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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacccggtcgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG

Basic information

species Selaginella moellendorffii
transcript EFJ15096
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 10
-------------------------------------------------------------------------------gtaacc-cggtcgagcccagttttttcagtct---gctgatctgagtccg--tggtgcat-ggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG
                                                                               || ||    |   ||     || ||| ||| |   |      ||| |||   |||||| | ||||||| ||||||||||||||||||||| |||| |||||||| |||||| | || |||||  | ||||| || || ||||| || || ||| || | ||||| |
gtaaaaaaaaaacatagtggtgattgaagtactaaagatccaatcaccagcatatagaatgatctgcactactttcttggtcacagtagcaaagtttctttcttttagtttcaaggaatattgactccacttggtgccttggcagGTGTACTACGTCTATGGTTTCATGTTGCTGGTGTTTGTCATCCTCATAATAGTCACCATATGTGTCACTATTGTGGGTACTTATTTCTTGTTGAATGCTG

upper sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 10
------------------------------------------gtaacccggtcgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG
                                          ||||            |||||| ||  |  |  |  ||    |||    ||     ||||| ||||| |||||||| |||||||| || || ||| |||| ||  ||||||| || ||||||||||| || ||||| || |||||  || ||||||| |
ttcaagtagtaaagcaactctttaatattcctgtgaatgctggtaaattaaatatatgcagtttcttatgcattttt-tccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

upper sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------------------------gtaacccggtcgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG
                                            | ||     | |      | | |||  |   | || ||||  |  ||  ||   | ||||||||||| || ||||| |||||| | || || |||||||| ||| |||| || ||||| |||||||| |||||||| || || |||||||| ||||| |
tctttaagtaggactaactttgtctttgctaatcatataacgacgaaagtaaattgtagt-ggctatttttgaaagttg-tctgtttttgtt-tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG

upper sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------gtaacccggtcg-agcccagtt--ttttcagtc--tgctga----tctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG
                                 |     |   | ||  ||  |  ||| ||||   || | |    | |  |    | ||||  ||||||| || || |||||||| || ||||| || || ||  |||| ||| | |||||||| ||||||||||| || ||||| || |||||| |||||||||| |
ctctctctctctatttttgagaaattcggactattgtttgacaggagttcaaattgtttgcagtggatgataaacattttttgctgtttgtgctgggcagGTGTATTATGTCTATGGCTTTATGCTACTGGTTTTCCTGATTCTCATAATTGTCACTGTTTGTGTGACAATAGTGGGAACATACTTCTTGCTAAATGCTG

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), 35 (downstream exon)
Score: 21

TCTCAAGCCATCCATCGTGGCGCTTATGGGAGGCTTACTCCCATTCGGGAGCATCTTCATAGAGATGTATTTCGTGTTCACGTCCTTTTGGAACTACAAGgtaacccggt ... tgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccggtcgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG
                          tgctgat  putative branch site (score: 21)
             agtttttt  TA-rich tract