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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaatgaaaattaaaaagggaaagttgagagctcatgctgtcttcttttaatttaaaacaaactaaaaagtttcaaagcacatgagctcagtaactgccaaaaaatacacagttctacactaataggcatcaatagtgatcttgataactattgcggttgacctgttttcag

Basic information

species Zea mays
transcript GRMZM2G094444_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094444_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g11510.1 (Oryza sativa), 5'ss of exon 3
------AAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaatgaaaattaaaaagggaaagttgagagctcatgctgtcttcttttaatttaaaacaaactaaaaagtttcaaagcacatgagctcagtaactgccaaaaaatacacagttctacactaataggcatcaatagtgatcttgataactattgcggttgacctgttttcag
      || ||||||||||||||| |||||||||| ||||  ||||||||||| | |||||||                                 ||| || | || |||   |   |||||||  |||||    |||     |  | ||  |||   ||    |   | ||   |      || |  | ||||  ||  |||||||| |   |      | |||  |||||||
GCTCAGAAAAATATATTCCAGATGATCAGGACAGTCTGGGTCTCTGATGGTCTGAAAGgttag--------------------------------ccattctctgttgtttgtttactaaacaaaggaaaaa----caacatgaagcaactttgtattagctctgaccaaaaccagt------tacttcgtatcagcagcaatcttgatgaaattcaatactcacccattttcag
















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|5566944|gb|AI881855.1|AI881855
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|101396104|gb|EB819979.1|EB819979
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|31355816|gb|CD440173.1|CD440173
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|93013218|gb|EB638738.1|EB638738
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|71328899|gb|DR801132.1|DR801132
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|91049487|gb|EB159905.1|EB159905
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|211518405|gb|FL045671.1|FL045671
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|91055834|gb|EB166252.1|EB166252
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|74244669|gb|DT652583.1|DT652583
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|211518397|gb|FL045663.1|FL045663
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|211518399|gb|FL045665.1|FL045665
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|213191961|gb|FM189272.1|FM189272
EST:     ATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: ATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|93284067|gb|EB676331.1|EB676331
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|211518406|gb|FL045672.1|FL045672
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|76288143|gb|DV027711.1|DV027711
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|149089237|gb|EE178440.2|EE178440
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|78117346|gb|DV535733.1|DV535733
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCCCAGGTGTTACTGGATCTCTTGCGACTGGCG
EST: gi|211518403|gb|FL045669.1|FL045669
EST:     GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAG                         GTTTTTACAGAGGAATCAGCCGCAGGTGTTACTGGATCTCTTGCGACTGGC
genomic: GAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaat ... ctgttttcagGTTTTTACAGAGGAATCAGCC-CAGGTGTTACTGGATCTCTTGCGACTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAATATATTCCAGATGGTCAGGACAGTTTGGGCTTCTGATGGTCTAAGAGgttagggaatgaaaattaaaaagggaaagttgagagctcatgctgtcttcttttaatttaaaacaaactaaaaagtttcaaagcacatgagctcagtaactgccaaaaaatacacagttctacactaataggcatcaatagtgatcttgataactattgcggttgacctgttttcag

- - - - - - CAGATG