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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcattcattttctcacagacttaccattttactttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ07568
intron # 35
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 2
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcattcattttctcacagacttacca-ttttactttgcag---------------------------------------------------
 || || |||   || || || || || ||||| ||||| ||||||||||| || || || ||||||||| ||||| | |||||||| |||||||| ||||||     |||  || || || | |   | | || |  | |  |  | ||                                                   
GCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGCAAACCATTGATATGAATCAGgtatgctgttgtctttatattttgatt-attgacgagctctcgtacgaagtttggtccttatacatataggagcaaatattatgtatattatatttatttg

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 38
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcattcattttctca---cagacttaccattttactttgcag------------------------------------------------
||| |||||||| ||| | |||||||| ||||| || |||||||||||||| ||||| ||||| |||||| ||||| | ||||| || || ||||| |||||     |||  | | ||||  |||    ||| |    |     |  ||| |                                                
ACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCCAAACAATTGACATGAATCAGgtgaagtttttgactaatttcatcataatagattgtgtaaggacccatgctgtattctcctgttgtgccccctcctattttgttagccattctgtcttat

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: GLYMA10G44150.2 (Glycine max), 5'ss of exon 36
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactacttt----gcattcattttctcacagactt-accattttactttgcag----------------------------------------------
 || |||||||| ||| | || ||||| ||||| || |||||||||||||| ||| | ||||| |||||| ||||| | ||||| || || ||||| |||||     |||    ||  ||  ||| | ||  | || | |||  ||  |||                                                 
GCCTGGAAATCCCAAATTGGGTGAAGGGAAGCCCGAGAATCAAAATCATGCAATTGTATTTACGCGTGGAAATGCAGTCCAAACAATTGACATGAATCAGgtgaagttttaatagctgtctgtttttgactaatttcatcataatagattgtgtaaggacccatgttgtattttccctttgtgccccccccccccccttt

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: AT2G36850.1 (Arabidopsis thaliana), 5'ss of exon 36
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcat-----tcattttctcacagacttaccattttactttgcag----------------------------------------------
 || ||| |||| |||||||| ||||| |||||||| |||||||||||||| ||  | ||||| || ||||| || || || |||||||||||||| |||||  | | |  | |     |||| ||    || | ||     || || ||                                                  
TCCCGGAGATCCTAAACTTGGTGAAGGGAAGCCTGAGAATCAAAATCATGCTATCGTGTTTACGCGGGGAGAAGCTATCCAGACCATAGATATGAATCAGgtttttcctcacttctttgtcatgtttcggcacatttctgtattgacattaagagagtcgtactgcggataagctaaacccgtcatgcatgtggccgata

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 33
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgt-actactttgcattcattttctcacagacttaccattttactttgcag--------------------------------------------------
||| |||||||| |||||||| ||||| || |||||||||||||| |||||  |||| ||||| |||||| ||||||| ||||| || || ||||| ||||| ||||  |    || || |  ||||| | | |  | |  ||||                                                       
ACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTCAAACGATTGACATGAATCAGgtcactaactctttttgatctattcacaaaataaaaaatggacttcttgtgttctgctgcatgaagtagattaagtttgttgaatttgggattgtgaaaa

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: Vv17s0000g10010.t01 (Vitis vinifera), 5'ss of exon 30
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgca--ttcattttctcacagacttaccattttactttgcag-------------------------------------------------
 || ||| ||||||| ||||||||||| ||||||||||| ||||||||||| || || || || ||||| || || || ||||| || |||||||| |||||    |||||||  ||  |||  |  ||    |    | | | || |                                                    
TCCTGGAGATCCAAAGCTTGGAGAAGGTAAGCCTGAAAACCAAAATCATGCTATAATCTTCACACGTGGGGAAGCTATTCAAACTATTGATATGAATCAGgtgagtctttgcacattgttttctttccaagtatcttgtgtgatttcggtttagtttcataaactgttgctataaaaacctggttttcagtagattatca

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: PP1S160_88V6.1 (Physcomitrella patens), 5'ss of exon 36
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcattcattttctcacagacttaccattttactttgcag------------------------------------------------------
 || ||       ||||| |||||||| || || ||||||||||||||||| || || ||||  ||||| |||||| | |||||||| ||||||||||||||   |   |||  |  ||||||      || |    | | ||  | |                                                       
CCCTGGGCCGTTTAAACTCGGAGAAGGAAAACCAGAAAATCAAAATCATGCTATCATATTTAGTCGTGGGGATGCAGTTCAAACCATTGATATGAACCAGgtttca---tgcgcttcttttcttttttcctcattcctctcctccggattgttctagatgcgtccttcttaacttatgttaagggctgtactataaattttct

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: PP1S145_49V6.1 (Physcomitrella patens), 5'ss of exon 34
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgt---actactttgcattcattttctcacagacttaccattttactttgcag----------------------------------------------------------------------------------------------------------------------
 || ||| |   ||   | || || |||||||||||||||||||| ||||||||||||||||| ||||| || ||  | || || || || ||||| |||||    |||| ||||       |   |   |    || |||||  |                                                                                                                            
GCCCGGAGAAGTAATTTTAGGGGAGGGCAAGCCTGAAAATCAAAACCATGCGATTATTTTTACTCGTGGGGAAGCCCTTCAGACTATTGACATGAATCAGgtttgtctaccttgcgaaggactctgcgtggtgcaactattttgatagctctctcctttcaaatcaaacatgaattagtggtttttatattttacctgcagaatttcagtagagtttgaacgttggtgggatttgacgtcatatttgtggataccctctcattgatgcag

upper sequence: EFJ07568 (Selaginella moellendorffii), 5'ss of exon 35
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 5'ss of exon 35
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtac-tactttgcattc--attttctcacagacttaccattttactttgcag---------------------------------------------------------------------------------------------------------------------------------------------
 || ||| |    |  || ||||| |||||||||||||| ||||| ||||| ||| | ||||| |||||||| || || ||||| || || ||||||||||||| | | |  |  ||    | |||| |   ||  |  | |   | |  |                                                                                                                                              
GCCTGGAGAAGTTATTCTGGGAGAGGGCAAGCCTGAAAACCAAAACCATGCAATTGTATTTACTCGTGGAGAGGCCATTCAAACTATTGACATGAACCAGgtacatccctctctctctagctctctctctctctcgctgtatatatatatatatatatatatatatatatatgttttagttcctttgtgacaaacttggggtggcgatttgttcgaacacctgcacagtagttacacagtttttcgttgatgagaagtgtcatcatatttcggagcacgttgcattgacgcag

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), 34 (downstream exon)
Score: 8

ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactacttt ... tactttgcagGACAACTATTTCGAAGAGGCCCTTAAAATGCGAAACCTGCTTCAAGAGTTTGACTCGAACCACGGTTTGCGTCCCCCGTCGATCTTGGGTGTTCGTGAAC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATACAAACCATAGATATGAACCAGgtactactttgcattcattttctcacagacttaccattttactttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG