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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGCACAATGATTAAGCACCCAATTGCTAGAGATGCAATTAATGGATACAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaatgtatttttactctatgtgtcttcctgcagctgtatttttatgctactctatgtgtgccacttaaatgttatttgtactaggattgtttg...

Basic information

species Zea mays
transcript GRMZM2G449355_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G449355_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g08220.3 (Oryza sativa), 5'ss of exon 6
TTTTGCACAATGATTAAGCACCCAATTGCTAGAGATGCAATTAATGGATACAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaatgtatttttactctatgtgtcttcctgcagctgtatttttatgctactctatgtgtgccacttaaatgttatttgtactaggattgtttg-------
||||| |||||||| |||||||| ||||||||| ||||| || |||| || |||||||||||| ||||| ||| | ||||||||||||| || || ||||||||||||||  | |||||| || || ||| ||| ||| | |   |||||      || |||    ||     | || | ||| |||         |||        
TTTTGTACAATGATAAAGCACCCGATTGCTAGAAATGCAGTTCATGGGTATAAGAAACTTCAGACTGTGTTGAGGATAGTTCTCCTGCGCCGCACAAAAGgtgataaaaactt-tttttattccatatgttttc-tgctgttccttttttgc----ctatatactagcttaggatatttcatt-gtaaggaagcaatttcaaccaca
















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|211322658|gb|FL233008.1|FL233008
EST:     CAAGAAACTTCAGGCTGTGCTGAANGTAGTTCTCCTGCGTCGTACGAAAG                         AAACTGTGAACAATGGCAAACCAATTAATAAATTTACCTCCTAAGACAATT
genomic: CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaa ... tttcatgtagAAACTGTGATCAATGGCAAACCAAT-AATAAATTTACCTCCTAAGACAATT
EST: gi|211322657|gb|FL233007.1|FL233007
EST:     CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAG                         AAACTGTGATCAATGGCAAACCAATAATAAATTTACCTCCTAAGACAATTA
genomic: CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaa ... tttcatgtagAAACTGTGATCAATGGCAAACCAATAATAAATTTACCTCCTAAGACAATTA
EST: gi|211322656|gb|FL233006.1|FL233006
EST:     CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAG                         AAACTGTGAACAATGGCAAACCAATAATAAATTTACCTCCTAAGACAATTA
genomic: CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaa ... tttcatgtagAAACTGTGATCAATGGCAAACCAATAATAAATTTACCTCCTAAGACAATTA
EST: gi|211322659|gb|FL233009.1|FL233009
EST:     CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAG                         AAACTGTGATCAATGGCAAACCAATAATAAATTTACCTCCTAAGACAATTA
genomic: CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaa ... tttcatgtagAAACTGTGATCAATGGCAAACCAATAATAAATTTACCTCCTAAGACAATTA
EST: gi|211322654|gb|FL233004.1|FL233004
EST:     CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAG                         AAACTGTGATCAATGGCAAACCTATAAYAAATTTACCTCCTAAGACAATTA
genomic: CAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaa ... tttcatgtagAAACTGTGATCAATGGCAAACCAATAATAAATTTACCTCCTAAGACAATTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGCACAATGATTAAGCACCCAATTGCTAGAGATGCAATTAATGGATACAAGAAACTTCAGGCTGTGCTGAAGGTAGTTCTCCTGCGTCGTACGAAAGgtgataaaaatgtatttttactctatgtgtcttcctgcagctgtatttttatgctactctatgtgtgccacttaaatgttatttgtactaggattgtttg

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG