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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgcttcaacacacaactaacacagctagtcaaatacag

Basic information

species Selaginella moellendorffii
transcript EFJ09183
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatatgagttgaat-gcttcaacacacaactaacacagctagtcaaatacag-------------------------------------------------------------------------------------------------------------------
 || || |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || |||||||| ||||| || || ||||| |        | |  |||     | |    || |     |  |||| | |||                                                                                                                   
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgt--------aatatgagttgaatgcttcaacacacaactaacacag-------ctagtcaaatacag--------------------------------
 || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || || |||||        ||    ||||  ||| || |  | | | |  |    |       ||   || ||  ||                                
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactgaaacatatccaaacttaa

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G379271_T01 (Zea mays), 5'ss of exon 3
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgt--------aatatgagttgaatgcttc----aacacaca-actaacacag-ctagtcaaatacag---------------------------------
 || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || || |||||        ||    ||||  ||| ||     ||  ||||   | |   |  ||   || ||  ||                                 
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgtttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcgtacactgaaaaatatccaaacttaat

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G036290_T01 (Zea mays), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaa--tatga------gttgaatgcttca-----acacaca-actaacacag-ctagtcaaatacag--------------------------------
 || || ||||| || || ||||| ||||| ||||| |||||||||||||| ||||| || || || ||||| || |||||||| ||| | || || ||||| |    |||      |||| ||  || |     || ||||   | |   |  |||  || ||  ||                                
AGAAGTTATTGAGGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAATCTATCATACACTCTATGGTTGAAACCCAGgtgagccctgaaccatggttgtatcttttactaaaacgcacatgttgaggtattctacccagatgtagtgctttgtacactaacatatccatgcttaatc

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaata--tgagttgaatgct----tcaacacacaacta-acacagctagtcaaatacag----------------------------------------
 || || |||||||| || || ||||||||||||||||||||| | ||||| ||||| || ||||| ||||| || ||||| || ||||| || |||||||||  |      ||  ||| |    | |   ||     | |  ||  || ||  |||||                                         
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTATGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtataaaccttattctatgttatgtttactgcattttgatatccatatattcggatacaaatggatgaggaaccatagccatagcacctacaagttccag

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgt---aatatgagttga----atgct--tcaacacacaacta-acacagctagtcaaatacag-------------------------------------
 || || |||||||| || || ||||||||||||||||| ||| | ||||| ||||| || ||||| ||||| || ||||| || ||||| || ||||||||   ||| | | |  |    ||| |  | | | ||     | |  ||  || |   || ||                                      
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTACGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtctaaatctaattctatgttatgttggttaccgcattttaatatccatatatttggatgcaaatggatgaggaaccatagtacctacaagctacaagtt

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 5'ss of exon 9
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgct--tcaacacacaactaacacagctagtcaaatacag-------------------------------
 |||||||||||||| || ||||||||||||||||| ||||| || || || ||||| || ||||| |||   || ||||| |||||||| || ||||||||  |        | | ||    ||   |  | |    | | |    ||| | |                                
TGAGGTCATTGAAGCGCATTATTTGTTTGGAGCTGAGTATGACGATATAGAGATTGTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacag

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S62_157V6.2 (Physcomitrella patens), 5'ss of exon 11
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatat--gagttgaatgcttcaacacacaactaacacagctagtcaaatacag----------------------------------------------------------------------------------------------------
 || || ||||||||||||||| | || || ||||| || ||||||||||| |||||| ||||||||||||| || || || |||||| | |||||||||||||       |||  |    |  |          | ||   | ||  ||||                                                                                                       
GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgt-gaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaattgctgacttctgggatgatgtctgtatcctctgttttatag

upper sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 5'ss of exon 11
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatatgagttgaatgcttcaacacacaactaacacagctagtcaaatacag------------------------------------------------------------------------------------------------------
 || || |||||||| || ||| | || |||||||| || ||||| ||||| |||||| | ||||||||||| ||||| || |||||| | ||||| |||||  |||    | |   |  ||    |   ||  |  | | |  ||  |                                                                                                          
GGAAGTGATTGAAGCCCATTATCTCTTCGGAGCTGATTACGATGATATTGATATTGTTGTTCATCCCCAATCAATTATTCATTCCATGGTGGAGACGCAGgtt-tatctcataatcaccgcagagaaattctttccaatcaaaccatgtttgaaagagttgttatttgattacagactggagtaacctttaacatttttcgatttggtcaaatggtttctgacttttgagatgatggatgtgacttgtctgatag

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), 33 (downstream exon)
Score: 16

CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatatgag ... tcaaatacagGATTCCTCCATCCTGGCGCAATTGGGGTGGCCTGACATGCGACTACCTATTCTTTACACACTCTCTTGGCCGGATAGAGTTCCATGCTCAGAAATCACCT




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