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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctgactgagatttctggttgcgaatctttaacaggtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA

Basic information

species Selaginella moellendorffii
transcript EFJ24458
intron # 25
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24458 (Selaginella moellendorffii), 3'ss of exon 25
lower sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 27
--------------------------gtatcctgac-tgagatttctggttgcgaatctttaacag--gtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA
                           |    ||||   || | |||     |   ||||| || |   ||| |||||| ||||| ||  | || ||| | |||||||| ||||||||||||||||| |||||  |||| || ||||||||
gtgtgttactgtttgaagaaaattctttccattgacaccagctctctaaagactg-tctttgactgtgtttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAGCAAGCAAGCCAAATACACCCCA

upper sequence: EFJ24458 (Selaginella moellendorffii), 3'ss of exon 25
lower sequence: AT5G15920.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------gtatcctgactgagatttctggttgcgaatctttaacag---------gtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA
                                 |  ||| ||   |    | ||         |||| |          | |||  |||| ||||||||| | || ||| | ||||||||||| ||||| || |||||||| ||||| || |||||||| ||
gtaaaaagtgtaaatgttttttttttaatgtaaaaactgtctcgaaacattagtcaaagtctcttaaaaatatacatttgcttgtgcagGTATGGATCCCATAAATGAAAGGAAGATGTTTCAACAATTGGTTAGAGCTGCTAGTCAACCAAACACACCACA
















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: 35 (upstream exon), 21 (downstream exon)
Score: 13

GAACGCTCGGTGTCAACTATACTCTACCTTGTCTCACTCCAAGACCTTACCCACTGTCCGTTTCGTGTTGTGGATGAGATAAACCAAGgtatcctgac ... gtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcctgactgagatttctggttgcgaatctttaacaggtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA
      atctttaac  putative branch site 
                                       aatctttaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctgactgagatttctggttgcgaatctttaacaggtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC