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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacaaatttcatattgtaaccttatgtataggcaacaaattatcccttttacatacatatgctctatctttatgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT

Basic information

species Oryza sativa
transcript LOC_Os01g67870.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 10
---------------gtactacaaattt-catattgtaaccttatgtataggc---aacaaattatcccttttacatacatatgctctatctttatgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT
                | ||    |  |   |||  ||| |  ||||||       ||| |||  |   || | |||| | ||| |   | || ||||||||||||||||||||| |||||||||||||||||||| || ||||||||||| || || ||||||||||||||||||||| ||||| ||   || ||||||
atactttgggtttcttttctgtgcacatgtttatgctaaaccaatgtatgcatcttaactaatactgttttcttcatatacatgtttgtttttcatgcagATACTGGAATTACCTCAGGAAACAAACTTTTGTTCTCGAGTCATATGTATCGAATGTAAACTGGATGATGAACCGTGCATTATTTACAAGCCATTGCTAT

upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA05G35860.1 (Glycine max), 3'ss of exon 9
gtactacaaatttcatattgtaaccttatgtataggcaacaaattatcccttttacatacatatgctctatcttta--tgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT
          |||   ||| | ||      || |   | |   ||  |   |||    |  ||   | | | || |  || ||||| ||||||||| | ||||||||||| |||||| | || |||||| || |||| ||||||||| |||||||||||||| | ||| |  | |||||||||
---------gtttgtgattatcactcgtcttacatttagcttctttgcgtatttgatgatttaatttattttttaacgtgtagATATTGGAATTACTTGAGGAAACAAACATTTGTTTTGGAGTCATATTTAACAAATGTTAACTGGGTGATGAACCGTGCATTGTTTACTACCCACTGCTAT

upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 10
gtactacaaatttcatattgtaaccttatgtataggcaacaaattatcccttttacatacatatgctctatctttatgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT
          |||   ||| | ||      || |   |     ||  |   |||    |  ||   | |     | || ||||| ||||||||| | ||||||||||| || ||| | || |||||| || |||| ||||||||| |||||||||||||| | ||| |  | |||||||||
---------gtttgtgattattactcgtcttaaattaagtttctttgcgtatttgatgatttaattttttaacatgtgtagATATTGGAATTACTTGAGGAAACAAACATTCGTTTTGGAGTCATATTTAACAAATGTTAACTGGGTGATGAACCGTGCATTGTTTACTACCCACTGCTAT

upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 10
----gtactacaaatttcatattgtaaccttatgtataggcaacaaattatcccttttaca-tacatatgctctatctttatgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT
     | ||   |  | | | ||  || | || | |||   || |  | |     || ||| |   ||| || | |  || |  ||||||||||| ||| | || |||||||| ||||| || ||||||||  |||| || ||||||||||| ||||||   ||  | |||||    || || |||
gtacattctcatatctacttgtttgaaacataag-atactgaatatttcagatgcttaacaatttctattcttttttgttttatagATACTGGAACTACTTGAGAAAACAAACCTTTGTGCTAGAATCATACATATCGAAAGTTAACTGGATAATGAACAAGGCTTTGTTTGCTGTCCATTGTTAT

upper sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 10
gtactacaaatttcatattgtaaccttatgtataggcaacaaattatcccttttacatacatatgctctatc-tttatgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT
||  |  | ||| | | ||  ||  || | | |     |||   ||| |||| |  ||   |   || | |   || || ||||||||||||||| | ||||| ||||| |||||||||||||||||  | || |||||||||||| | ||||| |||||| ||||| | || |||||||||
gtttttgatattcccttttcaaaatttgttttt---tcacatggtattccttgttgatcttttccctttttgacttgtgtagATACTGGAATTACTTGAGGAAGCAAACATTTGTTCTTGAATCATACATTTCGAAGGTTAACTGGGTTATGAATCGTGCATTATTTTCTTCCCACTGCTAT

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: 72 (upstream exon), 73 (downstream exon)
Score: 37

CATAAAAGGCTCATATCTTCACCACCTGTTGCAGTGTTTCCACACCCTCTTTCAAGTGATCTTAGTTTCTCCAGgtactacaaa ... ctttatgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtataggcaacaaattatcccttttacatacatatgctctatctttatgcagATACTGGAATTACCTAAGGAAACAAACTTTTGTTCTTGAATCATATGTATCAAAGGTTAACTGGATGATGAACCGTGCACTATTTGCATCGCACTGCTAT
                                       ctctatcttt  CT-rich tract
                        ttttacatacatat  TA-rich tract