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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctgcaaactgatagataaatttcaaagaggtgtattttttgtgctcgattgacatttgtttgttggttctttag

Basic information

species Oryza sativa
transcript LOC_Os01g59600.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 3
GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctgca-------aactgatagataaatttcaaagaggtg--tattttttgtgctcga---ttgac--------------atttgtttgttggttctttag
|||||||||||| ||||| ||||||||||| || ||||||||||  | |||        | ||  |   |    ||||  || |    |||||    ||| | |    ||||              ||||| | |||||||||||||
GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTGgtaagatttgcccttatctatcttttttctttggttcagggatgaagttatttggcttgcccaagtcctgactggatcacgatttgatttggtggttggttctttag

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 2
GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgt--aatgtctgcaaactgatagataaatttcaaagaggtgtattttttgtgctcgattgacatttgtttgttggttctttag-------------------
|||||||||||||||||| ||||||||||| || ||  ||||   ||   | |    |  |  ||  ||||  |       |  |   | |  ||  | |   |||  |   | || || |                     
GACTGTTGTTGGAATCAAGTGCAAAGATGGGATTGTTATGgtttgattcttcctccttcctctattgatttttatactactttgtcactttcttcagtggg--tttagtctctcgtgctgtgatttaaccttggaatgaagt
















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|88391292|gb|CI595546.1|CI595546
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAAATTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|33692105|gb|CF320344.1|CF320344
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88391006|gb|CI592914.1|CI592914
EST:     GACCTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GAC-TGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|218496122|gb|FG967266.1|FG967266
EST:     GACTGTTGTTGGAATCAAGTGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88425566|gb|CI569290.1|CI569290
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88407414|gb|CI583872.1|CI583872
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88738269|gb|CI761777.1|CI761777
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATA
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATA
EST: gi|88739654|gb|CI763162.1|CI763162
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGAT
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGAT
EST: gi|88393093|gb|CI616577.1|CI616577
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|58596536|gb|CK007064.1|CK007064
EST:     GACTGTTGTTGGAATCAAGTGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|58601557|gb|CK012085.1|CK012085
EST:     GACTGTTGTTGGAATCAAGTGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|29668732|gb|CB665007.1|CB665007
EST:     GAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|33657519|gb|CF280133.1|CF280133
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|12622988|gb|AU173201.1|AU173201
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88423678|gb|CI617030.1|CI617030
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAA
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAA
EST: gi|88763617|gb|CI773064.1|CI773064
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88722486|gb|CI745996.1|CI745996
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88300705|gb|CI589697.1|CI589697
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88420790|gb|CI564626.1|CI564626
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTC-TG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88454340|gb|CI569912.1|CI569912
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88718828|gb|CI742338.1|CI742338
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAG
EST: gi|29668731|gb|CB665006.1|CB665006
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|33686716|gb|CF314955.1|CF314955
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88396858|gb|CI578007.1|CI578007
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88400550|gb|CI595971.1|CI595971
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|87008998|gb|CI304941.1|CI304941
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAAT
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAAT
EST: gi|163919763|gb|EG714885.1|EG714885
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGGGATCTAATAGG
EST: gi|88722475|gb|CI745985.1|CI745985
EST:     GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTG                         GGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGG
genomic: GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctg ... ggttctttagGGTGTGGAGAAGCTAGTAACTTCGAAGATGATGCTGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGTTGTTGGAATCAAATGCAAAGATGGAATCGTCCTGgtaatgtctgcaaactgatagataaatttcaaagaggtgtattttttgtgctcgattgacatttgtttgttggttctttag

- - - - - - - - - - GCAAAG
- - - - - - - - - - -  AAGATG
- - - - - - - - - - - -  GATGGA