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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag

Basic information

species Selaginella moellendorffii
transcript EFJ23113
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagttttt--cttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag-----------------------------------------------
| || |  || ||   | |  | |  |||||||||||||| ||||||||||| || || || || ||||||||||| ||||| ||||| || || |||||||| |    |  || |  || | |  |||  |||  ||| || ||  |  | || || | |                                                  
CCGCCGCCGCCGCGCGCGTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTGCTGGGTCACGACTGgtacgcccctgcctccatcctagagattggattt-ttttttcttttctgtgggttttagcttttgcagcccggatcgttgacccttccttccctactcggtgtctttgcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os07g49310.2 (Oryza sativa), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgttct----tacgcgtctttgatcag---------------------
|||| |  || ||   | |  | |  || |||| |||||| ||||||||||| || || || || ||||||||||| ||||| || |||||||| |||||||| |    | |||      |   |  ||  | ||      | ||    ||   ||  || ||  |                     
CTGCCGCCGCCGCGCGCCTCCACAGCTGCCTCGCCTGGCCGCTCTACTGGGCGGCGCAGGGAACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtacgacggtattcatttccattttgattcctactccactctactacactagtagtaattaattcgttcatggaattggaattgcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os12g01370.1 (Oryza sativa), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttt--tcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag-------------------------------------------------
|  || |   ||    ||        |||   | |||||| ||||||||||| || || || || ||||||||||| ||||| || |||||||| ||||||||| || |  || |      |   |||   |||  |||||| |   | |   | |   ||||                                                  
CCACTCGGATTGACGTCTCCGTCGCCTGGGCGGCCTGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaatttctattcattcattcatcgcttccatttcttttctcatatatgcatatatgc-atcaatccatcgagatctccatgaaaaacaaattgaaaatgcatgcaaacacag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os11g01340.2 (Oryza sativa), 5'ss of exon 1
CTGCTGGTGCTGCTTA-CTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtt--tttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag----------------
| |||    |     | || | ||    |    |  ||||| ||||||||||| || || || || ||||||||||| ||||| || |||||||| ||||||||  |   ||  |||   ||     |   ||||  |||||| |   | |     |      ||                
CCGCTTCCTCCATCGATCTCGCATGGGCG-TGGGCATGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtatttctattcattcattcatcgcttccatttttttttctcatatatgcatcaatccatcgagatctccatgaaaaaag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os11g01340.3 (Oryza sativa), 5'ss of exon 1
CTGCTGGTGCTGCTTA-CTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttc--ttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag-----------------------------
| |||    |     | || | ||    |    |  ||||| ||||||||||| || || || || ||||||||||| ||||| || |||||||| ||||||||  | | |   |||   ||     |   ||||  |||||| |   | |     |      ||                             
CCGCTTCCTCCATCGATCTCGCATGGGCG-TGGGCATGGCCGCTCTACTGGGCGGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtatttctattcattcattcatcgcttccatttttttttctcatatatgcatcaatccatcgagatctccatgaaaaaagcatgcaaacacag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G128971_T01 (Zea mays), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgttt------ttgctttctcgttcttacgcgtctttgatcag----------------------------------------------------
| || |  || ||   | |  | |  |||||||||||||| ||||||||||| || || || || ||||||||||| ||||| || |||||||| |||||||| |  |     |  |||    |  ||        |||  | ||| || ||  |     ||  |                                                       
CCGCAGCGGCCGCGCGCCTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaggcctccagccctccacggtcccgtgcccaacattggatactcttttttttgtcctgttattttcattcatgccagttttaggcctttgactcctgctgcatatctgctgtttgcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgt-----tcttacgc----gtctttgatcag-----------------------
| || |  || ||   | |  | |  |||||||||||||| ||||||||||| || || || || ||||||||||| ||||| || |||||||| |||||||| |      |  ||   |   |    || |  ||| || |       ||   |    ||||||||   |                       
CCGCGGCCGCCGCGCGCCTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtacgcaccaatgttctggattgccctgttgttgtttttcatggaagctttggactctggtctttgacttgtgccgcatgtctgctgtttgcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA07G18350.1 (Glycine max), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaa------------gtttttcttctcccaaaaactt----gtttttgctttctcgttcttacgcgtctttgatcag---------------------------------------------------
|| ||| |||||||||  | ||||||||| | || ||||| ||||| |||||||| ||||| || |||||||||||||| ||||| || || ||||| |||||              |||||||| ||   |  |  |     |||     |    ||  ||  | ||     ||  |                                                   
CTTCTGCTGCTGCTTATCTCAATAATTGGTTGGTTTGGCCTCTCTATTGGGCTGCTCAAGGCACTATGTTCTGGGCTCTGTTTGTTCTTGGTCATGATTGgtactaactaataactatttttcttttcttcattatgttaaaatttggatgtagctgtattttggagtgcagaattgggtttcaaaaactgtgacttgatgggtttgtttgttgttttgtgtgtttcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA18G43210.1 (Glycine max), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgta------agtttttcttctcccaaaaacttgtttttgctttctcgttcttacgc---gtctttgatcag---------------------------------------------------
 ||||| |||||| ||  | ||||||||| | || ||||| ||||| |||||||| ||||| || |||||||||||||| ||||| || || ||||| |||||      | | ||| |  |  |   |  ||||| |   ||    ||   ||      ||     ||  |                                                   
-TGCTGCTGCTGCGTATCTCAATAATTGGTTGGTTTGGCCTCTCTATTGGGCTGCTCAAGGCACTATGTTCTGGGCTCTGTTTGTTCTTGGTCATGATTGGtactaataactatttttcttttcttcattttgttataatttggatgtagctagatggagtgcagaattgggtttcaaaattgtgacttgttgagtttacttgttgttttgtgtgtttcagt

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA03G07570.1 (Glycine max), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag-----------------------------------------------------------------------------------------------------
|||||| ||| |||||  | || |||||| | || ||||| ||||| |||||||| || || || ||||||||||| |||||||| || || ||||| |||||| ||     | ||  |   |  | |   || ||| |  || ||     | | | |  |                                                                                                      
CTGCTGCTGCAGCTTATCTCAACAATTGGGTTGTTTGGCCTCTCTATTGGGCTGCTCAGGGAACCATGTTCTGGGCCCTCTTTGTTCTTGGTCATGATTGgtaa-ttgccaatttcatattgatatctccatgtttttttattttt-tatttttattactaatgtagatctagattcaattgtatagattggcttttggggtggtaaagttggatttcaaaagtttgttatgataaccatggttggtgttttggatgtttcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA01G29630.2 (Glycine max), 5'ss of exon 2
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaa--gtttttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag------------------------------------------------------------------------------------
||| || ||| |||||  | || |||||| | || ||||| ||||| |||||||| || || || ||||||||||| |||||||| || || ||||| ||||||  ||   | |  |    |  |||   | ||  || ||  |    |      ||  ||                                                                                       
CTGTTGCTGCAGCTTATCTCAACAATTGGGTTGTTTGGCCTCTCTATTGGGCTGCTCAGGGAACCATGTTCTGGGCCCTCTTTGTTCTTGGACATGATTGgtaatagtcaatttcatattgattactccatcttttttactaatgtagatctagattcaattgtatagattggctttttggggtggtaaagttggatttcaaaagtttgttatgatgataaccatggttggtgttttggatgtttcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgta--agtttttcttc---tcccaaaaacttgtttt---tgctttctcgttcttacgcgtctttgatcag------------------------
|||||| |||||||||||| || ||||||||  ||||||| |||||||||   || ||||| || |||||||||||||||||||| || ||||||||||||||  |  |  || ||      ||    | |  ||    || |||    |   |     |  || | ||                         
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT3G11170.1 (Arabidopsis thaliana), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag--------------------------------------
||||||| ||||||||| | || |||||| | || ||||| ||||| |||   || ||||| || ||||| |||||||||||||| || || ||||||||||||  ||     | |  |     || || ||   | |||    |||  |  ||||   |                                        
CTGCTGGAGCTGCTTACCTCAACAATTGGATTGTTTGGCCTCTCTATTGGCTCGCTCAAGGAACCATGTTTTGGGCTCTCTTTGTTCTTGGTCATGACTGgtaaacttaaaaaccctaacttttttcttgttttctcctctgctttagtctcctttagcctttgatttggtcaactttggatgattccaaagaaccaatc

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtt-----tttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag---------------------------------------------------------
| || |  || |||||  | || || ||| | || ||||| |||||||||||||| || ||||| ||||||||||| |||||||| || |||||||||||||||  |     | |||      | | |  | || |  || | ||  |||      |   || ||                                                           
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtct-gtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv06s0004g06720.t01 (Vitis vinifera), 5'ss of exon 2
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag--------------------------------------------------------------------------------------------------------------------------------
||   |  |||   |||||| | |  ||| | || ||||||||||||||||||||||| || || ||||||||||| || ||||| || || ||||||||||||     |  |||    | |  || |  ||| || ||      |    ||    ||  ||                                                                                                                                
CTATAGCAGCTATATACTTGGACAGATGGGTGGTTTGGCCACTCTACTGGGCTGCCCAGGGAACAATGTTCTGGGCCCTGTTTGTTCTTGGACATGACTGgtaatcacatggtcttt--acactttctgcttggttgctgagaaatggtagtaaaagaaaagaaagcaaaacttgaaatcctacttcttcagtttctttcagtaacgtaatataattttactttgcttcttttgttgagtgcttttggcaatgaacttgaatgtcctttcttgatttttattttttgaag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv06s0004g06730.t01 (Vitis vinifera), 5'ss of exon 2
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagt-ttttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag-------------------------------------
| |  | |||   ||||| | | |  ||| | || |||||||| |||||||||||||| ||||| |||||||||||  | ||||| || || ||||||||||||    ||  || |  | |  | || | |||| || ||      |    ||     |  ||                                     
CAGTGGCTGCCATTTACTCGGACAGCTGGTTGGTTTGGCCACTGTACTGGGCTGCCCAGGGGACAATGTTCTGGGCATTGTTTGTTCTTGGACATGACTGgtaatcacttaattttagccattatttctgtttggttgctaagaaatggtggtaaaataaaagaaagtaaaactcttacctctactttttcaagtttctt

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgttc---ttacgcgtctttgatcag------------------------
| ||||  || ||||| || ||  |||||   || ||||| || ||||||   || || ||||| |||||||||||||||||||| || || |||||||||||| | | | |||| |   |   |  | ||   ||||  |  |   ||    || ||| ||  |                        
CGGCTGCAGCGGCTTATTTCAACCATTGGGCTGTTTGGCCTCTGTACTGGTTCGCTCAGGGGACCATGTTCTGGGCTCTCTTTGTTCTTGGTCATGACTGgtaa-tctattttcttcttgattttcctgttgaatttcaagacccaattctctgtttttaatgggattgtgttattctggattgtacag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: EDP09401 (Chlamydomonas reinhardtii), 5'ss of exon 4
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtttttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag----------------------------------------------------------------------------
                            |    | ||||| || ||||||| ||| || || || |||||||||||||| |||||| ||||||| ||||||| |||  | || | |  ||    | | ||    | | || |   |   |    |   |  |                                                                            
----------------------------GTGGATGTGGCCCCTGTACTGGGTTGCTCAGGGTACCATGTTCTGGGCTCTGTTTGTGGTCGGCCACGACTGgtgagtggtcctgcacataatg--tggcttcatgtctgtcctcactgtaccggctgagttggcctttcccgtcgacaccatgtagtgcagactccagcaaatcattaacgccccttcacttgccttttgcccacacag

upper sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S65_6V6.1 (Physcomitrella patens), 5'ss of exon 1
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagttttt-----cttctcccaaa--aacttgtttttgctttctcgttcttacgcg----tctttgatcag---------------------------
| || || |||||     |||| |  ||| | || |||||  | ||||||   || ||||| || ||||| ||||||||||| ||||| ||||||||||||||| | |       ||| | | | |   |   |        || ||||    | |||    | || |||  |                           
CCGCCGGCGCTGCAGCTGTGAACAGCTGGTTTGTGTGGCCGTTGTACTGGCTGGCGCAAGGAACCATGTTTTGGGCTCTCTTCGTGCTGGGCCATGACTGgtaattgtactataacttgttcgagattgagaggacacgcaattttcgtgagaatgcgggaatgttagatgtggaattctgagagtagccagacatgcca

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: 33 (upstream exon), 35 (downstream exon)
Score: 32

CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagttttt ... ctttgatcagTGGACACGGGAGTTTTTCCAATAACAAGAAGCTTAACCATGTCTTCGGCCACATTCTCCATTCTTCCATCCTGGTTCCATACCACGGGTG




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