Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ31084
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 5'ss of exon 22
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt-accacgtgat--agtgttcaagtttac---cgtttt-----ctttcttcgcag-----------------
||| || || || || || ||||||||||||||||| || ||||| ||||||||||| || ||||| ||||| || |||||||| |  ||||| || || |||  | ||| |    |  ||  || |||| || ||     | | ||     ||   || || |                 
TGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATATCAATGTCTAGTATTGCTTCAAAGgtactccctttatagagctatgcagagttccagattgttcacatcttgaatactccttttgctgatatctgattctgacag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 22
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcag----------------------------------
||| || || || || || ||||| |||||||| || || || ||||||||||||||||| |||||||| ||||| |||||||| |  ||  | || || |||     |||| |  |||| |   | | ||  |  ||||| ||| | |                                      
TGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATATCAATGTCGAGCATCTCTTCAAAGgtat---tttactaaatgattgctatta-gtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G157621_T03 (Zea mays), 5'ss of exon 22
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaagttta---ccgtttt---------ctttcttcgcag------------------------
|||||| || || || ||||||||||||||||| || || ||||| |||||||||||||| ||||| ||||| || |||||||| |  ||||| || || |||  |   | | |||| ||| |  ||||||||    ||| |||          || ||| || |                        
TGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATATCAATGTCAAGCATTGCTTCAAAGgta--cttgtgcaacgttatactcatcaagtttgttcccgatttggagtacttattactttgctgatttcaaccctgtaactataacag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G042074_T01 (Zea mays), 5'ss of exon 22
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcag--------------------------
||| || || || ||||| ||||| |||||||||||||| || || || ||||||||||| |||||||| || || || ||||| |  ||  | || || |||   |   |       |   | |     ||  | |||   | ||| |                              
TGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 5
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgt-aagcacttaccacgtgatagtgttcaagtttaccgttttct-ttcttcgcag----------------------------------
|||||| || ||||| |||||||| |||||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| |  ||  ||||||| || ||        |||  | |    || ||  |  | | | ||  ||  | |                                     
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttaaatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 22
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaag--------cacttaccacgtgatagtgttcaagtttaccgttt-tctttcttcgcag---------------------------
|||||| || ||||| |||||||| |||||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| |  ||  ||||||| || ||        ||||       |  || |||    |||  | |||  |  ||| |   |                            
TGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTTCCATGTCAAGTATCACATCTAAGgttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 20
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaag------cacttaccacgtg-atagtg--ttcaagtttacc-gttttctttcttcgcag----------------------------
|||||| || ||||||||||| || |||||||| |||||  ||||||| || |||||||| || |||||||| ||||| ||||| |  ||  ||||||| || |       | ||  | | ||| ||| ||  ||||  ||||   |||| || |     ||                             
TGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTTCTATGTCAAGTATCACATCTAAGgttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 18
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaa-gtttaccgttttctttcttcgcag--------------------------------------
|||||| || ||||||||||| || ||||| || |||||  | ||||| || ||||||||||| |||||||| ||||| ||||| |  ||| | ||||| || |    |  ||   |   |||||  |  | |  |   ||| ||  || || |                                      
TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 17
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttca------agtttaccgttttctttcttcgcag--------------------------
||| || || || || || || || |||||||| ||||| || || || || ||||| ||||||||||| || |||||||||||||  ||| | || || |||   |  |   |  | |   | ||        | ||    || | |||   |  ||                           
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 21
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtga-------tagtgttcaagtttaccgttttctttcttcgcag--------------------------
||| || || || || || || || |||||||| ||||| || || || || ||||| ||||||||||| || |||||||||||||  ||| | || || |||   |  |   | || |       | ||| |  | ||    || | |||   |  ||                           
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtattaatgttgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcag-------------------------------
||| ||||| || ||||| ||||| ||||| || || || || || || |||||||| ||||||||||||||||| ||||||||||  ||| | || || |||| | || |  | ||||||   ||    ||||   |||  |||  |    |                               
TGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCTCAATGTCCAGCATTACTTCGAAGgtaa-ctctcataaagtgatatgatttccttttatgctttcttttaatgattgtacttgaccatttacactaaatgctttgcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 21
------------TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCA---------TCTAAAgtaagcacttaccacgtgatag-----------tgttcaagtttaccgttttctttct-tcgcag
            ||| ||| | |||||||| |||||||||||||| ||||| || || || || |||||||| ||  ||||||| || |||||||| |   |  ||         |  |||||  |    |||||  | |||            |||||||  ||    | ||||   | | ||||
AATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGTCAATGTCAAGGgtaacagaatatccttgaaaagttggactctaccaatttatacacggaatctcttgttcaaacttgtgttcttctcaatattgcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 5'ss of exon 21
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgta---agcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcag----------------------------------------------
||| || || || || || ||||| ||||| || || || || || || |||||||| ||||| || |||||||||||||||||||  ||| | || || |||   | ||||||  |||   |    |     | ||  |||||||||      ||                                              
TGGACCGCCTGGTACGGGGAAGACAATGCTGGCAAAAGCTGTAGCAACCGAGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAGgtattgatcacttaaaacg--gttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagtggtttggtgagggagagaagta

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgta---agcacttaccacgtgatagtgttcaagtttaccgttttctttcttcgcag-----------------------
||| || || || || || ||||| ||||| || || || || || || |||||||| ||||| || |||||||||||||||||||  ||| | || || |||   | ||||||  |||   |    |     | ||  |||||||||      ||                       
TGGACCGCCTGGTACGGGGAAGACAATGCTGGCAAAAGCTGTAGCAACCGAGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAGgtattgatcacttaaaacg--gttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcact--------------------taccacgtgatag-tgttcaagtttaccgttttctttcttcgcag--------------------------
||| || || ||||| || ||||| |||||||||||||| |||||||| || ||||||||||| |||||||||||||||||||| |  ||  ||||||| || | || |                    || | | ||||   | |    | ||    |||| ||| ||| |||                          
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

upper sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 21
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttca---agtttaccgtt----ttctttcttcgcag----------------------------
||| ||||| || ||||| || || |||||||| ||||||||||| || ||||| ||||||||||| ||||| || |||||||| |  ||  | || || ||||  |  | |  |   || |||   |   || |  |  ||     ||||  || | |                             
TGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATATCAATGTCTAGTATCACTTCAAAGgtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcag

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: 33 (upstream exon), 35 (downstream exon)
Score: 16

TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcactt ... ttcttcgcagTGGTTTGGTGAGGCGGAGAAATATGTCAAGGCAGTATTTACTTTGGCCAGCAAAATCTCACCAAGCGTGGTGTTCGTTGACGAG




<











<


<