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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaatcctcctcttgtttacccgtcgatgtattttggaccatatagccgtccttggtctagcatcacgaacaacccacagatcacaacgttcccttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG

Basic information

species Zea mays
transcript GRMZM2G078458_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078458_T04 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os06g03676.1 (Oryza sativa), 3'ss of exon 14
gtattcaatcctcctcttgtttacccgtcgatgtattttggaccatatagccgtccttggtctagcatcacgaacaacccacagatcacaacgttcccttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG
|||    | || |  ||||   |    |||||||    || ||| | ||    |  ||  | | || |    || ||   |  |||||   | ||| |||||||||||||| ||||||||||||||||| ||||||| ||||||||||||  | |||| || ||| | ||||||  || | |  ||||||||    ||||
gtaacacacccacaacttgagaaat--tcgatgt-cagtgtacc-tgta----ttttttctatggcgttgtcaataatttattgatcaagcccttctcttttgcaagAATGACTGAACTTGAAGAGGGCACTGGAACTGAAGCATCTGACAGCCAACTACTTGAGAAATTCGATCTCAGTGATTCAGAAGACGCAACGAG
















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|71330008|gb|DR801741.1|DR801741
EST:     TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAA                         AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
genomic: TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAAgtattcaatc ... cttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
EST: gi|211219812|gb|FL295368.1|FL295368
EST:     TGCGGTGATCAGGGTGCACTGGTTTTGCTTGTGGATCTTCTCGGGGTCAA                         AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
genomic: TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAAgtattcaatc ... cttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
EST: gi|78108130|gb|DV526548.1|DV526548
EST:     TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAA                         AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
genomic: TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAAgtattcaatc ... cttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
EST: gi|71298468|gb|DR785212.1|DR785212
EST:     TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAA                         AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
genomic: TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAAgtattcaatc ... cttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
EST: gi|86469372|gb|DY235742.1|DY235742
EST:     TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAA                         AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
genomic: TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAAgtattcaatc ... cttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
EST: gi|78122645|gb|DV541029.1|DV541029
EST:     TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAA                         AATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT
genomic: TGCGGTGATCAGGGTGCACTGGGTTTGCTTGTGGATCTTCTCGGGGTCAAgtattcaatc ... cttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccttggtctagcatcacgaacaacccacagatcacaacgttcccttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG
                                       cgttccctttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcaatcctcctcttgtttacccgtcgatgtattttggaccatatagccgtccttggtctagcatcacgaacaacccacagatcacaacgttcccttttgcaagAATGGCTGAACTTGAAGAGGGCTCTGGAACAGAAGCATCTGACGCCGAACTGCTCGAGCAGTTCGATTCCATTCAGCCAGAAGACTACGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG