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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaggatgacttgtgtgttatttctttgctgactcgttttctgtttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG

Basic information

species Selaginella moellendorffii
transcript EFJ31365
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 12
------------------------gtaaaaggatga-cttgtgtgtt-atttctttgctgact---cgttttctgtttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
                         | |    |  | ||| ||| || || |||  | |       ||    ||   | ||||||||| || || |||||||| |||||  | || ||||| ||||||||| ||||||||||||| || ||||| || ||||| || || ||||   
gtttgtcaatcttttctttagaatattacgtaacaatcttttgtattgatatctaagataggatgacgaaaacttaatttcagTATACCATCGAGGAGAAAGTGATTGAGAGGGCATACAAGAAGCTTGCATTGGATGCTTTGGTCATTCAACAAGGCCGACTGGCAGAGCAGAAGA

upper sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------gtaaaaggatgacttgtgtgttatttctttgctgactcgttttctgtttct---cagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
                                              ||   ||  ||| | | |  ||   |  | || |    |||   ||||   |||||||| ||||| || || || |||||  | || || || |||||||| |||||||||||||| || |||||||||||| | || || |||| ||
gttttatttaatttattttaagatttaaaaacactggtttagcactaagcaatatcttctatttatttatataacagaatatgcttcatattctatgcagTATACAATTGAGGAAAAGGTGATTGAGAGAGCTTATAAGAAGCTTGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG

upper sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 12
--------------------------------gtaaaaggatgact-tgtgtgttatttctttgctgactcgtt-----ttctgtttct-cagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
                                 |  |  | | ||| ||||||||| |   |     | || ||     || |  |  | |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||||| ||||||| || || || ||| | || || ||||   
gtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA

upper sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
--------------------------------gtaaaaggatgact---tgtgtgttatttctttgctgactcgtt-----ttctgtttct-cagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
                                 |  |  | | |||   ||||||||| |   |       || ||     || |  |  | |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||||| ||||||| || || || ||| | || || ||||   
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA

upper sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
----------------------------------gtaaaaggatga--cttgtgtgttatttctttgctgactcgttttct----------gtttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
                                   | ||  | ||   |||    |||||||  |   ||  ||  | |||           || | |||||||| ||||| || |||||||||||| | || ||||| ||||||||||| |||||| ||||||| || || || ||| |||| |||||||   
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA

upper sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
---------------------------------gtaaaaggatg--------acttgtgtgttatttct-ttgctgactcgttttctg----tttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
                                  | ||  | ||        | || | |  ||||| | |   || ||| | |  ||    || | |||||||| ||||| || |||||||||||| | || |||||||||||||| || |||||| ||||||| || || || ||| |||| |||||||   
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA

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: 27 (upstream exon), 33 (downstream exon)
Score: 9

GAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAGgtaaaaggat ... tgtttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaaggatgacttgtgtgttatttctttgctgactcgttttctgtttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
                              tgctgac  putative branch site (score: 9)
                                    ctcgttttctgtttct  CT-rich tract
                     ttatttcttt  TA-rich tract