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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCGCCTGCGTGTGCCGCCGGTGGCGGGAGGCCGCCGTCTCCGTCGTGCGTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacggaagctgcggtttgagctggtcgctcgcacagaggtcagtagagtgccttaggctcttagctgacaattcaatgtgtgcggcggcgttggt...

Basic information

species Zea mays
transcript GRMZM2G068586_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068586_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g48370.1 (Oryza sativa), 5'ss of exon 1
CTGCGCCTGCGTGTGCCGCCGGTGGCGGGAGGCCGCCGTCTCCGTCGTGCGTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacggaagctgcggtttgagctggtcgctcgcacagaggtcagtagagtgccttaggctcttagctgacaattcaatgtgtgcggcggcgttggt----
|||||||||||||||||| ||||||||||| || |||||| |||||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||  |  |  | ||   | | || | || |       | |  |   || ||      | ||    |||        | || || || |  | |      
CTGCGCCTGCGTGTGCCGGCGGTGGCGGGACGCTGCCGTCGCCGTCGTGCGGCCGCCCGCGGAGTCCGGCAAGATCACCTTCCCGTCCTCGCTCAAGCAGgtgaggaaaggggggggggg--ggggtgat-gcccttctgctgttttgctaagagctcctatccctcgattgatgggggcttctg-gccgctgattcgaagtat
















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|211227913|gb|FL059245.1|FL059245
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227917|gb|FL059249.1|FL059249
EST:     TCCGCCGGCGGAGTCC-GCAAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: TCCGCCGGCGGAGTCCGGC-AAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227907|gb|FL059239.1|FL059239
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAA
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGA-GAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAA
EST: gi|71772807|gb|DR970732.1|DR970732
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227904|gb|FL059236.1|FL059236
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227909|gb|FL059241.1|FL059241
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAA
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGG-AGAGACCAATGCAGTGCTTTATCAAGAGGAA
EST: gi|211225858|gb|FL059235.1|FL059235
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227911|gb|FL059243.1|FL059243
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227905|gb|FL059237.1|FL059237
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211229973|gb|FL059252.1|FL059252
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227916|gb|FL059248.1|FL059248
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227912|gb|FL059244.1|FL059244
EST:     GTCCGCCGGCGGAKTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227908|gb|FL059240.1|FL059240
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227918|gb|FL059250.1|FL059250
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211229972|gb|FL059251.1|FL059251
EST:     GCCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|78109424|gb|DV527840.1|DV527840
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTT
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTT
EST: gi|211225857|gb|FL059234.1|FL059234
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCGCCTGCGTGTGCCGCCGGTGGCGGGAGGCCGCCGTCTCCGTCGTGCGTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacggaagctgcggtttgagctggtcgctcgcacagaggtcagtagagtgccttaggctcttagctgacaattcaatgtgtgcggcggcgttggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC