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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctactcgtcacttgtctgcatgtttttgttctcaacttataaatataatagctagttgataccccgcgctttgttgcgggatatgtatatgaata...

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 7
CAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctactcgtcacttgtctgcatgtttttgttc--tcaacttataaatataatagct---agttgataccccg-cgctttgttgcgggatatgtatatgaata
||||| ||||||||||| ||||  ||||| | |||||||||||||||||||||||||||  |||| || || |||||||| |||||||||||||| || ||||   ||||| |||| ||    |||||| ||||    |||   |  || |   ||| ||   | |   ||   |  |  | |  || |  ||   |  ||     
CAAGGACCTGAAACTGACCGTGGGACAGTAAAGAAGATAAGAGATGCCATAGATAACCAAACAGAAGTTACTGTTCAGCTGATAAATTATACAAAGAGCGgtaca-tactcttcacatgctcccatgttcttgtaagatcatgatgcaatttctatacctccaaatatttataacaacaatctagtgtgctatcgctgcat-----
















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|29624477|gb|CB629488.1|CB629488
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29630119|gb|CB635128.1|CB635128
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29681859|gb|CB678134.1|CB678134
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29624448|gb|CB629459.1|CB629459
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29641853|gb|CB646860.1|CB646860
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|2317379|gb|C22433.1|C22433
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     AGATCCCCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29628293|gb|CB633304.1|CB633304
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29678744|gb|CB675019.1|CB675019
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29630466|gb|CB635475.1|CB635475
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|2317377|gb|C22431.1|C22431
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29624450|gb|CB629461.1|CB629461
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
EST: gi|29646710|gb|CB651717.1|CB651717
EST:     AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTG                         GTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
genomic: AGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctact ... acttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGCCCTGAAACTGATCGTGCAACAGTTAGGAAGATAAGAGATGCCATAGATAACCAGGCAGAGGTCACAGTTCAGCTCATAAATTATACAAAAAGTGgtaggctactcgtcacttgtctgcatgtttttgttctcaacttataaatataatagctagttgataccccgcgctttgttgcgggatatgtatatgaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA