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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcgtctatgtgatttcgttgacgtctaacacaatctgtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ29370
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
-----------------------------------------------------------------------------------------------------gtagcgtctatgtgatttcgttg------acgtctaacacaat-ctgtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG
                                                                                                      ||| | ||       ||  |||      ||  ||    |  | || ||| |||| || |||||||| ||||| |||||||| |||||  ||||||| ||| | ||||| |||||||| ||||  ||||||||||| || ||  |||| ||||
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG

upper sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 16
------------------------------------------------gtagcgtctatgtgatttcgttgac------gtctaacacaatctgtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG
                                                | ||   | |  |   |||  ||||      || |  | |  | | || ||||| || |||||||| || || ||||||||||| ||| |||| || ||| | |||||||||||||| ||||  ||||| || || || ||  | || ||||
aattgtgcattcttctgttttttcatgtgcacattattgtgcagtattgcagttgccaacttccttcagtgactgaaatgttttcccccttgtattccagGAAGACTTCTATGCGGTCGTAGATTGGGCTTATAAAATTGACCCCTTGCGTTGCATCTCAATGCATGGGATTACAGAGCGTTACCTTTCTGGACAGAAAG

upper sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
-----------------------------------------gtagcgtctatgtgattt-----cgttgacgtcta-------acacaatctg-tttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG
                                           |   || ||  |||||     | || || ||||        |   || || |||||||| || |||||||||||||||||||||||||||||  |||| |||||  | || || |||||||| || | ||||||||| ||||||||  |||| ||||
atagattgagtcatgtagaaaggcatggtaatctccctgcataaaaatccataagatttttcagcatttacatctacaaatctgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 16
------------------------------------------------------gtagcgtctatgtgatttcgttgacgtctaacacaatctgtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG
                                                       |||  |   ||  ||   ||||   | |||         |||||||| || |||  ||||||||||||||||||  ||||| ||||||||||  | ||||| |||||||| || || |||||||| ||||||||  |||| ||||
ttccttataatttgacaatttgtaacgagtttccagatggattttggtatgttaatagatttgctgctataaagttgctttataatttctctgatttcagGAAGACTTCGCTGCTGTTGTGGATTGGGCACACAAAATTGATCCTTTATGCTGCATATCAATGCATGGAACTACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 16
-------------------------------------------gtagcgtctatgtgatttc---gttgacgtctaacaca-------atctg-tttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG
                                            |||  | | |   | | |    || ||  ||| || |       || || |||||||| || ||||||||||||||||||||||| || ||  |||| |||||  | || || |||||||| || | ||||||||| ||||||||  |||| ||||
ttccttataattggtcaggttttgttgtgttgttggcagcgatttagtatatttaaaaatccagcatttacagctaccaaactgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCATATAAGATTGACCCTTTACGCTGTATATCAATGCATGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

upper sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
----------------------------------------------gtagcgtctatgtgatttcgttgacg---tctaacacaatct-----gtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG
                                                |     |    | |||   |  ||   | |  ||   | |      ||  |||| || || ||||| || ||||||||||| |||||  ||||||||||| | ||||| |||||||| ||||  |||||||| ||| | ||  |||| ||||
gactcttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG

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), 30 (downstream exon)
Score: 21

CGGAACAAAACGCTGCGGAGATGGAAGCCTTGAATCAGGCTCTTCAAGAGCTTCTTGATGGCATTCAGgtagcgtcta ... tctgtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagcgtctatgtgatttcgttgacgtctaacacaatctgtttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG
                                  gtctaac  putative branch site (score: 21)
                                             tctgtttc  putative PPT