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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactgttcatattttgtcacattcagataatcaatcaatcaaaaagaacatgttgctgagttatgaatcattacag

Basic information

species Oryza sativa
transcript LOC_Os03g25940.4
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G075153_T03 (Zea mays), 5'ss of exon 11
CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactgttcatattttgtcacattca--gataatcaatcaatcaaaaagaacatgttgctgagttatgaatcattacag
|||| |||| ||| |||||||||||||| |||||||||||||| || || ||||| |||||||||||||| ||||||||||||||||||||||| |||||||| | |  ||| || ||| | | ||||||  || |||     | |       ||  |   |||  ||      | |  ||||
CTACGAGGAAATTCATTGATTCTGTTAAAATACCCTATCATGCGCCTTCTTTTGGAGGCTGTGAGAGCATAATTGATCAGCCTGCCATCATGTCCTACTGgtaagaa--gttgatgttt-gactcattcaatgaaaatggcatagttgtgctaaattttgagctctgtggcctgtaa--acag

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G113873_T02 (Zea mays), 5'ss of exon 10
CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactgttcatattttgtcacattcagataatcaatcaatcaaaaagaacatgttgctgagttatgaatcattacag
| || |||| ||| || ||||||||||||||||||||||||||||| || || || |||||||||||||| |||||||||||||| |||||||| |||||||| | |||   ||   |||||   ||| ||| | ||||  ||  ||  | |   |  ||||   || |||          
CCACAAGGAAATTCATCGATTCTGTTAAGATACCCTATCATGCCCCTTCTTTCGGAGGCTGTGAGAGCATAATTGATCAGCCTGCTATCATGTCCTACTGgtaagaacttaaca---tttgtggtattgagacattcaa--aacaaatgacatacttgtgctacattttgag---------

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G113873_T03 (Zea mays), 5'ss of exon 11
CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactgttcatattttgtcacattcagataatcaat-caatcaaaaagaacatgttgc----tgagttatgaatcattacag----
| || |||| ||| || ||||||||||||||||||||||||||||| || || || |||||||||||||| |||||||||||||| |||||||| |||||||| | |||   ||   |||||   ||| ||| | ||||  |||   | |      || | |    |||| | ||   | ||| |     
CCACAAGGAAATTCATCGATTCTGTTAAGATACCCTATCATGCCCCTTCTTTCGGAGGCTGTGAGAGCATAATTGATCAGCCTGCTATCATGTCCTACTGgtaagaacttaaca---tttgtggtattgagacattcaaaacaaatgacatacttgtgctacattttgagctctgtggc-ttataaacag

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA09G37020.3 (Glycine max), 5'ss of exon 9
CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg----ttcatatt----ttgtcacattcagataatcaatcaatcaaaaagaacatgttgctgagtt---atgaatcattacag-------------------------------------------------------------------------------------------------
| || |  | ||||||||||||  | || || || |||  |||  | || ||||| ||||||||||||||| | ||||| ||||| ||  |||||||||||||   | |     | ||| ||    ||||||  ||  ||| ||      |  | | ||   ||| | ||    |   |||   |  |   |                                                                                                 
CCACAATAAAATTTATTGATTCATTGAAAATCCCATATATTGCGGCCTCGTTTGGTGGCTGTGAGAGCATTGTGGATCAACCTGCTATTTTGTCTTACTGgtactcatttggattccatgttcaatttgtcatgtt--gatgattttgacactacacagggaatggtcctctacttgaatgtgaccctgtggtgaaagcatctttagctggtccttttggtttgttatagtgtcaaagtttaccttgtttttgttaatttaatttaattttcaacatattgtgcaacag

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA18G49660.1 (Glycine max), 5'ss of exon 10
CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactgtt----catattttg---tcacattcagataatcaatcaatcaaaaagaacatgttgctgagtt--atgaatcattacag-------------------------------------------------------------------------------------------------
| || |  |  |||||||||||  | || || || |||  |||  | || ||||| ||||||||||||||| | ||||| ||||| ||  |||||||||||||   | | ||    ||| ||||    |  |||   ||| ||    || |      | |   ||     | ||  |||   |  |  ||                                                                                                 
CCACAATAAAGTTTATTGATTCACTGAAAATCCCTTATATTGCGGCCTCGTTTGGTGGCTGTGAGAGCATTGTGGATCAACCTGCTATTTTGTCTTACTGgtactcatttttattccatgttttaagttgtcatgttgatgatttgacactactcggggaatggtcctctacttgaatgtgaccctgtagtgaaagcatcttttgctggtccttttgttaatttttagatttggcttggtggtggttgttgtatgtttaatttaattttcaacatattgtgcaacag

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv14s0108g01110.t01 (Vitis vinifera), 5'ss of exon 10
CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactgttcatattttgtcacattcagataatcaatcaatcaaaaagaacatgttgctgagttatgaatcattacag------------------------------------------------------------------------------
| || |  |  ||| ||||| |  | || || || |||  ||||||||| || || ||||||||||||||| ||||||||||||| || |||||||||||||||   |  |   |  | |     | |   ||||   |  |  |        |||    || | | |  |||||  | |                                                                               
CCACCATCAAGTTTGTTGATGCATTGAAAATCCCTTATATTGCCCCATCCTTCGGAGGCTGTGAGAGCATTGTTGATCAGCCTGCGATTATGTCTTACTGgtattccccttcattcctctcatgtagtagcataaatgaatacccctgtttggcattggtctcactgaataatcacaagacttgcacattgggtttcaccttgtccttgttacttggttctgattcttttaattgaattgttcgtgctttccaaaacag

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|25803371|gb|CA759332.1|CA759332
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|89184572|gb|CI006997.1|CI006997
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|15855064|gb|BI807876.1|BI807876
EST:     TTT-GGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCACGAGAGAAATCTATGGAATCAAGGACAACTTGATCA
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCA-GAGAGAAATCTATGGAATCAAGGACAACTTGATCA
EST: gi|88455535|gb|CI521755.1|CI521755
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTCCCATCATGTCTTAGTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|88254490|gb|CI353314.1|CI353314
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29673041|gb|CB669316.1|CB669316
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|88903949|gb|CI006182.1|CI006182
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|89168537|gb|CI038891.1|CI038891
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|86530519|gb|CI170725.1|CI170725
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29660677|gb|CB656952.1|CB656952
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29686154|gb|CB682429.1|CB682429
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|12623045|gb|AU173258.1|AU173258
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATNTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|58585673|gb|CF983981.1|CF983981
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|117251720|gb|CT861201.1|CT861201
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29625315|gb|CB630326.1|CB630326
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29641911|gb|CB646918.1|CB646918
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29639161|gb|CB644170.1|CB644170
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|88902302|gb|CI374910.1|CI374910
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|86413644|gb|CI019229.1|CI019229
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29645225|gb|CB650232.1|CB650232
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29614166|gb|CB619179.1|CB619179
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|2798534|gb|AA751828.1|AA751828
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29614914|gb|CB619927.1|CB619927
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|29613257|gb|CB618270.1|CB618270
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|88998108|gb|CI037993.1|CI037993
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
EST: gi|38475493|gb|CF959626.1|CF959626
EST:     TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTG                         GGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG
genomic: TTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactg ... atcattacagGGATTCAAAGGAGCAGAGAGAAATCTATGGAATCAAGGACAACTTGATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACTAGGAGATTTATTGATTCTGTTAAGATACCCTATCATGCCCCATCATTTGGGGGCTGTGAGAGCATTATTGATCAGCCTGCCATCATGTCTTACTGgtatggactgttcatattttgtcacattcagataatcaatcaatcaaaaagaacatgttgctgagttatgaatcattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA