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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttttgtgatcttctgtgggtgatctatacttacggaagatgttgtttgtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA

Basic information

species Selaginella moellendorffii
transcript EFJ31848
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------------------------------------------------------------------------------gtactttttgtgatcttctgtgggtgatctatacttacggaagatgttgtttgtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                                                                                                                                              ||   ||||  | |    | |   |||   ||| |  |      | || |   || |||||||||||||||| || ||||| || ||||| ||||||||||||||||| ||||| 
gtacttcttttgataactgctctattttttttctgtgtggctgtagattttttatccagctggttttgcaatcttcgggctggggtactgttttgggattgtattttgttctctatacaaaattagcaatatccagttccaggtttcttttcagttacagtattcctgaaa-atattatcttctattcttatgcttgcagTTCTTTATAACTTGTGCAAAATGTGAATGGCTGGACAACAAGCATGTGGTTTTTGGG

upper sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G057329_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------------------------------------------------------gtactttttgtgatcttctgtgggtgatctatacttacgg----aagatgttgtttgtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                                                                                                                         |  || ||||   |     |      |  ||  | |       |   | ||||   || ||||||||||||| || || || || |||||||| |||||||| |||||||| ||||| 
gtacgttcgccttctctaaaattgcatgtagccttaatgcctgactcagtcacactcagttgccttggcaatgcctattccttcaagccagtcatgtttaagaacaaaaaatgactagatatctttcttgtacaccctgttttagagtacatgatgaaaagcttacactcttgtgcttgcagTTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG

upper sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA09G11960.1 (Glycine max), 3'ss of exon 5
--------------------------------------------gtacttttt-----gtgatcttctgtgggtgat---ctatacttacggaaga------tgttgtt-tgtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                                              | ||| |     || || ||   | ||| ||   || | | ||  || ||      | || ||   || ||||||||||||| || || ||||| |||||||| |||||||||||||| || ||||| 
gtaactttctagtggtcacattctcacttacttccttttcctttccattttctcagtggtaatgttaaattggtaatactcttttcctattgatgaatcttctcttcttgcttgcagTTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGG

upper sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA13G26260.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------gtacttttt-----gtgatcttctgtgggtgat---ctatacttacggaaga-tgttgtttg------tgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                                                                            | ||| |     || || ||   | ||| ||   || | | ||  || || |||| | |       || ||||||||||||| || || ||||| |||||||| |||||||||||||| || ||||| 
gtaactttccagtggtcacattctcacttacttccttttccgtggtcacattctcacttacttccttttcctttccattttctcagtggtaatgttaaattggtaatactcttttcctattgatgaatgttctcttcttgcttgcagTTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGG

upper sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G37190.1 (Glycine max), 3'ss of exon 5
-------------------------------------------gtactttttgtgatcttctgtgggtgat---ctatacttacggaaga-tgttgttt------gtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                                            |     | || |  ||   | ||| ||   || | | ||  || || |||| | |       || ||||||||||||| || || |||||||||||||| ||||| |||||||| || ||||| 
gtaactttccagtggtcacactcacttccttttcctttcccttttgtcagtggtaacgttaaattggtaatgcccttttcctattgatgaatgttctcttcttgcttgcagTTCTTTATAACATGTGCAAAATGCGACTGGCTTGACAAAAAGCATGTTGTCTTTGGG

upper sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------------------------gtactttttgtgatcttctgtgggtgatctatacttacggaagatgttgtttg---tgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                                                                                     | | ||  | | | |  | | ||  ||   || | |  |    || | ||||   || ||||||| || ||||| || |||||||| ||||| |||||||||||||| || ||||| 
gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcag-gttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG

upper sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gtactttttgtgatcttctgtgggtgatctatacttacg-gaagatgttgtttgtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                                         ||  ||    || |  |   |  ||   | ||| | |   |||| |  | ||  || |||||||||| || ||| | ||||| |||||||| ||||||||||||||||| || || 
tattggtagatttgatcattgtaccttaaaaagattttaatgtttttgacttggttataaatttgtttaccatattcatttgaagctacttttgctgcagTTCTTTATCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGG

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: 35 (upstream exon), 24 (downstream exon)
Score: 11

GCTAACAGCGGCCCAAACACAAATGGCTGTCAGgtactttttg ... gtttgtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgtgatcttctgtgggtgatctatacttacggaagatgttgtttgtgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA
                            tacttac  putative branch site (score: 11)
                          tatactta  TA-rich tract