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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC

Basic information

species Selaginella moellendorffii
transcript EFJ07113
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g26740.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------gtgggatttttctctttgctcgtccctgatcgatg--gctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAG-CGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                                                   | | |||    | |||    |   |||| |  |   | |    |   | | ||||||||||| ||||||||||||||||| ||||||||||||||||||||     | |||||||  ||      | |  | |||| |  ||   ||        
gtctttatcaatgctttcagcttctttttttttttcctcctcatcatgttatagcattcggttttttagaagcatctgacccgtcttgttgcaatctgacttcagAGGTGCAAGCACTTTGAAATCGGTGGAGACAAGAAGGGCAAGGGAACTTCACTCTTCTAAGATGCTGATATTGCCCTGTTCCCCAATTCTCTGCCAGGAG-

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------gtgggatttttct--ctttgctcgtccctgatcgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGA--TGATGTTCTC
                                              | || ||| |   | || | |   || |   |     || ||     | ||||||||||| || |||||||| ||||| |||||||||||||||||||||    | |||||| |   | | | |  ||  |    |  |||   |  ||| || 
gtatttttgcaatgtgaagattcaagctgaaaattctcatgaatcagtatctttttagatgtgttggatgctcacttacataattattctg--tgcagAGGTGCAAGCATTTTGAAATTGGTGGAGACAAGAAGGGCAAGGGAACGTCTCTTTTCTAAAC-TAC-CTACTGGATACTGAAGTTGTGGGTCTACTGTGCTT

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------gtgggatttttct--ctttgctcgtccctgatcgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                                              | || ||| |   | || | |   || |   |     || ||     | ||||||||||| || ||| |||| ||||| |||||||||||||||||||||    | ||||||                                        
gtatttttgcaatgtgaagattcaagctgaaaattctcatgaatcagtatctttttagatgtgttggatgctcacttacataattattctg--tgcagAGGTGCAAGCATTTTAAAATTGGTGGAGACAAGAAGGGCAAGGGAACGTCTCTTTTCTAA----------------------------------------

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g33921.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------gtgggatttttct--ctttgctcgtccctgatcgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGA--TGATGTTCTC
                                                  | || ||| |   | || | |   ||     |     || ||    |  ||||||||||| || || || || ||||| ||||||||||||||||||||     | |||||| |   | | | |  ||  |    |  |||   |  ||| || 
gtattatttcattgtcaagactcaagctgaaaattgtcatgaatcaatcagtatctttttagatgtgttgggtgctatcttacattattattcttta--cagAGGTGCAAGCATTTCGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCTCTTTTCTAAAC-TAC-CTACTGGATACTGAAGTTGTGGGTCTATTGTGCTT

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g33979.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaa---------tccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                                          || |  |   |||||| |    || | |||| ||  |||||| |         | ||||||||||| || || || || ||||| ||||||||||||||||||||     | ||||||                                        
gtattatttcattgtcaagactccagagctgaaaattatcatgaatcattattttgctggatg-tgttggatg-ctcacttgcataattgttctctgcagAGGTGCAAGCATTTCGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCTCTTTTCTAA----------------------------------------

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaa---------tccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC-
                                          || |  |   |||||| |    || | |||| ||  |||||| |         | ||||||||||| || || || || ||||| ||||||||||||||||||||     | ||||||    ||  | | |    |   |    | | || || |||  
gtattatttcattgtcaagactccagagctgaaaattatcatgaatcattattttgctggatg-tgttggatg-ctcacttgcataattgttctctgcagAGGTGCAAGCATTTCGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCTCTTTTCTAAAT-TGCTTGCTACCTACTGGATACTATAGTTGTTGGTCTAC

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G160351_T01 (Zea mays), 3'ss of exon 3
-------------------------gtgggatttttctctttgctcgtccctgatcgatggcttt--cttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                          || |   |   |  |   | || | |    | |  ||||  | |  || | ||||||||||| |||||||| ||||||||||||||||| |||||||||||     |||||||||||      |  |    |     |||    |     ||  
gtctttacggccatgcttcattattttgtgccctcgtttgtgttttgttctttgaagctaactttgtcctttaacttcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAAGGCAAGGGAACCTCTCTGTTCTAAGCGTATCATAAACTTGCTCAGGGTCTCAAGTATCTGTCAG

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G160351_T03 (Zea mays), 3'ss of exon 2
---------------------------------------------gtgggatttttctctttgctcgtccctgatcgatggcttt--cttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                                              || |   |   |  |   | || | |    | |  ||||  | |  || | ||||||||||| |||||||| ||||||||||||||||| |||||||||||     ||||||||                                        
actctcaacacccgatcaaggtctttacggccatgcttcattattttgtgccctcgtttgtgttttgttctttgaagctaactttgtcctttaacttcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAAGGCAAGGGAACCTCTCTGTTCTAA----------------------------------------

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G009412_T02 (Zea mays), 3'ss of exon 3
-------------------------------------------------gtgggatttttctctttgctcgtccctgatcga-tggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCG-CGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC--
                                                 ||   | |||  | || ||||   | |    || || ||  | ||      ||||||||||| || ||||| || ||||| ||||||||||||||||||||     | |||||||   | |      ||   |  |  | ||||||           
gtgcagtgtctcattttcctgtgttaggcttgctgttgcacaaagtattgtctcactttgat-ttagctcactctttcctgactgactcacctgtgt-cacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCTCTCTTCTAAGTTTCTCATCGCCCA---TCTCGATGTTGGATCGAACCTGTGG

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G19320.1 (Glycine max), 3'ss of exon 3
-----------------------------------------gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC-----
                                          ||| || |      | |||  |   |  |   || || | |||    | ||||||||||| |||||||| || ||||||||||||||||||||||||||     |||||||   |   |||| | |   |||    |||   | |||||        
gttagtatatggtaaacaaaacaatggtttaaagtggttgtttggcatgtgctgtgtggctaatggtttgttcctgtctatgttgttg-tgcagAGGTGCAAGCACTTTGAGATTGGTGGTGACAAGAAGGGCAAGGGAACATCTCTGTTCTA---GTTTGCGAATTAGGATTCGCAGCTTT--TTATGTTTCAGCAAT

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA15G05670.2 (Glycine max), 3'ss of exon 3
-------------------------gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaatc---cagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCG----CGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                          | || |   | |  |   | |    || | | | | |    |  |  |    ||||||||||| |||||||| || ||||||||||||||||||||||||||     | |||||             |||| |    |      ||     ||||    
gtatatggaaagcaatggatgcttttttggttccatgtggtgtgtggctaatggttgttagttcctgtctatgttgtgcagAGGTGCAAGCACTTTGAGATTGGTGGTGACAAGAAGGGCAAGGGAACATCACTCTTCTAGTTTGAGAATTAGGATTTAGAGCTTTATGTTTCAGCAATGT----

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 3
-----------------------------gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaatc---cagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAA----GCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                              | || |   | |  |   | |    || | | | | |    |  |  |    ||||||||||| |||||||| || ||||||||||||||||||||||||||     | |||||             |||| |    |      ||     ||||    
gttagtatatggaaagcaatggatgcttttttggttccatgtggtgtgtggctaatggttgttagttcctgtctatgttgtgcagAGGTGCAAGCACTTTGAGATTGGTGGTGACAAGAAGGGCAAGGGAACATCACTCTTCTAGTTTGAGAATTAGGATTTAGAGCTTTATGTTTCAGCAATGT----

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 3
-----------------------------------------gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGC-GCGCGC---GATTC--AATTTTCCTCTCTTGGATGATGTTCTC---------------------------
                                          ||| || |      | |||  |   |  |   || || | |||    | ||||||||||| |||||||| || ||||||||||||||||||||||||||     |||||||    |||      |||||  |  |||      ||     |||||                              
gttagtatatggtaaacaaaacaatggtttaaagtggttgtttggcatgtgctgtgtggctaatggtttgttcctgtctatgttgttg-tgcagaggtgcaagcactttgagattggtggtgacaagAAGGGCAAGGGAACATCTCTGTTCTAGTTTGCGAATTAGGATTCGCAGCTTTTTATGTTTCAGCAATGTTGGAATCTTTTAGTTTCTCTCTGGATTTTTC

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA05G24930.1 (Glycine max), 3'ss of exon 3
----------------------------------------gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaatc-------cagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC--
                                            | |  ||  | ||       | || | ||||  |    ||    ||       ||||||||||| |||||||| |||||||||||||||||||| || |||||     | |||||   |      |||  | ||| |  | |   |   | |      
tacttttgcctcaaacagtaattttgccactgattcccaaacatgctcattgccgttttgaacacgtggttgatgcttgctatgtggttctgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCTCTCTTCTAGATGGAAT--ATTAGAATTTGCAATTTCACACACTCTCTGTAC

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G08030.1 (Glycine max), 3'ss of exon 3
--------------------------------------gtgggatttttctctttgctcgtccctgatcgatggcttt--cttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                                      || |  ||  || | | |||  | | || |      |||    ||     | ||||||||||| || ||||| |||||||||||||||||||| || |||||     |||||||                                         
gtataagcgtctcttcccgtcgtttcgtttttgtttttgtcgttttgatcgcgtggctgatgcttgctttcctccttctgtttttgcctgcagAGGTGCAAGCATTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACCTCTCTGTTCTAG----------------------------------------

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------gtgg-gatttttctctttgctcgtccctgatcgatggctttcttgcaaa-----tccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC--
                          ||   ||   ||| |   |||    ||| |   |    ||  ||         | ||||||||||| |||||||| |||||||| ||||||||||| ||||||||     | || ||||     |   ||||  | ||  || ||   || | |  |   
gtaatgtctgcgacattctttacctttgttaatcactctttagtctcagttctgtttcttacactttgtgtgtggtttttgcagAGGTGCAAGCACTTTGAGATCGGTGGAGACAAGAAGGGAAAGGGAACATCTCTCTTTTAAGTTGTTGT--TTCATCTATCTACTTTTTTTTGTTTTGTTTGG

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------gtgggatttttctctttgctcgtccctgat----cgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                               |||||| |  ||| |    |  || |      | ||| ||  |    | | ||||||||||| || || || |||||||||||||||||||| ||||||||     |||| ||||   |    ||   ||||||  |  ||     |  | || 
gtgcatagaacatagatcagttcattataccggatttgtaacttggtaatttgcttacattgtgttggtttgttgtttatttcagAGGTGCAAGCATTTCGAGATCGGTGGTGACAAGAAGGGAAAGGGAACATCTCTGTTTTAAGTTGGTTTCATCTTATTTTCTGCGATTTTTGTACTTGCTG

upper sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv01s0011g02080.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------gtgggatttttctctttgctcgtccctgatcga----tggctttc----ttgcaaatc-cagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC-
                                       ||  | | || |   |    ||  |  |  ||      ||||      ||| |  |  ||||||||||| |||||||| |||||||| || |||||||| ||||| ||     | || ||     ||   |        |       |  ||  |    |  
caaaaatttgtcaaatgtattttttaagttagcaaattttgaaactgtttttaataactgtttccaaatgaacctcagcttctgtcattggattttgcagAGGTGCAAGCACTTTGAGATCGGTGGCGATAAGAAGGGGAAGGGCACTTCTCTATTTTAGAT-TGCAAAACCAGGCAATTGCAGGGTCCATCTTCCATTTT

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), 32 (downstream exon)
Score: 24

GCCAAGACCACCAAGAAGATCGTGCTCCGGCTCCAGTGCCAGACGTGCAAGCGCGTGTCGCAGCACCCTCTAAAGgtgggatttt ... gcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggatttttctctttgctcgtccctgatcgatggctttcttgcaaatccagAGGTGCAAACACTTTGAAATCGGTGGTGACAAGAAGGGCAAGGGAACGAGCTTGTTCTAAGCGCGCGCGATTCAATTTTCCTCTCTTGGATGATGTTCTC
                         ccctgat  putative branch site (score: 24)
                                      ctttcttgc  putative PPT
       atttttct  TA-rich tract