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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacgggtgtcttctactcgagttcttaatgcgtgcatttgttttgtttcag

Basic information

species Selaginella moellendorffii
transcript EFJ22392
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 13
TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacgggtgtcttctactcgagttcttaatgcgtgcat-ttgttttgtttcag------------------------------------------------------------------------------------------------------------
| || ||||||||||| || ||||||||  ||||||| || |||||||| ||||||||||| || ||  || | ||| | || | ||| || || || |||    |      | |   ||   |       |  |   | ||| ||  |  || | |                                                                                                             
TTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAAGgc---atgtaaattttccctgaccattgctattgtatttacatgttactgagtatgatggacgctgaactttttgagtggtgtcccaagctgtgccattctggagagatataatttgaactgttcttgagataactcacaatactaaccatctttcgctatttcag

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GLYMA09G06890.1 (Glycine max), 5'ss of exon 27
TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacgggtgtcttctactcgagttcttaatgcgtgcatttgttttgtttcag------------------------------------------------
| |||||||| |||||||| ||||||||| |||||||||| ||  | || ||||||||||| || ||  || | |||||| |  | || ||||| || |||| |||      | | |  |  ||   || ||| || |  | | | | || ||  ||                                                
TTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcaga-----atttttatttttctgattattattggggacttatatattattgtagggttgcacagtgcttggaaaattagtgtcaacacagttggaaagccaa

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 27
TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacgggtgtcttctactc------gagttct-taatgcgtg-catttgttttgtttcag-----------------------------------
| ||||||||||||||||| ||||||||| ||||||| || ||  | || ||||||||||| || ||  || | |||||| |  | || ||||| || |||| |||        | ||||  |       | || ||  |   | || |||||  |||||||                                      
TTCTTTGGGTAAATCTTATCATGGATACTCTGGGAGCACTAGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGATCCCCAGTGGGTCGAAGgtcagagtttttatttttctgattattattgggtactacagatcatggcatttcatttgtttgctatattattgtagggttgcacagtgtttggaaaatt

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 29
TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgt------------tagacacgggtgtct---tctactcgagttc--ttaatgcgtgcattt-gttttgtttcag-----------------------------------
| |||||||| |||||||| ||||||||| | || || || |||||||||||||| ||||| || ||  ||||||||||| |  |||| || ||  | ||||             ||||  | |  |     |  | ||  ||||   ||  | ||||  |  ||||   ||||                                    
TCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAAGgtaccacttcttatcagacttgagcatgcgtgttaagtcttgttcaactatagagtgctctcagtttctcttcaatttgcacaataattggatttatcttttgctctcag

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 24
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacgggtgtcttctactcgagttcttaatgcgtgcatttgttttgtttcag-----------------------------------------------
| || ||||| |||||||| ||||||||| | ||||| || || || |||||||||||||| |||||  || | ||| | ||||| || || || || |||| |        | | |  |  | |       |||   | |  || | |    | ||                                               
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttt---tttttaatgttgggagatccaataaatactgtt-tataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca

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|169101664|gb|FE501208.1|FE501208
EST:     ACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAG                         GGAGCCCCTTGTCACGAATATAATGTGGAGAAATATTTTCGTACAG
genomic: ACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacg ... tttgtttcagGGAGCCCCTTGTCACGAATATAATGTGGAGAAATATTTTCGTACAG
EST: gi|169075222|gb|FE484104.1|FE484104
EST:     ACTGAGCCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAG                         GGAGCCCCTTGTCACGAATATAATGTGGAGAAATATTTTCGTACAG
genomic: ACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacg ... tttgtttcagGGAGCCCCTTGTCACGAATATAATGTGGAGAAATATTTTCGTACAG

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), 33 (downstream exon)
Score: 28

TGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCAGgttagacacg ... tttgtttcagGGAGCCCCTTGTCACGAATATAATGTGGAGAAATATTTTCGTACAG




<











<


<