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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGCCTGTGCGTGTGATTTAGATGATCCTGGAAATTTTAACCCTTTCCTTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacataaagcaccatgtattctcgtcggatcattataagacatttcagttttaatcactgttcacctactgcctatacagttgttttgcccgaat...

Basic information

species Zea mays
transcript GRMZM2G158097_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158097_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g36062.1 (Oryza sativa), 5'ss of exon 3
GGATGCCTGTGCGTGTGATTTAGATGATCCTGGAAATTTTAACCCTTTCCTTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacataaagcaccatgtattctcgtcggatcattataagacatttcagt-----tttaatcactgt-tcacctactgcctatacagttgttttgcccgaat
||||||||||||   ||||| || ||||||||  |||||||| ||||| || ||  | |||||||||||||||||||| ||||| |||||||| || ||||| ||  ||| ||||| |   | ||   ||    | || | || | ||  ||||     ||| | || |   | |  |   | |||  || |||| |  | |    
GGATGCCTGTGCAGTTGATTCAGTTGATCCTGACAATTTTAATCCTTTTCTGACCCACGCATTCCTCTCAAGCTTAGAGGAATCGGGTTCTGCAGTGAAGgtgagtgcatgaagcatcgcttgttg--gttccttaataagaacaaatcccagtggatgttttaccattacattatttttcgactacccatttgtat-acgca---
















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|76922721|gb|DV169140.1|DV169140
EST:     TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAG                         GAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
genomic: TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacat ... ctgatttcagGAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
EST: gi|89761707|gb|DY689615.1|DY689615
EST:     TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAG                         GAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
genomic: TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacat ... ctgatttcagGAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
EST: gi|71766887|gb|DR964824.1|DR964824
EST:     TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAG                         GAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
genomic: TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacat ... ctgatttcagGAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
EST: gi|78092697|gb|DV521071.1|DV521071
EST:     TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAG                         GAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
genomic: TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacat ... ctgatttcagGAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
EST: gi|50325272|gb|CO520398.1|CO520398
EST:     TTACTTATGCATTCCTCTCAAGCTTACAAGAATCAGGTTCTGCGGTCAAG                         GAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
genomic: TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacat ... ctgatttcagGAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
EST: gi|71318422|gb|DR795977.1|DR795977
EST:     TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAG                         GAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
genomic: TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacat ... ctgatttcagGAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
EST: gi|91873363|gb|EB403320.1|EB403320
EST:     TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAG                         GAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT
genomic: TTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacat ... ctgatttcagGAAACTGGCTGGTTACCTTTTCATATTGTTGCACGGGATGAGAATGGACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGCCTGTGCGTGTGATTTAGATGATCCTGGAAATTTTAACCCTTTCCTTACTTATGCATTCCTCTCAAGCTTAGAAGAATCAGGTTCTGCGGTCAAGgtaagcacataaagcaccatgtattctcgtcggatcattataagacatttcagttttaatcactgttcacctactgcctatacagttgttttgcccgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT