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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcccccagagctatcttttcaccttttgtttcttactgtttgttttaaacgattatcatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG

Basic information

species Selaginella moellendorffii
transcript EFJ13378
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13378 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 17
------------------------------------------------------------------------gtatcccccagagctatcttttcaccttttgtttcttactgtttgttttaaacgatt--atcatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG
                                                                        | ||    | ||       |||    | |  |||     || ||      |   |||   |     ||||||||||| ||||||||||||||||||||  | || || || || || |||   || ||||| |||||  ||||| |  |    ||    |  ||||  ||  
gttcgcatttgcactgtgtttagataaacaaaagctttattgaactcaacgaattacattaagatgatgatagaattgtaccgataacaacttttgattgtgatttggcgatgatttcagagagaaattgggtttgtgttgcagGTGCATCTTGATCACAAGCACATGGGGCTGGGAGGGGACGACAGCTGGTCGCCGTGCGTGCACGAGCAGTACTTGCTGCCGCCGGCGAGATACGCCTTCT

upper sequence: EFJ13378 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 17
----------------------------------------------------------------------------gtatcccccagagctatcttttcaccttttgtttcttactgtttgttttaaacgatt--atcatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG
                                                                            | ||    | ||       |||    | |  |||     || ||      |   |||   |     ||||||||||| ||||||||||||||||||||  | || || || || || |||   || ||||| |||||  ||||| |  |    ||    |  ||||  ||  
gtgggttcgcatttgcactgtgtttagataaacaaaagctttattgaactcaacgaattacattaagatgatgatagaattgtaccgataacaacttttgattgtgatttggcgatgatttcagagagaaattgggtttgtgttgcagGTGCATCTTGATCACAAGCACATGGGGCTGGGAGGGGACGACAGCTGGTCGCCGTGCGTGCACGAGCAGTACTTGCTGCCGCCGGCGAGATACGCCTTCT

upper sequence: EFJ13378 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA15G37670.1 (Glycine max), 3'ss of exon 11
-----------------------gtatcccccaga--gctatc--ttttcaccttttgtttcttactgtttgtt---ttaaacgattatcatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGT-CTTACCACGAAATTACGAGTTTG
                        |||  |||| |    |||   |||| |   ||  | |  | | |||| ||   || || |  |       |  ||| | || || ||||||||||||||||| || ||||| ||||||||||||   || || |||||| |  ||||  |  | | | |   |  ||    | | | 
tcctatttacaggaactaaaaatatatttcccaaattattattattttttattattattattgtgcagtttattatgtttaatgtcttatgggatcacagATTCATCTGGATCACAAGCACATGGGATTGGGTGGAGATGATAGTTGGTCACCATGTGTCCACAAACAGTATTTGATTCCTCCTGTGCCATACTCATTCT-

upper sequence: EFJ13378 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 17
-----------------gtatccc-ccagagctatcttttcaccttttgtttctta--ctgtttgt----tttaaacgattatcatac------ttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGT-CTTACCACGAAATTACGAGTTTG
                  |||    ||  |  ||| ||||    |  | ||  |||  |  ||| |    |||||    |||||          |||||| | || || ||||||||||||||||| || ||||| ||||||||||||   || || ||||||||  ||||  |  | | | |   |  ||    | | | 
ttacaagaagtaaaaatatatttagcccaaattatttttttttttcatattaattatgcaatttatcatctttaatgtcttatctcttatggcattgcagATTCATCTAGATCACAAGCACATGGGATTGGGTGGAGATGATAGTTGGTCGCCATGTGTCCACGAACAGTATTTGATTCCTCCTGTGCCATACTCATTCT-

upper sequence: EFJ13378 (Selaginella moellendorffii), 3'ss of exon 16
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 16
------------------------gtatcccccagagctatcttttcacctt-ttgtttcttactgt----ttgttttaa-acgattatcatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG
                         | | |   |    |  |||  ||  |  |||||  || | ||    ||||| ||     ||     |  |  |||||||| || || ||||||||||||||||| ||||| |||||||| |||  |||||| ||||| ||  | |||||  |   | |       |||   ||  
catgctacctgcctgcagctttccctgttcttgatttgttccttggcatatcattgttatttccagtcaccttgttatattgttatggcggtgttcccagGTGCATCTGGACCACAAGCACATGGGTTTGGGTGGTGATGATAGCTGGTCTCCCTGTGTCCATGAGAAATACCTGATTCCAGCGGTGCCATACTCATTCT

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: 32

AGGAAGTCCTCCATTGCAAATGAGTGCCAGCAACTACAGTACAGAGGAGCTGGATAGAGCAACTCATGAAGAAGAGCTGAATGCTGGACAGGACATTGAGgtatccccca ... atacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttcaccttttgtttcttactgtttgttttaaacgattatcatacttgcagGTGCACCTTGATCACAAGCACATGGGTTTAGGTGGCGATGATAGTTGGAGTCCCTGCGTCCACGATGAGTACCTCGTCTTACCACGAAATTACGAGTTTG
                 ttcttac  putative branch site (score: 32)
                              ttttaaacgattat  TA-rich tract