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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatgagacagagaattttcttgcgtagttctaatacgttcatgcttttaaatcttctgtccag

Basic information

species Selaginella moellendorffii
transcript EFJ31102
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os05g36000.1 (Oryza sativa), 5'ss of exon 3
TGTCACG-GCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatga-gacagagaattttcttgcgtagttctaatacgtt-catgcttttaa-atcttctgtccag-------------------------
 |  |   || || ||||| || || || || || ||||| || |||||||| || || |||||||||||||| || |||||||| ||||| ||||| |||||| | |  |||   |   |  | |    ||| ||   | |  | | |    | | ||||| |  ||||     |                         
-GGAATATGCTGTTGGGATCAAGAATGTTACAATAAATGATAACTTCTTCCCAGGGCATTTTCCGGAGAGACCTATAATGCCTGGTGTTCTTATGGTGGAGgtatacattgattttgtttgccagtacgtttgtgttcatatgttgcttaatttacatttaacaatttctaagttgtggttactttactggtgcttccctt

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G19200.1 (Glycine max), 5'ss of exon 2
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatgagacagagaattttcttg--cgtagttctaatacgttcatgcttttaaatcttctgtccag---------------------------
 ||  | ||||| |  || || || ||||| || |||||||| ||||| || || || ||||| || || || ||||||||||| ||||| ||||||||||||  |||  |||    |      |  |||    |||  ||| ||   ||  ||   ||   |  ||| |  |                            
AGTTTCTGCAGTGGCTATAAAGAATGTGACAATAAATGACAACTTCTTTCCTGGACATTTTCCAGAAAGGCCCATCATGCCTGGTGTTCTAATGGTTGAGgtactaaaatatgcactatgctcctacctttgttgtatctcttatttattt-tgtccttgccttgtctctaaacatgtcatgataaaatggaatcaatttg

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA05G24650.1 (Glycine max), 5'ss of exon 3
------TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatgagacagagaattttcttgcgtagttc-----taatacgttcatgcttttaaatcttctgtccag-----------------
       ||  | ||||| |  || || || ||||| || |||||||| || || || || || ||||| || ||||| ||||||||||| |||||||||||| ||||| | |   ||  ||       |   |||   || |||     || |   ||||||| |  || | || | || ||                 
TCCTGGAGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTTTTTCCTGGGCATTTTCCAGAAAGACCAATCATGCCTGGTGTTCTCATGgtttaggtaaacactaatatgagtctagctacccttttatatttcctttatattctcttcatgcctgcaatttttttatcaagtgtaaaaatctgtgctt

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA08G07870.1 (Glycine max), 5'ss of exon 3
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaa--acgatgagacagagaattttcttgcgtagttctaatacgttcatgcttttaaatcttctgtccag--------------------------
 ||  | ||||| |  || || || ||||| || |||||||| || || || || || ||||| || ||||| ||||||||||| |||||| ||||||||||| | |  | | |||  |    |  || | |      ||||  |   ||| ||| |  || | ||   |   |                          
AGTTTCTGCAGTGGCCATAAAGAATGTGACAATAAATGACAACTTTTTTCCTGGGCATTTTCCTGAAAGACCAATCATGCCTGGTGTTCTCCTGGTTGAGgtaaacactatgctgacccttttatattccctttccttttctcttgtcttcttgcctgaaactatttgattgtgaaagtgtaagttctgtgctttaatta

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT5G10160.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatgagacagagaattttcttgcgtagttctaatacgttcatgcttttaaatcttctgtccag---------------------------------
|||  | || ||||  ||||||||||| || || |||||||||||||| || || || || || |||||||| || |||||||||||||||||||||||||||     |  |    |     ||| |||    |   || || |  |  ||   |||  || |  | |  ||                                 
TGTATCTGCGGTAGCTATTAAAAACGTTACCATTAATGACAATTTCTTTCCTGGGCATTTCCCTGAGAGACCTATAATGCCTGGAGTTCTCATGGTTGAGgtaatttgcatttgccct----attctctcttcttactccaaaagttcaatctgtttgcatatatt-tatagttaaaagagaagctttttgagcctagacattta

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatg-----agacagagaatttt---cttgcgtagttctaatacgttcatgcttttaaatcttctgtccag--------------------
|||  | || ||||  ||||| || || || |||||||||||||||||||| ||||| || || ||  |||| ||||||||||| ||||||||| ||||||||  ||     |     ||    | | ||||   ||   | || || ||||  ||     |  ||  |   ||||                        
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 5'ss of exon 3
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgat----gagac----agagaattttcttgcgt-agttctaatacgttcatgcttttaaatcttctgtccag-------------------
 ||  | || || |  || || || || || || ||||| || ||||| || || || ||||| ||||| || || |||||||| ||||||||||||||||||        |    |   |    | | | |||| || | | ||||  | ||  || |   ||  |  | |   ||  |                    
AGTTTCTGCTGTTGCCATAAAGAATGTAACAATAAATGATAACTTCTTTCCTGGGCATTTTCCCGAGAGGCCAATTATGCCTGGTGTTCTCATGGTTGAGgtaatttcttgttcccgtaccttttaaatatttttttttctttagttgcattatttttaaagttacatgtatgaggtaaatgtttccatttttgctacaa

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgt-agaaaacgatgagacagagaattttcttgcgtagttctaatacgttca-----tgcttttaaatcttctgtccag----------------------
 |   | |  || |  ||||| |||||||| |||||||||||||||||||| || ||||| ||  || |||| ||||||||||| || |||||| ||||||| ||| | |  |  |   |  ||| |   || | || |  |||  |         | ||| ||   | | |  | |                       
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTCA-CGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatgagacagagaatt-----ttcttgcgtagttctaatacgttcatgcttttaaatcttctgtccag----------------------------
 |    |||| || |  ||||| || ||||| |||||||||||||||||||| |||||||| ||  || | || |||||||| || || || ||||||||||||  | |||      || |   ||     || |   || | | | | |||   ||||   |   |  | |||| |                             
-GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgta--agacgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgca-atgccaatgggt--tatgtcaatgtgtggcaacgttggcgcttctattgcc

upper sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S196_99V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatg--agacagagaattttcttg-cgtagttctaatacgttcatgct-----tttaaatcttctgtccag--------------------
 |   |||| || |  || ||||| ||||| ||||||||||| |||||||| || ||||| ||  || | || ||||||||||| || |||||||| ||||||  |    ||   ||  |    ||  |||||   |   | ||| |      |||      ||||  ||     |  |                     
GGAGTCGGCTGTTGCCATAAAAAATGTGACTATCAATGACAACTTCTTCCCTGGTCACTTCCCCCAGCGGCCCATCATGCCTGGGGTGCTCATGGTAGAGgtaagacgtcatttcagggatttgatcatcttgatatgaatgtaacattgcagtgcgcatggtttaggtcaataatgtaatagtgtgggcatttctattt

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: 32 (upstream exon), 11 (downstream exon)
Score: 4

TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacg ... ttctgtccagGCAATGGCTCAAGTTGGTGGACTCGTGATGCTCAAGCCCGAAGCTGGCGGCTCCAAGGAGATTTTTTTCTTTGCGGGCGTGGACAAGGTCCGGTTCCGCA




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