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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGGCGGCGCCGGCCACTCCCACCGTCCCACAGCAGCTTCGCGTCGGCTTCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgccgcctccgccgccgccgctgtttaaccgtctgcccatgtggtgtctgcgctcatgctcccgcttcatttttctttgcag

Basic information

species Zea mays
transcript GRMZM5G852968_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G852968_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 5'ss of exon 1
-CGCGGCGGCGCCGGCCACTCCCACCGTCCCACAGCAGCTTCGCGTCGGCTTCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgccgcctccgccgccgccgctgtttaaccgtctgcccatgtggtg----tctgcgctcatgct------cccgcttcatttttctttgcag--------------------
  ||| || ||||| || | ||  |    || |||||||| ||| |||| | ||| |||||||||||||||||||||||||||||||| ||||||||||||||   |  ||  |  |    | ||    ||||||        || |  | ||    | || |||| ||        |  ||| | | |||||||                        
AGGCGTCGCCGCCG-CCGCCCCGGCGCATCCGCAGCAGCTCCGCCTCGGGTGCTCCCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCCGGATCCGGCAAGgttgccatccatcctccttcctgctatcgtttaattacacttcccttcgttgcccttttgtgctcgtggctgacgacttgctgcttctttctttctgctgctgctgctgtccttgcag
















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|71757354|gb|DR955291.1|DR955291
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|101387332|gb|EB815682.1|EB815682
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|76014692|gb|DT941862.1|DT941862
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|149089024|gb|EE178175.2|EE178175
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|50337624|gb|CO532750.1|CO532750
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|78089192|gb|DV517576.1|DV517576
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|71439314|gb|DR820364.1|DR820364
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|148949372|gb|EC894828.2|EC894828
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|148990724|gb|EE032131.2|EE032131
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|211138817|gb|FL315878.1|FL315878
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|149101112|gb|EE187218.2|EE187218
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|13126490|gb|BG317060.1|BG317060
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|71301510|gb|DR786796.1|DR786796
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|71436978|gb|DR818028.1|DR818028
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|148987083|gb|EE030908.2|EE030908
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|148945255|gb|EC890464.2|EC890464
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|91877369|gb|EB407326.1|EB407326
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|148942891|gb|EC887934.2|EC887934
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|91049452|gb|EB159870.1|EB159870
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|78089320|gb|DV517694.1|DV517694
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|149111298|gb|EE294796.2|EE294796
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|76011527|gb|DT938697.1|DT938697
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC
EST: gi|71319071|gb|DR796286.1|DR796286
EST:     TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAG                         TTCTTCGTCGGAGGCAACTGGAAGTGC
genomic: TCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgcc ... ttctttgcagTTCTTCGTCGGAGGCAACTGGAAGTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGGCGGCGCCGGCCACTCCCACCGTCCCACAGCAGCTTCGCGTCGGCTTCTCGCGCCGCCGCGCCCAGCGCGTCGTCGCCATGGCTGGATCCGGCAAGgtgcgccgccgcctccgccgccgccgctgtttaaccgtctgcccatgtggtgtctgcgctcatgctcccgcttcatttttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA