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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgtccattgccgttttctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA

Basic information

species Selaginella moellendorffii
transcript EFJ30926
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 14
--------------------------------------gtctgtgtccattgccgttttctttattatgggttt--atggttatt------gctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA
                                      |  |  |    | ||  | |        ||| | |   | |||| ||       || ||||||| |||||||| || ||  ||||||||||||| || || ||||| ||||||||  | |||||| | || || |||||||| ||||||| ||||||||| |
acatacgtaaatggccatttcaaatgagaatatgtattgatttagcatctcgcaatgtgtacacacatgagctctaaaggttgtttatgtaactttgcagTTCATATTTTCAACTGCCATTGATGGGAAAATAAAGGCATGGCTATACGATAACATGGGTTCTAGGGTTGACTATGATGCCCCTGGTCACTGGTGCACTA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 14
--------------------------------------------------gtctgtgtccattgccgttttctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA
                                                    |  ||| ||    | |   || ||      |||||||    |  || ||||||| |||||||| || ||  ||||||||||||| || || ||| | ||||||||  | |||||| | || || |||||||| ||||||| ||||||||| |
acacacgtaaatggccatgtcaaatgagaatatgtattgatttagcatctcacaatgtacacacacatgcactctaaaggttgtttatg----taactttgcagTTCATATTTTCAACTGCCATTGATGGGAAAATAAAGGCATGGTTATACGATAACATGGGTTCTAGGGTTGACTATGATGCCCCTGGTCACTGGTGCACTA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 14
-----------------------------------------------gtctgtgtccattgccgttttctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA
                                                |   |   || |||| ||    ||| ||   |||  |  || |   | |||||||| ||||||| || ||  ||||||| ||||| ||||| ||| | ||||||||| | |||||| | || ||||||||||| || ||||  ||||| || |
tacatgagttacgagtacatattgtcgataattgtattattctagtaattaataaacactgcctttaatcttactaaatgtt-gtcattgtaattttgcagTTTGTATTTTCAACTGCCATTGATGGCAAAATAAAAGCCTGGTTATACGATAATATGGGTTCTAGGGTTGATTATGATGCCCCAGGTCATTGGTGTACTA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------------------------------------------------------------------------------------------gtctgtgtccattgccgttttct-ttattatgggttt-atggttatt-gctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA
                                                                                                            |   | |  ||| | ||| | |   |  ||   | |  |  ||||| |   | ||||| |||||||| |||||  | ||||||||||| ||||| |||||||| |||||||| |||||  |||| || ||||||||||| |||   ||||| || |
gtgcggcaaggattgaatcaaactatattttacatcaattattatactgttttaccaatccgtttgaagaacaataaagtagacgacacatttcatatagtattatcttgcctatgaatttctgttctttaccaaaatacatctcgttcttatttggatttcagTTCATATTTTCAACCGCCATAGATGGGAAAATAAAAGCCTGGCTTTATGATAATCTGGGTTCCAGAGTTGACTATGATGCTCCCGGTAAATGGTGTACGA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 13
---------------------------------gtctgtgtccattgccgttttctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA
                                   || |  |  | || || || |   ||||   | | |  || || || ||||||||||||| || ||||| |||||||| || ||||| || ||||| || |||||| | |||||||| || |||||||| || || || |  ||||| ||||
gtgcaggcatctcttgtttaaaaagacctgaaaaactttccctttcgctgtcttgtaatttatttttctcttttt-ttactatgcagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------gtctgtgtccattgccgttt--tctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA
                                                                 |   ||  |   |  ||  || | ||  |  |||| || || ||   || |||||||| ||||| || |||||||||||||| || ||||| ||| | || |||||  | || |||||||| |||||||||||||| ||||||||||||||||
gtaacaagtccattagctttggctattctaagtttgtcatgttttttcgccttcctgtaactactttcttctgtcatcccttggtcctgatgttctgtttgtgctt-ttatgcttcagTTTATCTTTTCAACAGCACTTGATGGGAAGATAAAAGCATGGTTATATGATAACTTGGGATCTCGAGTTGATTATGATGCTCCAGGTCGCTGGTGCACAA

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: 34 (upstream exon), 14 (downstream exon)
Score: 6

GTTTGGGAAGCCATGACCGCTCGCAAGATTTATGTATTTGAAGGTCATGAGGCAGCAGTGTATTCTGTATGTCCACATCATAAAGAAAGCATACAGgtctgtgtcc ... tgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgtgtccattgccgttttctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA
                                            ttgctct  CT-rich tract
                  ttttctttattat  TA-rich tract