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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatcacttttcttggctggttacttctagtaacatgctttttttgagtcacaataggtagttatcaaagaacggttttatcttgttgctttgaat...

Basic information

species Zea mays
transcript GRMZM2G107867_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 3
ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatcacttttcttggctggttacttctagtaacatgctttttttgagtcacaataggtagttatcaaagaacggttttatcttgttgctttgaat------
||||||||||||||| || || |||| ||| ||  | |||||||||||||||||||||||||| || ||||||||||| ||||| |||||||||||||||||| ||  |  |  || |  ||  | |||| |   |||| ||| |||| |  |     ||  |     |  ||     | ||  | |      |   ||       
ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctt-tcacttgtta-aacacgctcttttagcatt----tacttccaactttaatgcttgcttattttcaccattcaaaacctatgg

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 5'ss of exon 3
ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatcacttttcttggctggttacttctagtaacatgctttttttgagtcacaataggtagttatcaaagaacggttttatcttgttgctttgaat------
||||||||||||||| || || |||| ||| ||  | |||||||||||||||||||||||||| || ||||||||||| ||||| |||||||||||||||||| ||  |  |  || |  ||  | ||||   || | |||   | ||| ||     ||    |  | |||| |   | || | | |  |   |   ||       
ATATGTTGTGATGGAGTACTGCAAGTTTGGAGAACTGTTTGATTACATTGTTGAGAAAGGCAGGTTGCAGGAAGATGAGGCTCGCCGAATCTTCCAGCAGgtacttgaccttactcatttctt-tcactt---gttaaatgtgctcttttagcatttatttccaact-tcaatgcttgcttat-tttcatcattcaaaacctatgg

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 3
ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatcacttttcttggctggttacttctagtaacatgctttttttgagtcacaataggtagttatcaaagaacggttttatcttgttgctttgaat
|||| |||| ||||| |||   |||| ||| ||| | || ||||||||||| ||||| ||||| || ||||||||||||||||||    | || |||||||||          || ||  ||  ||   | || | |   |  |||||   ||||||      | ||  |||   |   | | || |||           
ATATTTTGTCATGGAGTATGTGAAGTCTGGAGAGCTGTTCGATTACATTGTAGAGAAGGGCAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtagg-------attgtttacta-ttttgtgtaattaagagactttttcatgtcacag-----attttccaagctaatttctgattttggaagcag----

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 3
ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtat-ttatcacttttct-tggctggt-tacttctag--taacatgctttttttgagtcacaataggtagttatcaaagaacggttttatcttgttgctttgaat
 |||||||||||||| |||   |||| ||| ||| | |||||||| ||||||||||||||||||||||| |||||||| ||||||    | ||||||||||| | || || |||| |  |  |  || |  || |||  || ||||   | |||||||   | |  || |||        ||  |  ||||    |         
TTATGTTGTGATGGAGTATGTCAAGTCTGGAGAGCTCTTTGATTATATTGTTGAGAAAGGCAGATTACAAGAAGATGAGGCTCGTAACTTTTTCCAGCAGgtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagt--gttgtttgtgtttgac--tcatatccgaatag-------

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G39440.1 (Arabidopsis thaliana), 5'ss of exon 2
ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatcacttttcttggctggttacttctagtaacatgctttttttgagtcacaataggtagtt-atcaaagaacggttttatcttgttgctttgaat----
 ||||||||||||||||||  ||||| ||| ||  ||||||| || ||||| |||||||| | |||||||||||| || |||||||   | || |||||||  |||   |  | | | |  |  ||| | | |  |   ||  |||  | |  |   |||     ||        |||  |||||| |      | |        
TTATGTTGTGATGGAATATGTTAAGTCTGGAGAACTATTTGACTATATTGTAGAGAAAGGTAAATTACAGGAAGACGAGGCTCGTCATCTTTTTCAGCAGg--tttggtatatatatag--tattta-tccaaacattttgtatttcataaaaccttatatccttttcgattggcaacacttttatttaaaccatatattctcag

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|71329108|gb|DR801263.1|DR801263
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
EST: gi|148999574|gb|EE036551.2|EE036551
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
EST: gi|89758870|gb|DY687889.1|DY687889
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
EST: gi|60359581|gb|DN226554.1|DN226554
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
EST: gi|211427354|gb|FL101767.1|FL101767
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAA
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAA
EST: gi|71447675|gb|DR828725.1|DR828725
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
EST: gi|211440538|gb|FL230375.1|FL230375
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
EST: gi|211440534|gb|FL230371.1|FL230371
EST:     TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAG                         ATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC
genomic: TTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatca ... tcatgaacagATCATATCTGGCGTCGAATACTGCCATAGAAACATGGTTGTCCACCGTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGTTGTGATGGAATATTGTAAGTATGGCGAGTTATTTGATTACATTGTTGAGAAAGGCAGATTACAGGAAGATGAAGCTCGTCGAATCTTCCAGCAGgtatttatcacttttcttggctggttacttctagtaacatgctttttttgagtcacaataggtagttatcaaagaacggttttatcttgttgctttgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC