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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcattgattcctcagttgtttcaggttgtaattgatcaactaaattaaggcaagttcagctgatcttctgtgcatgatgcag

Basic information

species Zea mays
transcript GRMZM2G160569_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g44070.2 (Oryza sativa), 5'ss of exon 7
CAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcattgattcctcagttgtttcaggttgtaattgatcaactaaattaaggcaagttcagctgatcttctgtgcatg-atgcag----
|||||||||||||| | ||  |||||||| |||||||| |||  |   ||||||| ||| ||||||| ||||||||||||||| || || ||||| ||||||  |    || |  | ||| |   | |  || |||    |||| |     ||| | || |  ||||| |  ||||| ||| |||  |    
CAAAGTGTGGCCCCCAAAAGGGCTGATCCGCAAGGTCTATGGCGAGGATGTAGGATGAATCATGCCTCCTGTAATAGCAACCAACTGCAATTTTTACAAGgtactgggctgttctcccagatccgtgaa-ttataaactgtcaatt----caagtctagattggctgaccccctgtgtatgtatgatggcag
















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|31998134|gb|CD661943.1|CD661943
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|148953387|gb|EE152881.2|EE152881
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTTTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|91056470|gb|EB166888.1|EB166888
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|60400656|gb|DN233463.1|DN233463
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|4887514|gb|AI677613.1|AI677613
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|5058593|gb|AI737069.1|AI737069
EST:     CAGCTCCAGTTTTTGCAAG                         GGTTCAGGANCCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: CAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|211266712|gb|FL294975.1|FL294975
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|101383816|gb|EB813963.1|EB813963
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTTTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|91051274|gb|EB161692.1|EB161692
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|31356908|gb|CD441265.1|CD441265
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|86471748|gb|DY238118.1|DY238118
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|93016716|gb|EB642236.1|EB642236
EST:     TAGGGCGAAGCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|149028341|gb|EE154630.2|EE154630
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|78025651|gb|DV494038.1|DV494038
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|149009226|gb|EE153857.2|EE153857
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGNNNNNNNGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|149101141|gb|EE187249.2|EE187249
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|76932739|gb|DV173141.1|DV173141
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|60401537|gb|DN234344.1|DN234344
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcattgattcctcagttgtttcaggttgtaattgatcaactaaattaaggcaagttcagctgatcttctgtgcatgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC