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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA

Basic information

species Oryza sativa
transcript LOC_Os01g59340.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
||||   || |   |  ||||   | | |||||||||   |    || ||||||||   |||       ||||||    | |||| | | | ||   |   ||||  | ||         |||     |||        |||  | | |   |||   |||      ||||  ||| |||||||| ||||| ||||||||||| |||||||| || ||||| |||||  ||||||| ||| ||||||||||||||||||||||||| || |||||||||||||
gtaaccccaaatctaaccttctattcttctgttatgctcctagtcctagatatgtt---cag-------gttttc---aataataattaggaca--ctaaggaacctgccatct------attctcacattaagctattcaaaaatgaa---ataattttg------ttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 6
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                         ||||||       |   || | | | || || |  | | |  |  |||| ||| | |  | | |   |        ||  |  | ||| | |   | |    |  || |||||||||| || ||||||||||| || ||||  |||||  | ||||| || || || || ||||| |||||||| |||||||||||||||||||| || |
-------------------------------------------------------------------------tcttatg------ttgtgtgattcttgtaaagtctaaatatga-aaaatctgtctctgatttatagaagatttccctatttgactttg-gttatgtat--acctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                                   |  |   |||  | |  |    |      ||    || |||   | | |         |   |    | || |          |||  |  ||  || |||||||||| || ||||||||||| || ||||| |||||  | ||||| ||||| || || ||||| |||||||| |||||||||||||||||||| || |
----------------------------------------------------------------------------------ctggttttgtcc-tcttatatcttgtgattactgcaaagtttaaatgtctgtctgtgtgattgataggacattcttccatttgactttgttatctgtgtagTTGGAAGGAGAGGCAACTGCTCGTGCCATTCGTTTAGCAGATTTTGTGAATACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                             ||    | |||   |  |||| |||| |       ||    || |||   | | |         |   |    | || |          |||  |  ||  || |||||||||| || ||||||||||| || ||||| |||||  | ||||| ||||| || || ||||| |||||||| ||||||||||| |||||||| || |
----------------------------------------------------------------------------catgttttgttctcttatattttgtgatc-------actgcaaagtttaaatgtctgtctgtgtgatttataggaaattctcccatttgactttgttatctgtgtagTTGGAAGGAGAGGCAACTGCTCGTGCCATTCGCTTAGCAGATTTTGTGAATACTCCTTTATATGTGGTTCATGTAATGAGCATTGACGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                                 ||||||   || | | | || || |  | | || |  | || ||| |||  | | |   |        ||  |  | ||| | |   | |    |  || |||||||||| || |||||||| || || ||||| |||||  | ||||| || || || || ||||| |||||||| |||||||||||||||||||| || |
-------------------------------------------------------------------------------ctaatatt-gtgtgattcttgtaaagtctaaatacgaaaatatatgtctatgatttatagaacatttccctatttgactttg-gttatgtat--acctatgtagTTGGAAGGAGAGGCAACTGCCCGTGCTATTCGTTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaag--tcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctg-cagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                               | || ||    |   ||      |||| ||||||    | | ||  |   | |  |   ||| |    |  |    | |||  |  ||   |     | |   |   | ||     || | ||| ||   |  || ||| | || || || || |||||| | |||||||| || ||    ||| | || || ||  | ||||||||||||||||||||  ||||||||||||| ||||
----------------------------------------------gtaatttgcgtcaagcattttccattttattatactgcctcctagattttttcttttctcctatatctgctcttgcctctgtaaagctttgtt-----gaagctactaaaac----aagatccttgtttgacaatgtcagCTCGAGGGAGAGGCCACTGCTAGAGCAATTCGTTTGGCTCGTTTTATTAACACGCCTCTCTATGTTGTTCATGTGATGAGTGTTGATGCAATGGACGAGA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccct--gcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                            | ||   | ||   ||   | |  |   || ||||   |      |||  || | ||  ||       | |  |  |||  ||    ||  || |||  || |  |||| | ||||| || ||||||||| | || ||||| || ||||  ||||| || || ||  | ||||| ||||||||||||||||||||||| ||||| || |
---------------------------------------------------------------------------ctttattctgtt---gttcttctaattgtct-gacagttc------tttccgtttatttcctggacgtcatgcttttatataatctgtcttttttttggcccttatgcagCTAGAAGGAGAGGCAACTGCTAGAGCTATTCGGTTGGCCAGTTTTGTTAACACGCCTCTCTATGTAGTTCATGTGATGAGCATTGATGCGATGGAAGAAA

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: 68 (upstream exon), 46 (downstream exon)
Score: 12

TCATGCAGAGAATGGGGATGCTGTTGCTGAGGGACAGCAACGAATGATCGATCTTGGGATAACTGGCCCAGAAGGACATGCTCTCTCAAGACCTCCAGTTgtaatttcac ... ttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
     ctctcac  putative branch site (score: 12)
                                   ctgcttcttgttccct  putative PPT
                    atagata  TA-rich tract