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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atatccacaaaaagctaatgctaaatgctattttaagtacttagcacaatgttttatagtaatggattgcattagatttccctataattgtttttggaggaaccatgccttcttttgcgagatttattaaggtccttaacttcaaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAGTG

Basic information

species Oryza sativa
transcript LOC_Os01g55590.1
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G460078_T02 (Zea mays), 3'ss of exon 6
atatccacaaaaagctaatgctaaatgctattttaagtacttagcacaatgttttatagtaatggattgcattagatttccctataattgtttttggaggaaccatgccttcttttgcgagatttattaaggtccttaactt-caaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAGTG
                                                |   |  || | | | | |   | | | | |       ||| | ||||| || | |   | ||  ||||  |    |||| | ||||||||||| ||| | ||||||| ||||| || ||||||||||||||||| ||||| ||||| |||||||||
------------------------------------------------agactacattgcattag-tgatagtggctcttatcgcgattatgtttggggggatc---cgtttctttgtcatcactattgaagtccttaactttcaagtgtacATGTGCATGGGCTTTTCAATGCTCTATTTGCGCCCCTTTATTCAGGATCAGTG

upper sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G460078_T01 (Zea mays), 3'ss of exon 6
atatccacaaaaagctaatgctaaatgctattttaagtacttagcacaatgttttatagtaatggattgcattagatttccctataattgtttttggaggaaccatgccttcttttgcgagatttattaaggtccttaactt-caaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAGTG
                                                    |  || | | | | |   | | | | |       ||| | ||||| || | |   | ||  ||||  |    |||| | ||||||||||| ||| | ||||||| ||||| || ||||||||||||||||| ||||| ||||| |||||||||
--------------------------------------------------actacattgcattag-tgatagtggctcttatcgcgattatgtttggggggatc---cgtttctttgtcatcactattgaagtccttaactttcaagtgtacatGTGCATGGGCTTTTCAATGCTCTATTTGCGCCCCTTTATTCAGGATCAGTG
















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|29617789|gb|CB622801.1|CB622801
EST:     ATGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACC                         ATGTGCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG
genomic: ATGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACCatatccacaa ... tcaaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG
EST: gi|88417003|gb|CI573718.1|CI573718
EST:     TGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACC                         ATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG
genomic: TGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACCatatccacaa ... tcaaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG
EST: gi|58605192|gb|CK033225.1|CK033225
EST:     ATGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACC                         ATGTGCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG
genomic: ATGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACCatatccacaa ... tcaaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG
EST: gi|58608782|gb|CK036815.1|CK036815
EST:     ATGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACC                         ATGTGCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG
genomic: ATGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACCatatccacaa ... tcaaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAG

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: 70 (upstream exon), 53 (downstream exon)
Score: 21

GTTCAAATTCTGTCAGAGGCATGGGGATATCGAAGTGAAGATCAATTTCTGCACTGTCTCCCACTGCACCatatccacaa ... tcaaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggaaccatgccttcttttgcgagatttattaaggtccttaacttcaaatttacATGTTCATGGCCTGTTCAATGCTCTATTTGCACCCCTCTATTCTGGATCAGTG
 gtccttaac  putative branch site 
                                       ttaacttcaaattta  TA-rich tract