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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACCTGAGGCTACCAGTGAAATCACTTTGAAACTTCAGCAATCACTAGATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatgagacttttgttttgtcagtttctacatgtgacgtgcattcaacacgtaactccactctaatctaaactattaatacatggaaaacatttac...

Basic information

species Oryza sativa
transcript LOC_Os07g22640.4
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22640.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G092129_T01 (Zea mays), 5'ss of exon 11
TCAACCTGAGGCTACCAGTGAAATCACTTTGAAACTTCAGCAATCACTAGATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatgagacttttgtt-ttgtcagttt-ctaca-tgtgacgtgcattcaacacgtaactccactctaa---tctaaactattaatacatggaaaacatttac
| || |||||  ||||   ||   |||| |||| || |  || ||||| ||| |  |||||| |||||||||||||||||| || |||||||||||| |||||||  || |  | |  || || | | | |  |||| | | || ||  |     |  |   |  |     |    ||| |  | |  |  ||   |||       
TGAATCTGAGATTACCCAAGACGCCACTCTGAAGCTGCTACATTCACTGGATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgggtttctacttattattaatgtgttacactttaacctgagtagcctatatccttgaagctagagatcctagaggacttgtgaataagaaat------
















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|29627155|gb|CB632166.1|CB632166
EST:     ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|29689585|gb|CB685860.1|CB685860
EST:     AATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: AATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|29624992|gb|CB630003.1|CB630003
EST:     ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|29665128|gb|CB661403.1|CB661403
EST:     ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|29662980|gb|CB659255.1|CB659255
EST:     ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|29658143|gb|CB654418.1|CB654418
EST:     TAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: TAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|88736008|gb|CI759516.1|CI759516
EST:     GGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: GGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|29657425|gb|CB653700.1|CB653700
EST:     ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
EST: gi|29685261|gb|CB681536.1|CB681536
EST:     ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAG                         GTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT
genomic: ATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatga ... tgcttttcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACCTGAGGCTACCAGTGAAATCACTTTGAAACTTCAGCAATCACTAGATTCTCTTAAAATTAAGGACACCAAGGATAGAGGAACATTACATCTTCAGgttagcatgagacttttgttttgtcagtttctacatgtgacgtgcattcaacacgtaactccactctaatctaaactattaatacatggaaaacatttac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA