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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ09736
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag----------------------------------------------------------
|        |||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||| || || || || ||  | ||||||||   | | ||   | |  |       | |  ||| |  ||                                                            
GCCGCTCGCCGCCATGGATGAGGAGTACGACGTGATCGTGCTGGGGACGGGCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctctcct-acccaatccatccgccgcctcccgtgctcggatcggtgctccccatcgtcgtcgatccgtagatcgccccccacttcatctcatctg

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcg-gagttggaagacatctctctcgcag--------------------------------------------------------
        | ||||||||||||||||||||||| || ||||| |||||||| ||||||||||||||||||||||| || || || || ||  | ||||||||  ||   |   | ||  |  |         |||||||| |                                                          
ACGAGCAGGAGCCATGGATGAGGAGTACGACGTGATCGTGCTCGGGACGGGCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacgtggctagggctctcgtctctctctctctctctctctctctctctctcacccgctcgccgccggctactagcttccgcagatgctcgccgtcgccg

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os07g16970.2 (Oryza sativa), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtggg-tttttctcgatcggagttggaagacatctctctcgcag--------------------------------------------------------
      |  ||||||||| | |||||||||||| || ||||| |||||||| ||||||||||||||||||||||| || || || || ||||| ||||||||||  |  ||||| |||    |         |||||||| |                                                          
CCGCCCGCCCGCCATGGACGTGGAGTACGACGTGATCGTGCTCGGGACGGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGATCGCCTCAAGgtggtctccttctccatctctctctctctctctctctctctctctctctctctctctctctctctcccgcccggatcgatctagctagggcatcgcgtca

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g16900.1 (Oryza sativa), 5'ss of exon 1
-GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagt---tggaagacatctctc--tcgcag----------------------------------------------------
 |    || | || |||||||||||||||||||| || |||||||||||||| ||||||||||||||| ||||||| || || || || ||| | |||||||||      || |      | |   | |||  || |      | |||                                                     
GGGAGCGGCG-GCGATGGATGAGGAGTACGACGTGATCGTGCTGGGGACGGGGCTCAAGGAGTGCATCATCAGCGGCCTCCTCTCCGTCGATGGCCTCAAGgtgaccgaatcccatctccaatctctcgaatgcaccctctgattgcaactcgacaatgcgttctactgctgctggtgcgtgcgtccgcattagtagatct

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G047431_T01 (Zea mays), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag---------------------------------------------------------
      | |||||||||||| |||||||||||| || |||||||| || || ||||||||||||||||||||||| || || || ||||| || ||||||||  |||   ||    ||  |     |   ||| |   | |                                                           
CCGCGCGCGCGCCATGGATGTGGAGTACGACGTGATCGTGCTGGGCACCGGGCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCTGTGGACCGCCTCAAGgtacgttacgctactacgacgcctccatcgatcccctcctctctctccctccgtcgtcggccacttctaataagatcgcgccctggtggttatccatttt

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G084440_T01 (Zea mays), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgt------gggt----ttttctcgatcggagttggaagacatctctctcgcag-------------------------------------------------
      | | |  |||||||||||||||||||| || ||| |||||||||| ||||||||||||||| ||||||| || || || || ||| | ||||||||      ||||    |     ||  ||    || | ||    |||    |                                                   
AAGAGAGAGAGAGATGGATGAGGAGTACGACGTGATCGTGTTGGGGACGGGGCTCAAGGAGTGCATCATCAGCGGCCTCCTCTCCGTCGATGGCCTCAAGgtctggccgggtgcagtgcgtgcgtgcgtgcatgcatgatgattcttcttcgttcggatccaaccgtcaatgtttgcgtaatataacaatgtgattgcacag

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttc------tcgatcggagttggaagacatctctctcgcag---------------------------------------------------
      |   ||||||||||||||||||||||| || ||||| || ||||| |||||||||||||||||||| || || || || || ||  | ||||||||| |    ||       || ||     |     |     | |||| ||                                                   
CAGCCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTGCTTGGCACGGGGCTCAAGGAGTGCATCCTCAGTGGTCTCCTTTCCGTCGACGGCCTCAAGgtgagcccgtcgatcgcccgctctcttctcctgcagccgccgctcgtagatccgtggctgccgtgctcggattttgggtccgcgtaatagtccggtgctt

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgg--------gtttttctcgatcggagttggaagacatctctctcgcag-------------------------------------------------
      |   ||||||||||||||||||||||| || || || || ||||| ||||||||||||||||||||||| || || || || ||  | ||||||||          | |    ||      ||  | |     |      |  ||                                                 
CCGGCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTACTAGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgcccgctcgcttcccctacagccgcagctagtacgatccatagctgccgtgctcggaatttgggtccgcgtataagtccggtgcttcaaggt

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G435373_T02 (Zea mays), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag---------------------------------------------------------
             ||||| |||||||||||||| || || ||||| ||||| ||||||||||||||||||||||| || || || || ||  | ||||||||| |       |   ||      |   ||  |  ||   |                                                           
-------------ATGGACGAGGAGTACGACGTGATCGTTCTGGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTCGACGGCCTCAAGgtgagcaccgaccacccgcctcccggtaacggcaatcggacctcaccccagtccccgagtccgatctgccactctcccccgcacgtacccggacgccgca

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA05G30140.3 (Glycine max), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgg-gtttttctcgatcggagttggaagacatctctctcgcag---------------------------------------------
   | | |    |||||||||||||||||| || || ||| |||| |||||||||||||||||||| |||||||| || || || || ||| | ||||||||    |||   |  |||    | |     | | ||| |   |                                              
AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtactatttccattcatcactttcgtttttcttttcttttcaatcgatccaatcctcgcatgctaattgctatttcttgttcgattcag

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G13300.3 (Glycine max), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag----------------------------------------------
   | | |    |||||||||||||||||| || || ||| |||| |||||||||||||||||||| |||||||| || || || || ||| | ||||||||  ||  |  ||  |      |      ||| |   |  |                                                
AGATCGATCGAACATGGATGAGGAGTACGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactcatcactttcctatttctttcattttcttttctatagatccaattctctcatgctaattcctatttcttgttcgattcag

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G07250.1 (Glycine max), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttc--tcgatcggagttggaa---gacatctctctcgcag----------------------------------------------------
             |||||||| |||||||| || |||||| |||| || ||||||||||| ||||||||||| || || || || || ||| | |||||||| | ||||    |   | ||| ||        |||  ||| |                                                         
-------------ATGGATGAAGAGTACGATGTAATTGTGTTGGGCACAGGTCTCAAGGAATGCATCCTCAGTGGCCTTCTCTCAGTTGATGGCCTCAAGgttgtttttctatttagttggactttttctctaacacttcttttcttaatgttagattggttttctatttggttgtacatgtatcatttaagaatgtcgt

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA07G30050.1 (Glycine max), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtt---tttctcgatcggagttggaagacatctctctcgcag-------------------------------------------------------
             |||||||| |||||||| || |||||| |||| || ||||||||||| ||||||||||| || || || || || ||| | |||||||| | ||   | |||      ||||   || | |||    ||   |                                                       
-------------ATGGATGAAGAGTACGATGTAATTGTGTTGGGCACAGGTCTCAAGGAATGCATCCTCAGTGGCCTTCTCTCAGTTGATGGCCTCAAGgtagtttaattctcttctctcgagtcccaaca-atcgaattcattgtttttctatttggttgtaatttttttctctaacacttcttattttaatgttagat

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA07G24480.1 (Glycine max), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtg------ggttt------ttctcgatcggagttggaagacatct--ctctcgcag----------------------------
             |||||||||| || ||| || || ||| |||| |||||||||||||||||||| |||||||| || || || || ||| | ||||||||        ||||      |  |  ||     ||  || | |||    |||||||                             
-------------ATGGATGAGGGGTGCGATGTGATCGTGTTGGGCACGGGTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCTGTCGATGGCCTCAAGgtactcatcagtttcctatttctttaattttcttttcaatagatccaattctcgcatgttaattcctatttgttgttcgattcag

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtg---ggtttttctcgatcgga-gttggaagacatctctctcgcag-----------------------------------------------------
 |          ||||||||| |||||||| || || ||| |||| || ||||||||||| ||||||||||| || || || || || ||  | ||||||||        |||||   ||     ||     || ||||  | | |                                                      
CTCCCTCAAAATCATGGATGAAGAGTACGATGTTATAGTGTTGGGCACCGGTCTCAAGGAATGCATCCTCAGTGGTCTTCTCTCCGTAGACGGCCTCAAGgtcttcatcctttctaattcactcatttttcaacttctccttggaaataagaggttttttggccctctactggagtcatgcttgtaatcgactatttttg

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: EDP02072 (Chlamydomonas reinhardtii), 5'ss of exon 2
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag---------------------------------------------
                 | |||||||| ||||| || |||||||| |||||||| |||||||||||| |||| || ||||||||||||||       |||||| |     || ||   | |   |||  |  |   |  ||                                               
----------------AACGAGGAGTATGACGTGATCGTGCTGGGCACGGGTCTGAAGGAGTGCATCATCAGTGGCCTGCTGTCGGTGGACAAGAAGAAGgtgcgggac-ctagacatgcgcgcgaatgctgcaaccgggcctgcttttcttcgcgcgctggccgctcaccatcgcaacctgttgcag

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S167_1V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTTTGGT--GCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtt--tttctcgatcggagttggaagacatctctctcgcag-------------------------------------------------------
  |   |   || |||||||||| |||||||| || ||||||||||| || || || ||||||||||||||||| ||||| || || |||||||||||||||||||||    |    |||||  ||||       |  |||  || |                                                       
--TGGAGCCGGCACCATGGATGAAGAGTACGATGTGATTGTGCTGGGCACCGGGCTGAAGGAGTGCATCCTCAGTGGGCTACTCTCCGTGGATCGTCTCAAGgtgggtgggatcgcagatcgtggttgatctgtgtgactcgggcggtgtggcgtagctgccggctctctgggtgtagcgtggatttgtggtcggcgaggga

upper sequence: EFJ11673 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtggg---tttttctcgatcggagt-tggaagacatctctctcgcag-----------------------------------------------------
       | || ||||||||| ||||| ||||| ||||| || || || || |||||||| || |||||||| || || || || || ||||||||||||||||    | || ||||||| ||   |   | |  | |      |||                                                     
CCGAGATTTCGTCATGGATGAAGAGTATGACGTGATTGTACTCGGCACTGGCCTCAAGGAATGTATCCTCAGTGGACTTCTCTCTGTCGATCGTCTCAAGgtggtgcctcttcctcgatctgaaccttttataggtttgcagatcagtgtttttgtttgtttgttttgtttttatttcctttctcttcttctccttaggt

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), 35 (downstream exon)
Score: 66

GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggttttt ... tctctcgcagGTGCTACACATGGACAGGAACGACTACTACGGGGGAGAATCGGCGTCTCTCAATCTTGTCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTGGTGCGCCATGGATGAGGAGTACGACGTCATTGTGCTGGGGACGGGTCTCAAGGAGTGCATCCTCAGCGGGCTGCTGTCGGTGGATCGTCTCAAGgtgggtttttctcgatcggagttggaagacatctctctcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA