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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaatccggctagtttgttggtcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

Basic information

species Selaginella moellendorffii
transcript EFJ30530
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G426306_T01 (Zea mays), 3'ss of exon 2
-------------------------gtatggaatccggctagtttgt-tggtcttttctattgattctcggggaatcgtggcg----atttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                         |    ||||   |  ||   |    ||    ||    ||   |   | | |||||| |    |||||| | | || |  || | ||| | ||||||    | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| ||||| |
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtccgccgagaattctgaattcgtggtgtttaatttctattgtagGTCAAATTAATCAGAATCGAGTGCAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAATGGCG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G003076_T05 (Zea mays), 3'ss of exon 1
-------------------------gtatggaatccggctagtttgt-tggtcttttctattgattctcggggaatcgtggcg----atttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG---------
                         |    ||||   |  ||   |    ||    |||   ||   |   | | ||| || |    |||||| | |||| | ||| | ||| | ||||||  | | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| || || |         
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCGGTGAGCCAG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
-------------------------gtatggaatccggctagtttgt-tggtcttttctattgattctcggggaatcgtggcg----atttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                         |    ||||   |  ||   |    ||    |||   ||   |   | | ||| || |    |||||| | |||| | ||| | ||| | ||||||  | | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| || || |
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G055462_T01 (Zea mays), 3'ss of exon 2
-------------------------gtatggaatccggctagtttgt-tggtcttttctattgattctcggggaatcgtggcg----atttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                         |    ||||   |  ||   |    ||  | ||    ||   |   | | ||| || |    |||||| | |||| | ||| | ||| | ||||||    | || || |||||||| ||||| ||||||||||| |||||||| || || |||||||| || || |
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcacagtaatgtccgccgagaattctgaattcgcggtgtttaatttctattgcagGTCCAATTAATCAGAATCGAGTGCAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA08G07670.1 (Glycine max), 3'ss of exon 1
--------------------------------gtatggaatccggctagtttgtt-ggtcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                                 |||||      | |     |   | | || || |  || ||      |||| |  |   ||   || ||| | |||||  | || ||  | |   | || || |||||||| ||||| ||||||||||| ||||||||| |||||||  |||| |||||| 
gaatttagtgaggaacttggtagaatgtgtgcttatgggtgtttgtttccaagccagattttgtcaaaggaatc---aataatcataacttgtttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGAT

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA08G07670.2 (Glycine max), 3'ss of exon 1
--------------------------------gtatggaatccggctagtttgttgg-tcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG----
                                 |||||      | |     |   | | || || |  || ||      |||| |  |   ||   || ||| | |||||  | || ||  | |   | || || |||||||| ||||| ||||||||||| ||||||||| |||||||  |||| ||||||     
gaatttagtgaggaacttggtagaatgtgtgcttatgggtgtttgtttccaagccagattttgtcaaaggaatc---aataatcataacttgtttattctcagGTGCAACTGGTACGAATTCAAAGGAGGGTACCTGAGTATGGGTGGACAACGCAGAAGGTTTTCCATTTGATGAATTTTGTTGTCAATGGATGTAA

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA05G24420.1 (Glycine max), 3'ss of exon 1
------------------------gtatggaatccggctagtttgtt---------ggtcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                         ||||   |   |   |||||||         | | || || | ||| ||      |||| |      ||   |  ||| | |||||  | || ||  | ||  | || || || ||||| ||||||||||||||||| ||||| ||| |||||||  |||| |||||| 
aattttgtgaggaatttggtagaaatatgtgcttatgggtgtttgtttccaagccagattttctcaaatgaatc---aataatcataatttgtttattatcagGTGCAACTGGTGCGAATTCAAATGAGGGTACCTGAATATGGGTGGACGACGCAGAAGGTTTTCCACTTGATGAATTTTGTTGTCAATGGAT

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------gtatggaatccggctagtttgttggtcttttctattgattctcggggaatcgtggcgat-----ttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                                                                                                       || |     |  | |  ||||| |       |   |  ||      ||    |         || | | | |||| ||| |  |  | ||  |  |  | || || || |||||||||||||||||||||||||| ||||| || |||||| | || || ||||
gtaccgtttacttgtccttctggttttgaattgggattggaattagggaatgtgttgatttggaatcggaagattaggcatttaaggatatgaaattgaggaaatagttgttgtatggagtgttgattagagaaaaaaaccctaaattgattaaagtttcatttgtttttttgtagATTCAATTGGTAAGAATACAATTGAGAGTTCCAGAATATGGCTGGACGACGCAGAAGGTCTTTCATTTTCTCAATTTCATGGTTAACGGAG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------gtatggaatccggctagtttgttggtcttttctatt--gattctcgg---ggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                           | | ||    |  | ||| ||| | |||| | ||   |||        |  ||  |  |    | | |   || | |||||  | |||||  |  |  | ||||| |||||||| ||||| ||||||||||| ||||| || || |||||||| || ||||| |
tttctttatgaatcttcttttccataaacgaaacagagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------gtatggaatccggctagtttgttgg----tctt---ttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                        | |||| |   ||| | ||||||     ||||   || |   | |      |   || | |   |      ||||||| ||||| ||  |||| ||  |  | || || |||||||| ||||||||||||||||| |||||| |  |||| ||| | || |||||||
gaattgtttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv00s2255g00010.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------gtatggaatccggctagtttgttgg----tctt---ttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                        | |||| |   ||| | ||||||     ||||   || |   | |      |   || | |   |      ||||||| ||||| ||  |||| ||  |  | || || |||||||| ||||||||||||||||| |||||| |  |||| ||| | || |||||||
gaattgtttttcactgccgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG

upper sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S295_30V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------gtatggaatccggc------tagtttg---ttggtcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                       || |    || |||      |||| |         ||| ||| || | |   |    |   ||   |      ||  || | ||||| || ||||| ||||| || || || |||||||||||||| || ||||| ||||| ||| || |||||||| |||| |||||| 
ccctttcaatttgtcaatgtggcgtgtctgctctggcagcacatagtcttaaccaaagcttctctttttagttgtgaactaatatgttaaaaatgttc--agGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT

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: 29 (upstream exon), 35 (downstream exon)
Score: 20

GGAGGATTGGTGGTACACTCTCAACGAGTCCAAGGCATGGCAGAATCGATTCTACTACTCGCTCTCCGGCGCCTATCTCCTTGTAGCTCTCGTCGCCCTGgtatggaatc ... tctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgttggtcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
                 tattgat  putative branch site (score: 20)
                                           tttctctcgc  putative PPT
            ttttctatt  TA-rich tract