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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttgcctaccatgtccctgcgtcctggagatgtcaagtcgtcaacggagatttgatctgacaaatgcttcctgcacttggcgccaacatttgttttttgtgtggctgcaactgtgaacccatttaacttacatcag

Basic information

species Zea mays
transcript GRMZM2G009021_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009021_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g46555.1 (Oryza sativa), 5'ss of exon 3
GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttgcctaccatgtccctgcgtcctggagatgtcaagtcgtcaacggagatttgatctgac-aaatgcttcctgcacttggcgccaacatttgttttttgtgtggctgcaactgtgaacccat--------ttaacttac-atcag
||| || || || ||||| ||||| ||||||||  | ||||||||| |||| |||||||||||||||||| | ||||| ||||||||| ||   |||||   |     ||  ||| || ||    | | | |  |||    ||||  ||||||||| |||| |   |  |||  ||  |||||  ||| | ||||||| ||| |  |         ||  |||||  ||||
GCCTGGGGATACTATTCTAATTGCTGCTGGTGGCACACATGTTGCACGTAATATCCAAATAAAGAAGCCTCTCTGCATTgtaagtttttccattcatgtttgttatatctcaaga-gtgaaagtttgatctggtatt----ctgatgaaatgcttcttgcattacacagcaa--ttcttttttgttgttgatgcaactttgagcttacgcttgtcatttgcttactgtcag
















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|211344537|gb|FL091805.1|FL091805
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGA
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGA
EST: gi|211342145|gb|FL091793.1|FL091793
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211344534|gb|FL091802.1|FL091802
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342144|gb|FL091792.1|FL091792
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342151|gb|FL091799.1|FL091799
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342143|gb|FL091791.1|FL091791
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342152|gb|FL091800.1|FL091800
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342147|gb|FL091795.1|FL091795
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGA
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGA
EST: gi|30087498|gb|CB885704.1|CB885704
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342146|gb|FL091794.1|FL091794
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342153|gb|FL091801.1|FL091801
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGG
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGG
EST: gi|211344538|gb|FL091806.1|FL091806
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342149|gb|FL091797.1|FL091797
EST:     GTGGTTCC-ATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGA
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGA
EST: gi|211344536|gb|FL091804.1|FL091804
EST:     GTGGTTCCCATGTTGTATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTA
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTA
EST: gi|211344543|gb|FL091811.1|FL091811
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211344540|gb|FL091808.1|FL091808
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGC-TATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|37396358|gb|CF635468.1|CF635468
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|30087497|gb|CB885703.1|CB885703
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211344542|gb|FL091810.1|FL091810
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATATTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211342148|gb|FL091796.1|FL091796
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGA
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGA
EST: gi|29945972|gb|CB815913.1|CB815913
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|29945970|gb|CB815912.1|CB815912
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT
EST: gi|211344539|gb|FL091807.1|FL091807
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGAC-TGCTCACGTGG
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGG
EST: gi|211342150|gb|FL091798.1|FL091798
EST:     GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATA                         ATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGC
genomic: GTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttg ... cttacatcagATTGGCGGGGGCGATCTTCCTGATGACACTGTATTGACCTGCTCACGTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGGTGACACCATTCTTATTGCGGCTGGTGGTTCCCATGTTGCATGTAACATCCAAATAAAGAAGCCTATTTGCATAgtaagttttgcctaccatgtccctgcgtcctggagatgtcaagtcgtcaacggagatttgatctgacaaatgcttcctgcacttggcgccaacatttgttttttgtgtggctgcaactgtgaacccatttaacttacatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC