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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggaaatgcctatcttataaaagtgtacatttaatacatatataaaagtggacattttgttgaggagataattacttcagtcttcaccttatgtttagTTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAAGAGTTGGAAGGGCTAAAAGACACCTTGCAATCCGAACGACAAAGTTCCA

Basic information

species Zea mays
transcript GRMZM2G423861_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 12
aatggaaatgcct---atcttataaaagtgtacatttaatacatatataaaagtggacattttgttgaggagataattactt-cagtcttcaccttatgtttagTTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAAGAGTTGGAAGGGCTAAAAGACACCTTGCAATCCGAACGACAAAGTTCCA
  | | ||    |   |  | ||   | |||| |||||  |   |   | ||      | ||   |       |  | |||    |||||    || | | ||||||   || ||  |||||  ||||||||||||||||| ||| |||||| |||| || ||||| || |  || ||||||||||| ||||| |||||    |
-gttgcaacatattgaagataatggcattgtatatttagcatgga---agaaaccattacttacatagctcatttgtcactggttgtcttttttttttttatagTTGAATGAGGAGTTACAGAAGAAGACAAAACAAGAAAGAGATATGCAAAAAGAATTAGAAGGTCTGAGGGATACCTTGCAATCTGAACGGCAAAGCATTA
















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|211028431|gb|FL442904.1|FL442904
EST:     TCCAAGAACTGACAAAAACAGTTGAGGAATCTCAGAAGCAAGCAGATCAG                         TTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAA
genomic: TCCAAGAACTGACAAAAACAGTTGAGGAATCTCAGAAGCAAGCAGATCAGgtaagcacct ... ttatgtttagTTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAA
EST: gi|18649769|gb|BM498588.1|BM498588
EST:     TCCAAGAACTGACAAAAACAGTTGAGGAATCTCAGAAGCAAGCAGATCAG                         TTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAA
genomic: TCCAAGAACTGACAAAAACAGTTGAGGAATCTCAGAAGCAAGCAGATCAGgtaagcacct ... ttatgtttagTTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagtggacattttgttgaggagataattacttcagtcttcaccttatgtttagTTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAAGAGTTGGAAGGGCTAAAAGACACCTTGCAATCCGAACGACAAAGTTCCA
                                     tcttcacctt  CT-rich tract
                        ataattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggaaatgcctatcttataaaagtgtacatttaatacatatataaaagtggacattttgttgaggagataattacttcagtcttcaccttatgtttagTTGCGAGAAGATCTACAGTTGAAGACAAAACAAGAAACAGAGATGCAAGAAGAGTTGGAAGGGCTAAAAGACACCTTGCAATCCGAACGACAAAGTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG