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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCCCTTGCGTCTGACTTCATGTATAACCATATGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgtttatagatgttttacatttcagatagcattgcattagctattgagctcctccaagtagtgtatcttttcaccatttttatttgtataattgaatgttcttgtggaaataaattctgttgcag

Basic information

species Zea mays
transcript GRMZM2G174696_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174696_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 5'ss of exon 9
GTTTCCCTTGCGTCTGACTTCATGTATAACCATATGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgtttatagatgttttacatttcagatagcattgcattagctattgagctcctccaagtagtgtatcttttcaccatttttatttgtataattgaatgttcttg--tggaaataaattctgttgcag------------------------------------------------------------------------
||||||||||||||||||||||||||||| || |||||||| || || ||| |||||||||||||||| ||  ||||||||||||| ||||||| ||      | | ||  ||  ||||| || |||   | |||||||  |||| ||  || |||| ||||      |  ||||| ||  ||  | |   ||  | | |  ||  | |||                                                                             
GTTTCCCTTGCGTCTGACTTCATGTATAATCACATGTCAAGGGACGTTACTTCCAGCTTTGGTTATGACTATATGCTTAGGCAGgttagtgtttcta------tcaaatagcaagtagcaatgtattctttcttgagcttatcca-gttttgcatctcttcatggacct-gtttgtgtatatgggtatctgtgaatagtacaaagctgtgtactcttgctcctgcagttccttgttttctgatatttccgtttagtagttttgaatttatcaatgaattttactgcag

upper sequence: GRMZM2G174696_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv03s0097g00590.t01 (Vitis vinifera), 5'ss of exon 9
GTTTCCCTTGCGTCTGACTTCATGTATAACCATATGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgtttatagatgttttacatttcagatagcattgcattagctattgagctcctccaagtagtgtatcttttcaccatttttatttgtataattgaatgttcttgtggaaataaattctgttgcag
|||||  | || || || |||||||| ||  |||||||||||||||| ||||| || ||||||||||||||| | ||| | ||||| |   ||| |||   |   | |  |    || |     ||||  | ||| ||   | ||  ||   |||   ||||    ||||  |     |||  | ||||| |                      
GTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAGgtaa---tttctagtattgcaaaaactttcttatctagatattatgt-ttgtgcctttgcatata---tattacttcaattgtttttgtcacgcaat-aattgttcct----------------------
















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|32919687|gb|CF024499.1|CF024499
EST:     AGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: AGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|37398312|gb|CF636468.1|CF636468
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|211276272|gb|FL458556.1|FL458556
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|6095402|gb|AW120069.1|AW120069
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|6095403|gb|AW120070.1|AW120070
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|211352868|gb|FL030242.1|FL030242
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|71428446|gb|DR809496.1|DR809496
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|32911927|gb|CF016739.1|CF016739
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|60338504|gb|DN205477.1|DN205477
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCTTAAGAGGCAAAATAGACTGGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|5607738|gb|AI901405.1|AI901405
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|6095404|gb|AW120071.1|AW120071
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|60355450|gb|DN222423.1|DN222423
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|83279399|gb|DV943407.1|DV943407
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
EST: gi|32919688|gb|CF024500.1|CF024500
EST:     TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG                         TGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG
genomic: TGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgttt ... tctgttgcagTGCCGCCTAAGAGGCAAAATAGACTCGAATGGTGTTGTTGCCGCATACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCCCTTGCGTCTGACTTCATGTATAACCATATGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAGgtcagtgtttatagatgttttacatttcagatagcattgcattagctattgagctcctccaagtagtgtatcttttcaccatttttatttgtataattgaatgttcttgtggaaataaattctgttgcag

- - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - GAGATG