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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttatacgagcgctaccgtaatgtttagtttttctaacagtttctacag

Basic information

species Selaginella moellendorffii
transcript EFJ24096
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24096 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os10g35290.1 (Oryza sativa), 5'ss of exon 17
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttata--cgagcgctaccgtaatgt---ttagtttttctaacagtttctacag-------------------------------------------------------------------
|||    ||| | || || || || ||  | ||||| |||||||  || ||||||||||| |||||||||||||||||||| || |||||||| || |||||   ||  |      | || || |||   | | ||| ||   ||   |  | |                                                                    
TCATGAAGAAATCCACCCTACAGCCATTCTTAGTGTAGTTGCAAATTTGACACCTTGGTCTGATCACAATCAAAGTCCTCGGAACATGTACCAATGTCAGgtcagtagccagatcttcccttactgtaaatcaatttctcatgcataatgaaaattgctcacgcataatgaatgctgagaccttttttttctagacctgctaacctgcttgcttgttcacag

upper sequence: EFJ24096 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G388892_T02 (Zea mays), 5'ss of exon 18
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttatac----------gagc--gctaccgtaatgtttagtttttctaacagtttctacag--------------------------------
|||    ||  | || || || |||||  | ||||| ||||| |   | ||||||||||| |||||||| ||||||||| | || |||||||| |||||||||  |||          || |  |      || || || |||  ||   |  |   |   |                                
TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcagaagtcagatcttgtccttatagtgattggttgatcatgctttcctttttggactaacccccagtcatcctccttgtttgcag

upper sequence: EFJ24096 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA17G23500.1 (Glycine max), 5'ss of exon 13
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtt-tata----cgagcgcta-ccgtaatgtttagtttttc--taacagttt--ctacag-------------------------------
|||    ||| | ||||| || |  ||| | ||||| ||||| |   | ||||| ||||| ||||| ||||| ||||| ||||||||||||||||| |||||| ||||       |  ||   | |  | |  |  | | |  || |||| |  |||||                                
TCATGAAGAAATTCATCCAACAGTAATGCTTAGTGTAGTTGCTAATCTCACACCATGGTCAGATCATAATCAGAGTCCACGAAATATGTACCAGTGTCAGgttctataatcttttgtactggtcttggtatccaaatctacgttagcagtatagctacatttttttcactctgggggtgtttatgatgtag

upper sequence: EFJ24096 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA13G26190.1 (Glycine max), 5'ss of exon 22
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtt-tata----cgagcgctac-cgtaatgtttagtttt--tctaacagttt--ctacag--------------------------------
||||   ||| | ||||| || |  ||| | ||||| ||||| |   | ||||| ||||| ||||| ||||| ||||| ||||||||||||||||| |||||| ||||       |  ||   | |  | |  |  | |  | || ||||||  |||||                                 
TCACGAAGAAATTCATCCAACAGTAATGCTTAGTGTAGTTGCTAATCTCACACCATGGTCAGATCATAATCAGAGTCCACGAAATATGTACCAGTGTCAGgttctataatcttttgtacttttcttggtatccaaatctactttagcagtttagctacaatttttttcactctgggggtgtttatgatgtag

upper sequence: EFJ24096 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv13s0084g00600.t01 (Vitis vinifera), 5'ss of exon 18
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttatacgagcgc---------------taccgtaatgtttagtttttctaacagtttctacag----------------------------------------------------
|||    ||  | ||||| || |  ||| | ||||| ||||| ||  | |||||||||||||||||||| || || || || |||||||||||||| ||||||| | |  ||                 | |  |||||| |  |  | ||   |  ||| |                                                       
TCATGAAGAGATCCATCCCACTGGAATGCTCAGTGTTGTTGCTAGTCTTACACCTTGGTCGGATCACAACCAGAGCCCGCGTAATATGTACCAGTGTCAGgttttttcttgcatgttgactgaaaaaggtcctataatgtattatgctcctgttatcttcaaatttaactaactgttgtgttttgttttcttctttttctcttaaaatgattggtag

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: 26 (upstream exon), 33 (downstream exon)
Score: 3

TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttatacga ... gtttctacagATGGGAAAACAAACGCTAGGCTTTGCTTCACAGGCTTTGAAGTTTAGAACGGATCACAAAATGTACAATCTTCAG




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