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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtacttgtccttcctgtgtttacccccttaagaatgccagttgtaatgacttgaacattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG

Basic information

species Zea mays
transcript GRMZM2G168506_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 5
gtagtgtacttgtccttcctg--tgtttacccccttaa------gaatgccagttgtaatgacttgaacattccat--agGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG
||||| ||| ||||||   |   | | |||    |||       | ||  |  ||| | | ||| ||  |||   |  |||||||| |||| ||||||||||| || || |||||||| ||||| | ||| ||||||||||
gtagtttacctgtcctctttaactttctacagtgttagccacttggatttcccttgcagtaactcgactattttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG
















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|74238562|gb|DT646476.1|DT646476
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|50334166|gb|CO529292.1|CO529292
EST:     CTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: CTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|61119514|gb|DN560475.1|DN560475
EST:     TGGAGAGA-CATCTTTCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: TGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|30088239|gb|CB886444.1|CB886444
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|32834904|gb|CD974582.1|CD974582
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|33103527|gb|CF063487.1|CF063487
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|148987376|gb|EE031220.2|EE031220
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|74239750|gb|DT647664.1|DT647664
EST:     CCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: CCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|71304282|gb|DR788255.1|DR788255
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|31998069|gb|CD661904.1|CD661904
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|166512308|gb|EG321376.1|EG321376
EST:     TCTTCCCCAATGCAGA-                         GGGAAGCTATTGACAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAA
genomic: TCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTG-CAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAA
EST: gi|4647604|gb|AI622679.1|AI622679
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|12972561|gb|BG268043.1|BG268043
EST:     CCTATCAAATGTCGAGAAGGGTGGAGATACTTATTTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: CCTATCAAATGTCGAGAAGGGTGGAGAGAC-CATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|94475795|gb|EB704753.1|EB704753
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|76913826|gb|DV165269.1|DV165269
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|83278553|gb|DV942561.1|DV942561
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
EST: gi|60398051|gb|DN230867.1|DN230867
EST:     ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAG                         GGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC
genomic: ACCTATCAAATGTCGAGAAGGGTGGAGAGACCATCTTCCCCAATGCAGAGgtagtgtact ... cattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgtgtttacccccttaagaatgccagttgtaatgacttgaacattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG
                 ttaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgtacttgtccttcctgtgtttacccccttaagaatgccagttgtaatgacttgaacattccatagGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA