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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGTAGAACCTCCCAAGATGCAAGCACCGAAGCCAACTGCACCATTAAAAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcggataatatcccattggagagttcagatgttgtatgagggacatgcacatattttaccatgatattgcag

Basic information

species Zea mays
transcript GRMZM5G807639_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 8
GAAAGTAGAACCTCCCAAGATGCAAGCACCGAAGCCAACTGCACCATTAAAAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaagg-cggataatatc-ccattggagagttcagatgttgtatg----agggacatgcacatattttaccatgata--ttgcag
  |||   |  | || ||     || | || |||    ||   |||   ||||| |||||| |||||||||| ||||||||||||||||| || ||| |||||||  |   |   |||  || | |   |  ||||| || | |     ||| ||| ||| || ||| |||||  ||  ||||||
AGAAGAGAAGTCACCAAAAGCAGAACCTCCCAAGATGCCTCTGCCACCCAAAACCTCCCCTACAGAACCACAGCTCCCTCCAAAAGAACGAGAACGGAGGgtaagatcaactttcatcatcaataggttgcacagatttttttttttacaggtacaagcatatctttaaccattttaatttgcag
















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|67031724|gb|CO460473.1|CO460473
EST:     CGTCCCCTTCAGGAAC-ACAACTCCCCTCCAAAAGAACGGGAGCGGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAAGATTC
genomic: CGTCCCCTTCAG-AACCACAACTCCC-TCCAAAAGAACGGGAGCGG-CGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTC
EST: gi|211169877|gb|FL077606.1|FL077606
EST:     CAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: CAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|31349005|gb|CD433362.1|CD433362
EST:     AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|67025111|gb|CO453860.1|CO453860
EST:     AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|6056485|gb|AW090875.1|AW090875
EST:     GGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: GGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|7031253|gb|AW461141.1|AW461141
EST:     AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGG                         GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|32834807|gb|CD974485.1|CD974485
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcgga ... gatattgcagGTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGTAGAACCTCCCAAGATGCAAGCACCGAAGCCAACTGCACCATTAAAAACGTCCCCTTCAGAACCACAACTCCCTCCAAAAGAACGGGAGCGGCGGgtaaggcggataatatcccattggagagttcagatgttgtatgagggacatgcacatattttaccatgatattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC