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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtgcatcgcaaaagcctagcctctagctgtactaaaagtggttgctatgttttctggaacgcgcatgagagctgcacatctttatattagaga...

Basic information

species Zea mays
transcript GRMZM2G015730_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015730_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g17930.3 (Oryza sativa), 5'ss of exon 10
ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtgcatcgcaaaagcctagcctc-tagctgtactaaaagtggttgctatgttttctggaacgcgcatgagagctgcacatctttatattagaga---------
||| |   | | |||||  |||| |||||||| ||||||||  ||||| | ||||||||||| |||||| ||||||| |||||| | ||||| ||||||| | ||  | |     |   || | ||  |    || |  |||   |||    | | | |    |  ||||||    |           | || |            
ATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAGgtaa-atgtctaaccttcca-tgtaccttcacatgcataatggaagctcttgtgcaggtctttctttcttgcatgatgattaattgaacccttgtttgctttctccgcag
















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|60350738|gb|DN217711.1|DN217711
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|211265994|gb|FL478571.1|FL478571
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|24766462|gb|CA401615.1|CA401615
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|67019010|gb|CO447759.1|CO447759
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|74244820|gb|DT652734.1|DT652734
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|24769021|gb|CA404150.1|CA404150
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|148952378|gb|EC898193.2|EC898193
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|37400434|gb|CF637568.1|CF637568
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|60339601|gb|DN206574.1|DN206574
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
EST: gi|31354045|gb|CD438402.1|CD438402
EST:     AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG                         CGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA
genomic: AGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtg ... tgccttgcagCGTGAGCTAACGAAGAAGCAAATAGAGAAATTGAAAAACCAAAAGGAGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAGgtaatacgtgcatcgcaaaagcctagcctctagctgtactaaaagtggttgctatgttttctggaacgcgcatgagagctgcacatctttatattagaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA