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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactcttaaaaaacattcaagttatttttctaactttgattttcagaaacttcagataagctatgctggtcaatggattttatctccatctcttcttgctttag

Basic information

species Oryza sativa
transcript LOC_Os08g32630.5
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32630.5 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM5G851815_T01 (Zea mays), 5'ss of exon 14
GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactcttaaaaaacattcaagttatttttctaactttgattttcagaaacttcagataagctatgctggtcaatggattttatctccatctcttcttgctttag
||||||||||| ||||||||||| || |||||| |||| ||||||||||||||| ||||||| ||||| |||||||| ||||||||||||| || || ||||    |||  || |  |         |  | | || || ||    |      | || |                                   
GATGTAATACAGTTTGGACCTCTTGTGAAAACTTTGGGGCTAGTAATGATCACTAGACCACAAATTTTACCTTCCATATTTAAGCAGgtaggcttttgaaaaggcatcattttctcatgaggctgaagtctgttagtaatttattctgtttcctcctag-----------------------------------
















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|29670150|gb|CB666425.1|CB666425
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTTAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGG
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
EST: gi|29670151|gb|CB666426.1|CB666426
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
EST: gi|22305644|gb|BQ906866.1|BQ906866
EST:     TCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTGTTTAAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCACTTTTGTGATGCTTG
genomic: TCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATT-TTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCA-TTTTGTGATGCTTG
EST: gi|29677474|gb|CB673749.1|CB673749
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
EST: gi|88244952|gb|CI244801.1|CI244801
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
EST: gi|88847633|gb|CI018324.1|CI018324
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG                         GCTGGACCTGGGGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
EST: gi|88245161|gb|CI245010.1|CI245010
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
EST: gi|88841109|gb|CI001071.1|CI001071
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
EST: gi|29679962|gb|CB676237.1|CB676237
EST:     GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAG                         GCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT
genomic: GTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 72 (downstream exon)
Score: 17

GATGTAATACAATTTGGACCTCTGGTTAAAACTCTGGGTCTAGTAATGATCACTCGACCACAGATTTTGCCTTCCATTTTTAAGCAGgtagactctt ... cttgctttagGCTGGACCTGGAGTCATTCTTAACTGGTCAGGCCATTTTGTGATGCTTGGTTACTATACATTCCTTTCCACCTTTATAGACCCAATCCTCAG




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