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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggcgatatggagaatcgttatatagggatctttgacctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC

Basic information

species Selaginella moellendorffii
transcript EFJ19778
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------gtgggcgata--tggagaatcgttatatagggatctttgacctg-----gttgtaattgatgc-agGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
                                                           |     |||  |  | |||   | |  |    |  |  ||         || || ||  | | || | |||||||| ||      |||    || || |||| |||||||||||| || || ||||| || ||||||||||| |||||||| ||   |||| |  
gtcagaatttcttcggatgtccattattacacagaacatttgttatataaaggcaaagctaattaatacttctataataactgtggatatcttctcaactcttcaacattatactttgtcccagATATGGAGAGTTGCTCCTACTCCACCAAATGACAAGTACCAGTACACGCACTTCGCGCACAAAATAAACAGCTTCGATACGGCGCCGAAGAAGCTATTGG

upper sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA07G15930.3 (Glycine max), 3'ss of exon 8
----------------------------------------------gtgggcgatatggagaatcgttatatagggatctttgacctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
                                                  || || || |   |  || | |   | |   ||     |||  | |     ||| | |||||||| || ||    || ||||| || ||||||||||||||||||||||| ||||||||||||||||| ||||| || || ||   | |  |  
tgtcactgtatgatttccgcttcattgggttgtcatcaccttttgttctagcaatttgaattgtttttttgttaagttacctgt----gtttcattctgcacagATTTGGAGAGTTGCTGATACCCCGAAGAAGGACAAGTTCCAGTACACGCATTTTGCACACAAGATTAACAGCTTTGACACTGCTCCCAAGAAGTTGTTGG

upper sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 8
------------------------------------gtgggcga--tatggagaatcgttatatagggatctttg-----acctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
                                    ||   |    | ||    |||  | |  |    | |||      | |   |   | |     ||| | |||||||| || || |  |||||||| || || |||||||||||||||||||| ||||||||||||||||| ||||| || || ||   | |  |  
tttagtgtcactctatgatttctgcttggttgggttgtcatcaccttttgttccatcaatttgaattatttttttgaagtaaccattcccattctgcacaGATTTGGAGAGTTGCTGATGCCCCCAAGAAGGACAAATTCCAGTACACGCATTTTGCACACAAGATTAACAGCTTTGACACTGCTCCCAAGAAGTTGTTG-

upper sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------------------------------------------------------gtgggcgatatggagaatcgttatatagggatctttgacctg--gttg--------taattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
                                                                                     ||  | | || |     | || ||  ||   |||   | ||  ||||        |  ||  | |||||||||    | || || || ||||| ||||| || || |||||||| || |||||||||||||| |||||||||||||| |||||      |||  |  
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG

upper sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------gtgggcgatatg-gagaatc---gttatatagggatctttgac-ctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
                                |   |  | ||  | ||||   |||  ||       ||| |  |||  | |  || ||  |||| |||| | | || || || || ||| | || || |  || ||||| || ||||||||||||||||| ||||||||||| || || ||   |||  | |
gtttgccaaatcttcctctgtcattgactcaattctctttttgtaaaaatctcagtttgatgaaacattttaatgctgccttttgttcat--agGTATGGAAACTCGCTGATGTGCCAAAGGATGACAAATATCAATACACTCACTTTGCTCACAAGATTAATAGCTTCGACACTGCCCCGAAAAAGCTGTTGC

upper sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------gtgggcgatatggagaatcgttatatagggatctttgacctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
                        |    |  | || | | |   ||| |||  | ||||    |  | || | |    ||||||||||  || || || | ||| ||||||||||| | ||| ||||| ||||||||||||||||| || || || ||||| || || ||   ||||||  
gttttatcaatttctctcctctaagcaaaccctctgcatacta--tatctagtcacctttctaattat-gttacttccacagGTGTGGAAGGTTGCTGAAGCTCCAAAGAACGATAAATACCAATACACACATTTTGCTCACAAGATCAATAGTTTTGACACTGCCCCTAAAAAGCTACTGT

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: 31 (upstream exon), 34 (downstream exon)
Score: 36

GGAGCCCAAGCTTCTGCTTACGGGGAAGTGGAACTCATTTATGAGTTACCAGCCCTGCGATTCCGAAGGCGAGCCGTTAGCAGGATCTGAGCTGAAGGAGgtgggcgata ... attgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgatatggagaatcgttatatagggatctttgacctggttgtaattgatgcagGTGTGGAGAGTAGCGGACGTTCCCAAGAACGATAAGTTCCAGTACACGCATTTTGCTCACAAGATTAACAGCTTCGACACGGCGCCAAACGGGCTACTTC
                                            aattgat  putative branch site (score: 36)
                 ttatata  TA-rich tract