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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttcctgtttgattcttttagtagctccttctaagAGGGTAATTCTCAGGAGCAAGTGATTGGTGTGACCATTGGAAACAATGTGTCTGGTTTCTTCCTGGACAAG

Basic information

species Selaginella moellendorffii
transcript EFJ06477
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06477 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA05G04600.1 (Glycine max), 3'ss of exon 6
------------------------------------gtttgttttcctgtttgattcttttagtagctccttctaagAGGGTA-ATT--------CTCAGGAGCAAGTGATTGGTGTGACCATTGGAAACAATGTGTCTGGTTTCTTCCTGGACAAG-------------------------------------------
                                    |  | |||     | | | | ||||||   || | |  | || | |  |||        |  |||  |   || |||||||||||| |||||||| ||||| |||||| |||||||    |                                           
atgaattatattaaaataaatcatagcatgtcttatgaatatttataattgttaatattttagagtcttcattgatgatgctgcattggttctaccctagGTCCTGTTGGTTGGTGTGACCACTGGAAACAGTGTGTTTGGTTTGTTCCTGGCAGTGGTATTTCCATATTCAAAGGGGAAGAAATTCATTTACATGCTAC

upper sequence: EFJ06477 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT4G16570.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------------------------------------------------------------gtttgttttcctgtttgattcttttagtagctcc--ttctaagAGGGTAATTCTCAGGAGCAAGTGATTGGTGTGACCATTGGAAACAATGTGTCTGGTTTCTTCCTGGACAAG-------------------------------------------
                                                                                                             | |||||   |   |   |  ||| |  |  |    || |       |  |   |||| |  || || |||||||||||||||||||| ||||| ||||||  ||| |||  ||                                           
gtgagttacaccttactgtgacttatgtcaattctcacgctgttatatggtttagaggaatccctttttcccccagttgcagtacattcagctccattgcgatcgaataggttgttgatc-actgagtcatttgaccaattttggttttcttttcttgttaaacagGTGTTAGAGACTGGTGTGACCATTGGAAACAGTGTGTTTGGTTTACTCCAGGAACAGGCGTGTCCATATCCAAAGGAGAAAAAGTTCATTTGCATGCTTC

upper sequence: EFJ06477 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv02s0154g00540.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------gtttgttttcctgtttgattcttttagtagctccttctaagAGGGTAA-TTCTCAGGAGCAAGTGATTGGTGTGACCATTGGAAACAATGTGTCTGGTTTCTTCCTGGACAAG-------------------------------------------
                                             | |    |  |||       |  || |||    |  |     | |   || | ||| ||  | ||||||||||||||||||||||||||||| |||||  |||| ||  |||                                           
tgttgaaccaagtagagatcatcttttgagttccttcatataaactatagagttttgtgctcacataataatagaatttgttggtttgatgtcttattagGTGCTGGGGATTGGTGTGACCATTGGAAACAATGTGTTTGGTTCATTCCAGGGAAAGGTATATATGTGTCCAAACATGAAGAGGTGCATTTACATGCAAT

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), 31 (downstream exon)
Score: 9

GTGGGTGCTGCAGCTTGACAAAGATGGCTTGATTTGCTACTCAACTGCTCCTCGTTGGGTCAAAGgtttgttttc ... tccttctaagAGGGTAATTCTCAGGAGCAAGTGATTGGTGTGACCATTGGAAACAATGTGTCTGGTTTCTTCCTGGACAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgttttcctgtttgattcttttagtagctccttctaagAGGGTAATTCTCAGGAGCAAGTGATTGGTGTGACCATTGGAAACAATGTGTCTGGTTTCTTCCTGGACAAG
                          gtttgat  putative branch site (score: 9)
                                            ctccttct  putative PPT
                               attctttta  TA-rich tract