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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCGCCTGCGTGTGCCGCTGGTGGCGGAAGGCCGCAGTCTCCGTTGTGCGTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacgaaagcttcggtttcagctgttcgctcgcacatggtcagtagagtgtcttaggcacttacctgccgattcagcgtgtgcggcggcgttggtc...

Basic information

species Zea mays
transcript GRMZM2G062154_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062154_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g48370.1 (Oryza sativa), 5'ss of exon 1
TTTCGCCTGCGTGTGCCGCTGGTGGCGGAAGGCCGCAGTCTCCGTTGTGCGTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacgaaagcttcggtttcagctgttcgctcgcacatggtcagtagagtgtcttaggcacttacctgccgattcagcgtgtgcggcggcgttggtc--
 | |||||||||||||||  |||||||| | || || ||| |||| ||||| || || |||||||||| ||||||||||||||| ||||||||||||||||||| ||  || |    ||     | || |  |   |   || |  |   || |       | ||    ||  |        ||  ||  |           
CTGCGCCTGCGTGTGCCGGCGGTGGCGGGACGCTGCCGTCGCCGTCGTGCGGCCGCCCGCGGAGTCCGGCAAGATCACCTTCCCGTCCTCGCTCAAGCAGgtgagga--aagggggggggggggggtgatgcccttctgctgttttgctaagagctcctatccctcgattgatgggggcttctggccgctgattcgaagtat
















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|38687992|gb|CK145023.1|CK145023
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGTGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|211111224|gb|FK952889.1|FK952889
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|74244974|gb|DT652888.1|DT652888
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|211111223|gb|FK952888.1|FK952888
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|211112130|gb|FK952891.1|FK952891
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|211111218|gb|FK952883.1|FK952883
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|71431617|gb|DR812667.1|DR812667
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAA
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAA
EST: gi|149040587|gb|EE046828.2|EE046828
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|211111222|gb|FK952887.1|FK952887
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|74239976|gb|DT647890.1|DT647890
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAAGGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|86466002|gb|DY232375.1|DY232375
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAAAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
EST: gi|71329294|gb|DR801349.1|DR801349
EST:     GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC
genomic: GTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacga ... caaaacacagCCAGGGCCTAGGGAGAACCCAATGCAATGCTTTATCATGCGGAATAAGAAC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCGCCTGCGTGTGCCGCTGGTGGCGGAAGGCCGCAGTCTCCGTTGTGCGTCCTCCGGCGGAGTCCGCCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgatgacgaaagcttcggtttcagctgttcgctcgcacatggtcagtagagtgtcttaggcacttacctgccgattcagcgtgtgcggcggcgttggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC