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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaaagattgtgtgtaacatggataaatacatagttataatggccacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGATGGAGAATGATGATGGCGGTAATCCTGCTTTGCTTGGTAGCTGTAATG

Basic information

species Zea mays
transcript GRMZM2G151268_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151268_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 3'ss of exon 1
gtaaaagattgtgtgtaacatggataaatacatagttata-atggccacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGATGGAGAATGATGATGGCGGTAATCCTGCTTTGCTTGGTAGCTGTAATG
 |      |  |  ||  || | |  | |||||     || ||    | |  || ||  | ||   |    |  |  ||   |       ||| ||| |||||||||||||||||||| ||||| || ||||| |||||||||||| ||||  |||||||||||||||| || ||||| ||||||||||||||||| ||||
-tgtgctctcttcagtttcaagaaccattacattacattacatacgaaaaccctcctattaccataaggcgtgatcttgtcttgcactcttgcttgagtagGCTGAGCTAAGAGCAAGTGTGTTCGAGGCCATAGAAGAGGAGGATAGGGTAGTGGAGAATGATGATGGTGGGAATCCCGCTTTGCTTGGTAGCTGCAATG

upper sequence: GRMZM2G151268_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G55000.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------------------------------------------------------------------gtaaaagattgtgtgtaacatggataaatacatagttataatggccacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGATGGAGAATGATGATGGCGGTAATCCTGCTTTGCTTGGTAGCTGTAATG
                                                                                                     |   ||  |   ||  |    |||  |   ||  |    || |  |  | | | ||| || |  | ||| || |||  | | | ||  ||  ||  |||||||||||  | ||||| ||||||||||| |||||||| |||||| | ||||| |||||  |||| ||      ||| ||| || | || ||||||||||
gtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatacatacattactctttttctagggttcctgctattcagatcgaa--atgctcgatattgttaattgcctatgcatctggaatcttgct-gatagtttatttg--tgtttg--tagGCTGAGCTCCGTGCAAGTGTGTTTGAAGCAATTGAAGAAGAGGATAGAGTGATAGAGAACAATGAAGGACCGCCTCCAGCTCTGTTGGGAAGCTGTAATG
















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|211533622|gb|FL412539.1|FL412539
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211305553|gb|FL417499.1|FL417499
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211029306|gb|FL370361.1|FL370361
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGAT-ACG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|29945213|gb|CB815527.1|CB815527
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211511056|gb|FL378831.1|FL378831
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211355840|gb|FL403701.1|FL403701
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211317656|gb|FL416767.1|FL416767
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211533628|gb|FL412545.1|FL412545
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211156585|gb|FL395419.1|FL395419
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211036668|gb|FL370397.1|FL370397
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211191821|gb|FL384737.1|FL384737
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211254949|gb|FL427088.1|FL427088
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|9952754|gb|BE639217.1|BE639217
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211163025|gb|FL401335.1|FL401335
EST:     GCTCGTCACCCTGCACCCTCGAGAAGAAGGGCGTTCTCG-MAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: GCTCGTCACCC-GCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211403469|gb|FL414956.1|FL414956
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211076740|gb|FL399053.1|FL399053
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211537120|gb|FL426924.1|FL426924
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGATGGAGAATGATGATGGCGGTAATCCTGCTTTGCTTGGTAGCTGTAATG
                         tcttgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagattgtgtgtaacatggataaatacatagttataatggccacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGATGGAGAATGATGATGGCGGTAATCCTGCTTTGCTTGGTAGCTGTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA