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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAAgtgagtataatgatattatttttcttcacttggttcgtctttgttagcctttcagcagtataacttgaatttgacatgatcactcccaccacgcag

Basic information

species Oryza sativa
transcript LOC_Os05g06460.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 13
--------------TGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAAgtgagtataa-tgatattatttttcttcacttg-gttcgtctttgttagccttt--------------cagcagtataacttgaatttg-acatgatcactcccac-cacgcag
              |||||| || ||||||||||| || ||||||||||||||||| |||||||| ||||| |||||||||||||||||||| ||||||||||||||  ||||||||||| |   ||||| | | ||| ||     |  ||| |||||||| |  | |               ||||||  | ||||||  || |||| |||  | |       ||||
TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAatgccatcgccctaggaactcgtgtgcaagtgagtgtcgctgataatctattttttattgagcattcatctttgttggattctgtcatactcgtagctagcagttcatcttgaacctgtacataatcgtttctgtatttgcag

upper sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 13
TGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAAgtgagtataa-tgatattatttttcttcacttg-gttcgtctttgttagccttt--------------cagcagtataacttgaatttg-acatgatcactcccac-cacgcag
|||||| || ||||||||||| || ||||||||||||||||| |||||||| ||||| |||||||||||||||||||| ||||||||||||||  ||||||||||| |   ||||| | | ||| ||     |  ||| |||||||| |  | |               ||||||  | ||||||  || |||| |||  | |       ||||
TGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAGGAACTCGTGTGCAAgtgagtgtcgctgataatctattttttattgagcattcatctttgttggattctgtcatactcgtagctagcagttcatcttgaacctgtacataatcgtttctgtatttgcag

upper sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 13
TGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAAgtgagtataatgatattatttttcttcacttggttcgtctttgttagcctttca--gcagtataacttgaatttgacatgatcactcccaccacg-cag-------------------------------------------------------
|||||||||||| || || || || || || || || ||||| |||||||| ||||||||||||||||| ||||| || ||  ||||||| ||  | || || | | |    |   ||  | ||     |  |    |     ||||    | |  |  | ||    || |||||   |  |     | |   |  ||                                                        
TGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAGGAACACGTATTCAGgtaaattttcctaccatagctgtcacatgtgagagactgggatttagttcgtaatggttgcatgtgctgcatttggtttatttttgtcgatagcaacaagaaactttttatccgtctatatggtaactcccaacattgttgtgctacaatgcag

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|25807039|gb|CA763000.1|CA763000
EST:     ACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACATTGTTCGAGGTGCTGGAC
genomic: ACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAAgtgagtataa ... caccacgcagGACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGAC
EST: gi|29680626|gb|CB676901.1|CB676901
EST:     ACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGAC
genomic: ACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAAgtgagtataa ... caccacgcagGACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGAC

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: 71 (upstream exon), 70 (downstream exon)
Score: 10

TGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAGGAACTCGGTTGCAAgtgagtataa ... caccacgcagGACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGACGAACTCTTTAAAGCAGCCAAG




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