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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtctgcgtctctctctcgaccccaacagattactcccaaagcctcaatcgcaacactagcgacgacacactcactctagcgcttttgtttgcacttcgcag

Basic information

species Zea mays
transcript GRMZM2G116185_T07
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116185_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g50900.1 (Oryza sativa), 5'ss of exon 4
AGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtctgcgtctctctctcgaccccaacagattactcccaaagcctcaatcg----caacactagcgacgacacactcactctagcgcttt----tgtttgcacttcgcag
 |||||||| ||||| |||||  ||||||||||||||| |||||||||| | |||||||||||||||||  |  |||| |||| |||||||||||| |||||||||  | || |||      | | |  | ||| |   |   ||  ||| ||| |       || || | || |   ||    | | |  |  |    | | |||   | ||||
TGGGAAAGTTGCAGCTGACCATGGCCACAAGTGGGTGTCCCAGGAGGCCAATGAGCACGAGATCAACCTGGTTACCTCATGGAACAACCCTGCCGATTCTgtaagctgcagcatcttctcacctatctaatcagttcggttaaaactcctaaattgatgcttgcaataacaacaattaacatgtttttgttccgtataatttctgctgattgcag
















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|71441211|gb|DR822261.1|DR822261
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|50330624|gb|CO525750.1|CO525750
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|93015353|gb|EB640873.1|EB640873
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|88754599|gb|DY538740.1|DY538740
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|76291868|gb|DV031436.1|DV031436
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|93016819|gb|EB642339.1|EB642339
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|78092357|gb|DV520731.1|DV520731
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|71299044|gb|DR785510.1|DR785510
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|94474694|gb|EB703652.1|EB703652
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|86473098|gb|DY239468.1|DY239468
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|101393157|gb|EB818509.1|EB818509
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|78084496|gb|DV512889.1|DV512889
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|74244543|gb|DT652457.1|DT652457
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|76011281|gb|DT938451.1|DT938451
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|149058752|gb|EE156770.2|EE156770
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|50336433|gb|CO531559.1|CO531559
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|88751941|gb|DY536082.1|DY536082
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|76910706|gb|DV163993.1|DV163993
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|71316516|gb|DR794932.1|DR794932
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|89251137|gb|DY622923.1|DY622923
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|74244764|gb|DT652678.1|DT652678
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|148933880|gb|EC877854.2|EC877854
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|71442161|gb|DR823211.1|DR823211
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
EST: gi|71323162|gb|DR798249.1|DR798249
EST:     AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCT                         CATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG
genomic: AGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtct ... cacttcgcagCATCCGAGGACATGGGAGGCTCAGTTCAAGTCTGGCATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAAAGTGGCAGCCGACCACAGCCACAAGTGGGTGTTCCAGGAGGCCCAGGAGCACGAGATCAACCTCATCTCCTCCTGGAGCAACCCTGCCGACTCTgtaagcgtctgcgtctctctctcgaccccaacagattactcccaaagcctcaatcgcaacactagcgacgacacactcactctagcgcttttgtttgcacttcgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA