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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatttgcgaatttgtacactgcgggtccactatagttcgcgagctagcttgtgctgaactccgatggagtatatgactaccgtgactattatccgcagGGCAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACCTTCGAAGGGAGGCTGTCATGGAAAAAGAAAATACTTGCGTTCATCTTCG

Basic information

species Zea mays
transcript GRMZM2G140782_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140782_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g03040.1 (Oryza sativa), 3'ss of exon 3
agaatttgcgaatttgtacactgc-----gggtccactatagttcgcgagctagcttgtgctgaactccgatggagtatatgactaccgtgact-attatccgcagGGCAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACCTTCGAAGGGAGGCTGTCATGGAAAAAGAAAATACTTGCGTTCATCTTCG
      ||| ||    | || ||         |   | |  ||| || | ||    | ||||  |  | | ||   |||    | ||     || |   |   ||||| ||  | || ||||||||| | |||||||| ||  | |||| ||| ||||| || ||||||||||||||||| ||||| ||||| || ||||||||||
----gctgcaaaaggcttcattgttcttgaaatttgcaaatgtttgcta-ctgttatctgctatatactg-tgtgttattcatccacatctcctgaacctgtacagGGAAAGAGGATTGAGAATGGCGTGTATTTGGGGCCTGTTGGGTCCTTAACCTTTGAGGGGAGGCTGTCATGGAAGAAGAAGATACTCGCATTCATCTTCG
















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|74244076|gb|DT651990.1|DT651990
EST:     AGAAAGGGCAGTATTTCCCAGTGACAGCAGTCCAACGCTTCGATGCTGCG                         GGCAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACC
genomic: AGAAAGGGCAGTATTTCCCAGTGACAGCAGTCCAACGCTTCGATGCTGCGgtgagctgag ... ttatccgcagGGCAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACC
EST: gi|211449237|gb|FL468489.1|FL468489
EST:     GAAAGGGCAGTATTTCCCAGTGACAGCAGTCCAACGCTTTCGATGCTGCG                         GGGAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACC
genomic: GAAAGGGCAGTATTTCCCAGTGACAGCAGTCCAACGC-TTCGATGCTGCGgtgagctgag ... ttatccgcagGGCAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcttgtgctgaactccgatggagtatatgactaccgtgactattatccgcagGGCAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACCTTCGAAGGGAGGCTGTCATGGAAAAAGAAAATACTTGCGTTCATCTTCG
                                         actattat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatttgcgaatttgtacactgcgggtccactatagttcgcgagctagcttgtgctgaactccgatggagtatatgactaccgtgactattatccgcagGGCAAACGCATCGAGAATGGCATATATTTGGGCCCCATCGGGTGCTTGACCTTCGAAGGGAGGCTGTCATGGAAAAAGAAAATACTTGCGTTCATCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - ctgcggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa