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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGTATTGGAGCTTTGTGGACTGGCCTCGGTCCAAACATAGCACGCAATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttgattctttcaccttgtattcttgtggccactttctatgtgtgttactgttcatcactttgttctgtttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g74640.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74640.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G852877_T01 (Zea mays), 5'ss of exon 5
GAAGGTATTGGAGCTTTGTGGACTGGCCTCGGTCCAAACATAGCACGCAATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttgattctttcaccttgtattcttgtggccactttctatgtgtgttactgttcatcactttgttctgtttgtgcag----------------------------------------------------
||||||||||||||||||||||||||||| ||||||||  | ||||||||||| |||||||| ||| |||||||||||||||| || ||  |||||||||| ||| |||| ||| | |  |  |  | | ||| ||| | | | |   | | | |||||||  ||||||||||||  |||||                                                    
GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattgactctcttatgtctt--tgtggtgaccattatatttcattatcattgttcattcctttgttctgttcatgcagatgtttctaaaacttcctgggtttactgataacgtttttacgcatcttttag

upper sequence: LOC_Os01g74640.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G852877_T02 (Zea mays), 5'ss of exon 5
GAAGGTATTGGAGCTTTGTGGACTGGCCTCGGTCCAAACATAGCACGCAATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttgattctttcaccttgtattcttgtggccactttctatgtgtgttactgttcatcactttgttctgtttgtgcag
||||||||||||||||||||||||||||| ||||||||  | ||||||||||| |||||||| ||| |||||||||||||||| || ||  |||||||||| ||| |||| ||| | |  |  |  | | ||| ||| | | | |   | | | |||||||  ||||||||||||  |||||
GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacctattgactctcttatgtctt--tgtggtgaccattatatttcattatcattgttcattcctttgttctgttcatgcag

upper sequence: LOC_Os01g74640.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G165629_T02 (Zea mays), 5'ss of exon 5
GAAGGTATTGGAGCTTTGTGGACTGGCCTCGGTCCAAACATAGCACGCAATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttgattctttcacct-tgtattcttgtggccactttctatgtgtgttactgttcatcactttgttctgtttgtgcag
||||||||||||||||||||||||||||| ||||||||  | ||||||||||| |||||||| ||| |||||||||||||||| || ||  |||||||||| | | | || ||| | |  | | | |  ||||    |  ||  ||   | | | |||||||  ||||||||||||  |||||
GAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAGgtacatatcgactctcttatgtctttgtggttgttattatatttcat---tatcattgttcattcctttgttctgttcttgcag

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|29663991|gb|CB660266.1|CB660266
EST:     ATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTA
genomic: ATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttg ... gtttgtgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTA
EST: gi|29682716|gb|CB678991.1|CB678991
EST:     ATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTA
genomic: ATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttg ... gtttgtgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTA
EST: gi|33684429|gb|CF312668.1|CF312668
EST:     ATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAG                         ATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTA
genomic: ATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttg ... gtttgtgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTA

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), 65 (downstream exon)
Score: 19

GAAGGTATTGGAGCTTTGTGGACTGGCCTCGGTCCAAACATAGCACGCAATGCTATAATTAATGCTACCGAGTTGGCCAGCTACGACCAACTCAAACAGgtgccttttg ... gtttgtgcagATGTTTCTAAAACTTCCTGGGTTTACTGATAACGTTTTTACCCATCTTTTAGCTGGACTTGGTGCTGGATTTTTTGCTGTTTGCATTGGCTCTCCAGTGG




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