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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatttgttcctcgttgttttcttgtttgttttttggtttccgtgttgctaagatggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA

Basic information

species Selaginella moellendorffii
transcript EFJ19424
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os03g58590.1 (Oryza sativa), 3'ss of exon 12
gtgagtgatttgttcctcgttgttttcttgtttgttttttggtttc-cgtgttgctaagatggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA
|| ||    |  | ||   |  |    ||   |  | |   |||||  | |    | |  |  |   | ||| |   |   |||||||| || |||||||||||||| ||||| || ||||| ||||| ||||||||||| |||||||| || || || || ||  | ||||||||||| ||| 
gtaagcctctattcccatatcttcaaatttaatcctgtagagtttcatgggcacttcacttaattactctgttttcttcaccagGCTTTCCGTATTGTCAACAAGGAGTGGGAATACTCACATAAGAAGGGCTTCAAGTGCACATTCGAACGTGGGATTCTCCACCTCTATTTCAACTTCAAGC

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G072156_T01 (Zea mays), 3'ss of exon 11
gtgagtgatttgttcctcgttgttttcttgtttgttttttggtttccgtgttgctaag----atggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA
|| || | ||||| |||     | || |  | | || ||  ||  || | |   |  |    ||  |   | ||| |   |   |||||||| || ||||| |||||||| ||||| || ||||||||||| || ||||||||||| || ||||| || || || ||| | ||||||||||| ||| 
gtaagcg-tttgtgccttacaatgttttgttctattcttctgtggccttatccatgggcggtattttcactttgttttgttccacagGCTTTCCGTATTGTGAACAAGGAGTGGGAATACTCACACAAGAAGGGGTTCAAGTGTACTTTTGAGCGTGGGATTCTCCATCTCTATTTCAACTTCAAGC

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA03G34590.1 (Glycine max), 3'ss of exon 12
gtgagtgatttgttcctcgttgttttcttgtttgttttttggtttccgtgttgctaagatggtgtgt-gtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA
|| |||    | ||   | ||  |||  ||   | |||||  ||| |       | |  |  |   |  | | |    |  |||||||| |||||||| ||||| |||||||||||||| || |||||||| || |||||| |||| || || || || || ||||| || ||||| || ||  
gtaagt---ctattatcctttaattttatgaaggatttttaattttcaatcaatttacttatttccttattttttccatgacagGCTTTCCGCATTGTTAACAAAGAATGGGAGTATTCTCATAAGAAAGGTTTTAAGTGTGCATTTGAACGTGGAATTCTGCATGTGTACTTCAATTTCAAAC

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA19G37280.1 (Glycine max), 3'ss of exon 12
gtgagtgatttgttcctcgttgttttcttgtttgttttttggtttccgtgttgctaagatggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA
|| |||    | ||   | ||  |||  ||   | ||||   ||||  |     ||      |   | ||| |    |  |||||||| || || || ||||| |||||||| ||||| || |||||||| || ||||||||||| || || || || || || || || ||||| || ||  
gtaagt---ctattatcctttaattttatgaaggattttaattttcaatcaatttacttatttccttatgttttccatgacagGCTTTCCGGATCGTTAACAAAGAATGGGAATATTCTCATAAGAAAGGTTTTAAGTGTACATTTGAACGTGGAATTCTGCACGTGTACTTCAATTTCAAAC

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT1G03910.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgagtgatt-tgttcct--cgttgttttcttgtttgttttttg-gtttccgtgttgctaagatggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA
|| |||  |  |   | |   || | |||| |  |    | | | |||  | |  |||| | ||  | | | ||| ||  ||| ||||| || || ||||| || || |||||||||||||| ||||||||||| ||||| || || || ||||| || || || ||| | || |||||||||||  
gtaagtactcgtaaccattatgtgggtttcatcatcacctctcgtgttatcattgtgctcaaatt-tatttttgtttgctttt-cagGCGTTCCGGATTGTGAATAAAGAATGGGAGTATTCTCACAAGAAAGGTTTCAAATGCACGTTTGAGCGTGGGATTCTGCATTTGTACTTCAACTTTAAAC

upper sequence: EFJ19424 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv08s0007g04370.t01 (Vitis vinifera), 3'ss of exon 12
gtgagtgatttgttcctcgttgttttcttgtttgttttttggttt----ccgtgttgctaagatggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA
|| |||| | | |  ||  |  |||| |||||| | ||    |||         ||||| || || |     |   |       ||||| || || ||||| || || |||||||| ||||| || ||||| || || ||||| |||||||| || |||||  | ||||||||||||||||| ||| 
gtaagtgctctttatctgctaattttattgtttttgttgctatttagagttagattgctcagttgcttctccta-atccacg-acagGCATTCCGGATTGTGAATAAAGAATGGGAATATTCTCATAAGAAGGGGTTTAAGTGCACATTCGAACGGGGTATTTTGCATGTTTATTTCAACTTCAAGC

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: 33 (upstream exon), 30 (downstream exon)
Score: 10

TGACAAAACGAAGGCACCGACTTATGCGATCGAGAGAGATGGAAGCAGCGGGGAGACGTGCCTCATCAGATTTCACGCAGGCCCTCCATACGAAGATATTgtgagtgatt ... gtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgttttttggtttccgtgttgctaagatggtgtgtgtgtgtgtgtttgcagGCTTTTCGCATTGTCAACAAGGAATGGGAGTATTCACACAAGAAAGGCTTCAAGTGTACATTCGAGCGAGGTATCCTTCATGTTTATTTCAACTTTAAGA
      tttttt  TA-rich tract