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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtattttaagagttagtggacatcaattttataataagataggatatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 7
ttgtattttaagagttagtggacatcaattttataataagataggatatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
 |   |  |   || ||| ||  |  ||| |    |||   |    | | |  |       |||| | |  || | |    |  |  || |||||   |||||| || || |||||||||||||||||||| || ||||||||||| |||
ctagttgcttgtagatagaggctactaatgtgcagatatctttatttctatggtaatgagttaaactgaaatttcttgtggttgtgtatcacttgagtagGTAAGAAATTCTGGAACCTCTTTCACTTGCAGCCTATGCGTGATCAGAAG

upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 9
--ttgtattttaagagttagtggacatcaattttataataagatagg-atatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
  ||  || | | || |   |   |||   ||| | |  || ||    || |  |   |   ||  || |    || |    |||| |      |     ||||||||||||| |||||| | ||||| ||||| || ||||||||||| |||
gttttcatatcatgaatcc-ttttcatagttttcaaaggaaaatgactatttaacaacttgaagctaaatatggttgctaatattattctgc--ccaattcagGTAAAAAGTTCTGGAACTTGTTTCATTTGCAGCCTATGCGTGATCAGAAG

upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G40550.1 (Glycine max), 3'ss of exon 7
ttgtattttaagagttagtggacat-caattttataataagataggatatgtcttttc-acagtaaagttaccttcccttcattacttcattacttggac-agGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
   | | |||      |  ||| ||  |  | | |||   ||      ||    || | |   | |    || | |  || |  | |||  |  |    | ||| || ||||| |||||||| ||||| |||||||| ||||||||||| |||
---tttcttagcgtacaaaggatatatagctatttaacgtgaagatcaataatgttgcgattattattccacttgctattgaagatttctctgttcaatccagGAAAGAAGTTCTGGAACCTGTTTCATTTGCAACCTATGCGTGATCAGAAG

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtcttttcacagtaaagttaccttcccttcattacttcattacttggacagGTAAAAAGTTTTGGAACCTCTTTCACTTGCAACCAATGCGTGATCAAAAG
                taaagtta  TA-rich tract