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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaagtttcttcgtcgttcctgtttagaaatttcttgcttcttttgacagGTTGAACGAGTTATTGGTATGGTTGATGGAGCTGTGCTCGTTGTCGATGCTGGCGAGGGGCCGCTTGCACAAACAAAGTTTGTGGTCGCCAAAGCTCTAA

Basic information

species Selaginella moellendorffii
transcript EFJ08344
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 2
--------------------------------------gtatgaaagtttcttcgtcgttcctgtttagaaatttcttgcttcttttgacagGTTGAACGAGTTATTGGTATGGTTGATGGAGCTGTGCTCGTTGTCGATGCTGGCGAGGGGCCGCTTGCACAAACAAAGTTTGTGGTCGCCAAAGCTCTAA
                                        ||| |  ||     ||  |      |  ||   ||      | | ||| ||||||||||||||| |||| ||||| || ||||||||  | ||||| |||||||| ||||| ||  | |||||||| || |||||| |  | |||||| | |
gtatgtggtcctcatataattttctatgttttgaaccaaaatgtagattctgatgtgatatacaatatgatcattaccaaatttgttg-cagGTTGAACGAGTTGTTGGAATGGTGGAAGGAGCTGTCTTGGTTGTTGATGCTGGAGAGGGACCTTTAGCACAAACTAAATTTGTGCTTTCAAAAGCTTTGA

upper sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT2G31060.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------------------------------------------gtatgaaagtttcttcgtcgttcctgtttagaaatttcttgcttcttt-tgacagGTTGAACGAGTTATTGGTATGGTTGATGGAGCTGTGCTCGTTGTCGATGCTGGCGAGGGGCCGCTTGCACAAACAAAGTTTGTGGTCGCCAAAGCTCTAA
                                                                                                                                                 ||    ||    |  ||  |  || | |    ||||  ||  | |   | | |||||||||||||  ||||||||||||| |||||| |  | ||||| |||||||| || || || |||||||| || ||||||||  | ||||||||  | |
gtgaggtatgatactgatcttacttttagcgtattatttgattctcatgctcgtttttagtagaaatgcatattagtggacaaaagataaattaattagaagttctcaatacctactcatggtctgttgacattaggatactccttactgtagaacataggtgctatctttgtgactattttgtgtatttgaattatagGTTGAACGAGTCGTTGGTATGGTTGAAGGAGCTATATTAGTTGTTGATGCTGGAGAAGGCCCTCTTGCACAGACTAAGTTTGTTCTTGCCAAAGCCTTGA

upper sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------------------------------------gtatgaaagtttcttcgtcgttcctgtttagaaatttcttgc-ttcttttgacagGTTGAACGAGTTATTGGTATGGTTGATGGAGCTGTGCTCGTTGTCGATGCTGGCGAGGGGCCGCTTGCACAAACAAAGTTTGTGGTCGCCAAAGCTCTAA
                                                                                                                                            ||    ||    |  ||  |  || | |    ||||  ||  ||    | | |||||||||||||  ||||||||||||| |||||| |  | ||||| |||||||| || || || |||||||| || ||||||||  | ||||||||  | |
gtatgatactgatcttacttttagcgtattatttgattctcatgctcgtttttagtagaaatgcatattagtggacaaaagataaattaattagaagttctcaatacctactcatggtctgttgacattaggatactccttactgtagaacataggtgctatctttgtgactattttgtgtatttgaattatagGTTGAACGAGTCGTTGGTATGGTTGAAGGAGCTATATTAGTTGTTGATGCTGGAGAAGGCCCTCTTGCACAGACTAAGTTTGTTCTTGCCAAAGCCTTGA

upper sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------gtatgaaagttt-cttcgtcgttcctgtttagaaatttcttgcttcttttgacagGTTGAACGAGTTATTGGTATGGTTGATGGAGCTGTGCTCGTTGTCGATGCTGGCGAGGGGCCGCTTGCACAAACAAAGTTTGTGGTCGCCAAAGCTCTAA
                                                | ||  || |  ||  || | ||||  |    |||| |||  |   || |  ||||||| || ||| |||| |||||||| ||||| ||  | ||||| |||||||| || || || ||||||||||||||||||||  | || |||||  |||
ggtgtaagctttacttacacactggtttgcaagttttcttgtttttattttgctagatcactaagttgatccttgt--ataattactttttctgttggttagGTTGAGCGGGTTGTTGGCATGGTTGAAGGAGCAGTTTTAGTTGTAGATGCTGGTGAAGGTCCCCTTGCACAAACAAAGTTTGTCCTTGCAAAAGCCTTAA

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), 35 (downstream exon)
Score: 6

TATACTTCTATGATCTGGGGAACCAGTTCTCTCAACATTGTTGATACTCCTGGTCACGCAGATTTTGGTGGAGAGgtatgaaagt ... cttttgacagGTTGAACGAGTTATTGGTATGGTTGATGGAGCTGTGCTCGTTGTCGATGCTGGCGAGGGGCCGCTTGCACAAACAAAGTTTGTGGTCGCCAAAGCTCTAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgaaagtttcttcgtcgttcctgtttagaaatttcttgcttcttttgacagGTTGAACGAGTTATTGGTATGGTTGATGGAGCTGTGCTCGTTGTCGATGCTGGCGAGGGGCCGCTTGCACAAACAAAGTTTGTGGTCGCCAAAGCTCTAA
                                   tttcttgcttctttt  CT-rich tract
                           tttagaaatttctt  TA-rich tract