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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgtggctttccgtgtagttcttctctaaatttctgtcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ06058
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 10
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgt--gtttttgtggctttccgtgtagttcttc--tctaaatttctgtcgcag--------------------
 || ||||| |||||||||||||| || ||||||||||| || || ||||||||| | || || || ||| | || || ||||||||||||||||| |||||  |||||       | ||  | | |  |||   |||  | |  |  |                       
ACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAATGAGAGTCGCTGGTGTTCTTCATATCTTTCAGTTTGAAACTAAGCAGgttagttttaaatctctaccaggaaataattcatactatgtgtaggctgtgaaataaccatctgatatttag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgtggctttccgtg-tagttcttctctaaat---ttctgtcgcag-----------------------------------
 || |||||||||||||||||||| || |||||||| || || || ||||||||||| || || || ||| | || || ||||| |||||||| || ||||| || |   |  |    |   |||||  |     |     | ||||   |                                    
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagcttcgaggcaatagtttataatacagccgatcctgttatatcatccatagctgttagaataacgatgactttttag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgtggctttccgtgtagttcttctctaaatttctgtcgcag----------------------------------------
  | |||||||||||||||||||| || |||||||| || || || ||||||||||| || || || ||  | || || ||||| |||||||| || ||||| || |   |  ||||   | | |  |||   |    ||||   | |                                        
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaag--tttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 12
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtt-------tttgtggctttccgtgtagttcttctctaaatttctgtcgcag------------------------------------------------------------------
| | || ||||| |||||||||||||| |||||||| ||||| |||||||||||||| || || || ||| | ||||| |||||||||||||| || ||||| ||       |  | | | |||           | ||| |||||| | |   |                                                                  
GTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGAGTTGCAGGTGTTCTTCACATATTTCAGTTTGAAACAAAGCAGgtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 12
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgtggctttccgtgtagttcttctctaaatttctgtcgcag--------------------------------------------------------------------------
  | |||||||| |||||||||||||| |||||||| ||||| |||||||||||||| || || || ||| | ||||| || ||||||||||| || ||||| ||    ||            || ||  ||  | ||  |      |                                                                          
ATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGGGTTGCAGGTGTTCTTCACATATTCCAGTTTGAAACAAAGCAGgtattggcatgttcagggacactgtactcttcctagttcttaatttcgacctttggacttgactcatatcttcattactttgaagttattttattttattggtattttatcattctttgaag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA16G21340.1 (Glycine max), 5'ss of exon 15
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgt------ttttgtggctttccgtgtagttcttctctaaat-ttctgtcgcag------------------------
| | |||||||| |||||||||||||| |||||||| ||||| |||||||||||||| || || || ||| | ||||| || ||||||||||| || ||||| |      |||  ||   || |    | ||  | |  || | || |||| ||                         
GTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataatacctttgttgatgttgcacaaactttctttggaattattttgtcacactggtattttatctcttggttgtag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA09G32740.1 (Glycine max), 5'ss of exon 12
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgt-----ttttgtggct--ttccgtgtagttc-----ttctctaaatttctgtcgcag---------------------------
| | |||||||| |||||||||||||| || ||||| ||||| || ||||||||||| || || || ||| | ||||| || ||||||||||| || ||||| |      ||||| | |  |  |    |   |     |||| |  | || | | ||                             
GTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataatacctttgttgatgatgtcacacaaacccttgtttctttggaattattttgcctcactgatattttatctatttgttgtag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 11
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgttt----ttgtggctttccgtgtagttcttctctaaatttct---gtcgcag-------------------------------------------------------------------------------
 || ||||| || ||||||||||| || |||||||| || || |||||||| ||| | || || || ||  | ||||| || ||||||||||||||||||||  ||    || ||  ||||  | |   | |     | |||| |   ||   ||                                                                               
ACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGATGAGAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAGgttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 5'ss of exon 13
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgt-gtttttgtggcttt-ccgtgtagttcttctctaaatttctgtcgcag-----------------------------------
 ||  | ||||| ||||||||||| || ||||| || || || ||||| ||||||||||| ||||| ||  |||| |||||||||||||| ||||| |||||  |||| ||  ||    | ||   |     |  ||||  || |   |                                    
ACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAATGCGTGTAGCGGGTGTACTGCATATTTTTCAGTTTGAGACTAAGCAGgttattttcgtacctagatcttgctttgtacttgcaaatccctatattattttggagatttatttttggtttgtcttgtgagcag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 5'ss of exon 13
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgtggc---tttccgt-gta-gttcttctctaaatttctgtcgcag---------------------------------------------------------
|||  | || ||||||||||| || ||||| ||||| || || |||||||| |||||||| || |||||| | || ||||| ||||| ||||| || ||||| ||| |    |   | |  || ||| | || | || ||  | |||  |  |                                                         
GCTGCGTGATATCATGCAATTCGGCAGTAGTAATACTGCCGTTTTTTTTAAGATGCGTGTTGCTGGAGTTCTTCATATTTTCCAGTTCGAAACAAAGCAGgtatttataaatcaagtgtaagtcgtacggtcatatccaagctgctgcggtggttttatgagtcatttataacttggtaatttatgatgtgtgggattggcttcaaacag

upper sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgttt-ttgtggctttccgtgtagttcttctctaaatttctgtcgcag------------------------------------------------------
| |  |||| |||||||| ||||| ||||| || || || || |||||||||||||| || || |||||  | || ||||||||||| ||||| || ||||| | | || |   | ||  ||  ||  | ||| ||  |||||  |                                                         
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatg--gtcatactc-aagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag

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), 29 (downstream exon)
Score: 7

GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgt ... tctgtcgcagGGCGAAGAAATATGCGTGGCTCTCCAGACACACATAAACGATGTGATGCTGCGGAGATATTCAAGAACGCGTTCTGTTGCTAACGGCGCCATACAAAGCA




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