgttttgttcaaacgcaaaattttt

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|149015235|gb|EE045022.2|EE045022
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211399668|gb|FL004442.1|FL004442
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|149015481|gb|EE045355.2|EE045355
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|101395193|gb|EB819526.1|EB819526
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211283517|gb|FL004412.1|FL004412
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|149087114|gb|EE176653.2|EE176653
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211285334|gb|FL004433.1|FL004433
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211399660|gb|FL004434.1|FL004434
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAA-G                         TTTGTRGWCGGATTCGGAGATAAGGTCTCTCCAACTGATATCGAGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGG
EST: gi|30087195|gb|CB885403.1|CB885403
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|19437016|gb|BM953426.1|BM953426
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211283515|gb|FL004410.1|FL004410
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211283510|gb|FL004405.1|FL004405
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|67028224|gb|CO456973.1|CO456973
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|78085799|gb|DV514192.1|DV514192
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|19436438|gb|BM952848.1|BM952848
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211285332|gb|FL004431.1|FL004431
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211010592|gb|FL355819.1|FL355819
EST:     TAATACGGATGATGCCAAATATGTTATAAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTTGGGAGATAAGGTCTCTCCA
genomic: TAATACGGATGATGCCAAATATGTTATAAA-TGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATT-GGGAGATAAGGTCTCTCCA
EST: gi|28930845|gb|CB334206.1|CB334206
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAAGGTCTCTCCAACTGATATCGAGGAAGGG
EST: gi|211283518|gb|FL004413.1|FL004413
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAA-CAAATTGCAAAG                         TTTGTGGTCGGATTGGGAGATAA
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatg ... aatcctgcagTTTGTGGTTGGATTGGGAGATAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCAAGATGTACAAAGATTATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATTGCAAAGgtatgacatgcctttgccattttatttccatcgcatgtcacctagaaactacacttttcttatgcctctttttgaatcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG