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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtagtctgtgacctctcacacgctctcacacacatatgtagcctttggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g54020.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 12
gtctgtagtctgtgacctctcacacgctctcacacacatatgtagcctttggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
|| | |    | |  | |||    ||||||| |  || | | |   | ||  ||     |||||||||||  |||| ||  ||  ||||||  |||| |||||||||||||||||||| |||||||  ||||||||||| || ||||||||||| || | ||| ||||| |||
gtttctctcttctcgcttct---gcgctctctc-tacctctcttttcattattat---ggaaactcattccattgaactcata--tttcagTATGGAGTTTGACAACCCAGAGAGGCCGGAATGCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAG

upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA04G09130.1 (Glycine max), 3'ss of exon 12
------------------------------------------gtctgtagtctgtgacct-ctcacacgctctcacacaca-tatgtagcctttggtacat----aagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                           ||  |  |   | |  | ||      || | |  |    | | | |  |||||||  |    ||   |||  | || || |      | ||| ||| ||||||||||||||| | |||||||||||||| ||||||||||| || || |||||| ||                     
tgattgatgatcttagtcctcagaggtttagtctataaatgcttccatttttcataattttcttgttttctataaatctttctttttggtgtttggtaagTTCTCAAATTACTTGTGCACTTTATGACAAATCTTACAGTTTGGAATTTGACAACTCTGAGAGGCCTGAATGTAACAATCTTCTTTCCATATACCAGCTT---------------------

upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G09240.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------gtctgtagtctgtgacctctcacacgctctc-----acacacatatgtagccttt----ggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                                            |  || | |   | | |  | ||  | | ||     |      | | | |  |||     || |  ||   |||  | || || |        ||| ||||||||||||||||||| | |||||||||||||| ||||||||| | || || |||||| ||||| |||| || || ||||||
gttagtacttgtaatattaccatatgatgatcttagtcctcagaggtttagtctataaatgcttgcatttgttcatcatttacttgttttctataaatctttctttttggtgtttcgctagttctcaaattacttgtgcactttatgacaattcttacagCTTGGAATTTGACAACTCTGAGAGGCCTGAATGTAACAATCTTGTTTCCATATACCAGCTTATTTCAGGAAAGACGAAAGAG

upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G25840.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------------------------------------gtctgtagtctgtgacctctcacacgctctcacacacatatgtagcctttggtacataaga---aactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                              | |  | | |  ||| |  |  | |  ||      | |  |   |  | ||  |||     ||  | |    ||    |||| ||     ||||| ||||||||||  | ||||| ||||||||||||||||| ||||| || || |||||| || |||| || |  ||||||
gtgagcgctacttatgtcgctaaaaaatttcttgcaatgcacaaagttttttttttttcctttttcttgttaccatttcagttttcaaattgagatatctaatgttgaaagcttctgcttcttgttgttccaacagGCTTG-AATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAG

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: 42 (upstream exon), 48 (downstream exon)
Score: 13

GTTATCATGAATAAGATTAAGCGCTGCAAAACTGACTCGTTCCCAGGgtctgtagtc ... tacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgtagcctttggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                  atttgac  putative branch site (score: 13)
                                             tacctttc  putative PPT
                   ataagaaa  TA-rich tract