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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaataataatgatttgttctgagtggcatgtttttagaaattatgctgcag

Basic information

species Selaginella moellendorffii
transcript EFJ06565
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 11
AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaat---------aataatgatttgttctgagtggcatgtttttagaaattat--gctgcag----------------
 ||| ||||| || ||| | ||||||||||||||  | || || |||||||| || ||| | |||||||| ||| | |||||||| |||||||||||||||||           |||  | |||| |||| | |   |   |||  ||| |||   | |   |                
CAGGGAGTGAAAAATTTGTTTTCTTGCTTTCGACTAGGGCAGGTGGTCTTGGGATAAATCTTGCTACTGCTGATGTTGTTATTCTTTATGACAGTGACTGgtatgtccttttcaaatcgtaattttttctcattc-tacaatttgtgaagttaaaggttatggttatttggtttcacag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 8
AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaataataatgatttgttctgagtggcatgtttttagaaattatgctgcag----------------------------------------------
 |||||||||||||||| | ||||| ||||| ||  | || || || ||||||||||| ||||| ||||| ||| | ||  ||||||||||||| || |||||    |     |||||| ||       |  ||||     |||| |   |                                               
CAGGAAGTGAGAAGTTTGTTTTCTTACTTTCAACTAGGGCAGGTGGCCTTGGTATCAACTTGGCCACTGCTGATGTTGTGGTTCTCTATGACAGCGATTGgta----tgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatgaaccttatgttcctagtacttctgtgcctccag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 11
AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaataataatgatttgttctgagtggcatgt---ttttagaaattatgctgcag---------------------
 |||||||||||| ||  | |||||| | || ||  |||| || || |||||||||||| | |||||||| ||| | || || |||||||| ||||||||||||   |  |  | ||| |   ||    | |   | ||     ||||||   |                      
CAGGAAGTGAGAAATTCGTTTTCTTGTTATCCACTAGAGCTGGAGGACTTGGTATCAATCTTGCTACTGCAGATGTTGTGATCCTCTATGATAGTGACTGgtaaggctctttttgtgtccattgtaatttatgagtgttttcttttatgcctaatgaggtgggtggattatggcag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 11
AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaataataatgatttgttctgagtggcatgtttttagaaattatgctgcag--------------------------------------------
  ||||||||||| ||| | ||||| || || ||  |||| || ||||||||||||||| | |||||||| ||| | || || || |||||||||||||||| |  ||       | || |        | ||||   |   || |     |                                            
CCGGAAGTGAGAAATTTGTGTTCTTACTGTCAACTAGAGCTGGAGGTCTTGGTATCAATCTTGCTACTGCAGATGTTGTCATCCTTTATGACAGTGACTGgtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtag

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|169107316|gb|FE504142.1|FE504142
EST:     GGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTG                         GAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACA
genomic: GGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaataataa ... tatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACA
EST: gi|169028023|gb|FE435914.1|FE435914
EST:     GGCATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTG                         GAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACA
genomic: GGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaataataa ... tatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACA

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: 28 (upstream exon), 33 (downstream exon)
Score: 5

AAGGAAGTGAGAAGTTTATATTCTTGCTTTCGACCCGAGCCGGCGGTCTTGGTATCAATTTGGCTACTGCCGATATCGTTATTCTCTATGACAGTGACTGgtaataataa ... tatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG




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