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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag

Basic information

species Selaginella moellendorffii
transcript EFJ38013
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 5'ss of exon 6
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag--------------------------------------------------
|||||||||||||| || ||||| || ||||| ||||||||||||||||| ||||| ||||||||  ||||   |  |         |||  |    |   || | |                                                   
TTCTTTATAACTTGTGCAAAATGTGAATGGCTGGACAACAAGCATGTGGTTTTTGGGgtaagttcc-ctcattttgaatgctttgtgctctcggagcaacattccaacagcatgtacttgtctacagtatgtttttttacttacagagtaaatatatg

upper sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 6
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag-------------------------------------------------
||||||||||| || || || || |||||||| |||||||| |||||||| ||||| ||||| |    | |  |    ||| |     |  ||  |  |  ||   |                                                  
TTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGGgtaagcttacttgattcaaatgcttccttttttgtgaacactccttaggataattggttttattgcaagtatgtatatgcatacctacagtattagggtt

upper sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 6
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag----------------------------------------------------
||||||||||| || || ||||| |||||||| |||||||||||||| || ||||| ||| |  |||| | | ||| || | || |  | |     |  ||    |||                                                    
TTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGGgtatg--cttcactatcttcagttgcatatattaaatatt-cttcaaacagcctgaatgcgaatttagtttttcttcaaggatgggtttgttacacagtacaa

upper sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 6
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag--------------------------------------------------------
||||||||||| || || ||||| |||||||| |||||||||||||| || ||||| ||| |  |||| | | ||| || | ||      ||  |  || || ||||                                                         
TTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGGgtatg--cttcactatcttcagttgca-----tatattaaatattctccaaacagcctgaatgtgaatttagtttttcttcaaggatgcgtttgttacatagtacaa

upper sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA15G37190.1 (Glycine max), 5'ss of exon 6
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag-------------------------------------------------
||||||||||| || || |||||||||||||| ||||| |||||||| || ||||| ||| | |   ||       |||        |  ||  |   | || | ||                                                  
TTCTTTATAACATGTGCAAAATGCGACTGGCTTGACAAAAAGCATGTTGTCTTTGGGgtatgcttcactatcttcggagtgcggttgcatatattaattattcttcaaacagcctgaatgtgaatttagttgttcctcaatgtttgttacacagtac

upper sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: AT2G38730.1 (Arabidopsis thaliana), 5'ss of exon 5
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag----------------------------------------------------
||||| || ||||| || |||||||| ||||| |||||||||||||| || ||||| ||| |||||  | || ||  |  ||     || ||||  |||       |                                                     
TTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGGgtacgttctctttaagct--atttaattttcttatgca-tatgaccggtaatagtattgatatatgactcattgcaatttcttcttttgattttgatgtacag

upper sequence: EFJ38013 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 5
TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttcttctcaaacttgagctacaaaactcatgctctattttttccag--------------------------------------------------
|||||||| || ||| | ||||| |||||||| ||||||||||||||||| || || ||| |||||       ||||  || |     || |  |  | | |||| |                                                   
TTCTTTATCACATGCTCGAAATGTGACTGGCTTGACAACAAGCATGTGGTATTCGGGgtatgttctctaatctcttgccct-ctgggttctttgtaaagtctttcaatatgctgaaaccaaaaatattatgtcttttacaagaccaatgtctgttctt

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169086717|gb|FE494354.1|FE494354
EST:     TAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA                         AGGGTTTTGGGCGACGGACTTTTAGTGGTGCGAAAGATCGAAAACGTCCAG
genomic: TAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttctt ... ttttttccagAGGGTTTTGGGCGACGGACTTTTAGTGGTGCGAAAGATCGAAAACGTCCAG
EST: gi|169052927|gb|FE460642.1|FE460642
EST:     TAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA                         AGGGTTTTGGGCGACGGACTTTTAGTGGTGCGAAAGATCGAAAACGTCCAG
genomic: TAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttctt ... ttttttccagAGGGTTTTGGGCGACGGACTTTTAGTGGTGCGAAAGATCGAAAACGTCCAG
EST: gi|169052928|gb|FE460643.1|FE460643
EST:     TAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA                         AGGGTTTTGGGCGACGGACTTTTAGTGGTGCGAAAGATCGAAAACGTCCAG
genomic: TAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttctt ... ttttttccagAGGGTTTTGGGCGACGGACTTTTAGTGGTGCGAAAGATCGAAAACGTCCAG

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: 34 (upstream exon), 26 (downstream exon)
Score: 4

TTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGAgtaagttctt ... ttttttccagAGGGTTTTGGGCGACGGACTTTTAGTGGTGCGAAAGATCGAAAACGTCCAGACTGGTCAGAGCAACAAGCCAAAGCTCCAATGCACAATTTCGCAATGTG




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