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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcgggaactcaaaagttcggtttttccattcttccag

Basic information

species Selaginella moellendorffii
transcript EFJ28417
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os04g31070.1 (Oryza sativa), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcgggaactcaaaagttcggtttttccattcttccag---------------------------------------
  | ||||||||| | || || |||||  | ||||| |||||||| || |||||||| ||||| |||||||| || || ||| |||| || ||||| |||||||||||  | | | | ||    |  |   |    |   | |  |||    |   || ||                                        
CAGGCATGGTGATCTTCTTAATAAGTACATGTACCTTACTGGACGTGTTGACATGAAACAAATTGAGAAGACAATACAATACCTGATTGGGTCTGGGATGgtaagagctaata-tctatttaggcatgatgatattattttcctttttacttaagtttacaatgctattgtggataaccttgttatcaatagccatgtctc

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os02g30200.1 (Oryza sativa), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcgggaactcaaaagt----tcggtttttccattct-tccag---------------------------------------
 || || || ||  |  | |||||||| ||||||||||| ||  | |||||||||| |||  ||||||||||||| |||||| | || || || || ||||||||        | | | ||  | ||   | || | ||||    | | ||||    |||| |  |                                        
CCGGCACGGCGACCTGATGAACAAGTACCTCTACCTCACCGGCAGGGTCGACATGAGGCAGGTCGAGAAGACGATACAGTACCTCATTGGCTCCGGCATGgtaagcattt---gctccctccgtttc---accttacaagtcgctttgattttctttttctatttaaactttttaaagtttaattaagattatagaaaatattagc

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g69080.1 (Oryza sativa), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcggg------------aactcaaaagttcggtttttccattcttccag--------------------------
  | ||||||||  | || ||||| |||||||||||||||||  | || |||||||  ||||| |||||||| || |||||  | || || ||||||||||||| ||          |||||||    |             |||| |  | || |   ||  ||||| |                              
CAGGCATGGTGACCTCCTGAACAAATATCTCTACCTCACTGGTAGGGTGGACATGAGACAAATTGAGAAGACAATTCAGTATCTTATTGGCTCTGGAATGgtaacagttttcttccgcttctttgctagcctagctatatttaactgattattttgaaattgtcattcatgagtttttccctcaagcaattgttttcctc

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G026793_T01 (Zea mays), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttct---ttctcgggaactcaaaagttcggtttttccattcttccag-----------------------------------
  | ||||||||  | || || |||||  | ||||| |||||||| || |||||||| ||||| |||||||| || |||||  |||| ||||| ||||||||||| |   |     | || |   |  ||  | | |   |  |  | |||| || ||| | |                                     
CAGACATGGTGACCTCCTTAATAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATTCAGTATCTGATTGGTTCCGGAATGgtaagcgattaagtactattatatatcttcaaggattttgatatctgtttttccctttccttccatttatagcttttcaatgaatcatgaaatcaccgac

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AC215690.3_FGT002 (Zea mays), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaag-agcccagagtttcttctttctcgggaactcaaaagttcggtttttccattcttccag-------------------------------------
  | ||||||||  | || ||||||||  | ||||| |||||||| || |||||||| ||||| |||||||| || || ||  |||| ||||| ||||||||||| ||   |    | ||  | |||      | |     |||  ||| |   ||      |                                     
CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactactggtatctgtctttcccttcccttccatttataactttcaatgggtcatgaaatcattcacatttttgcttttgataacca

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT3G02630.1 (Arabidopsis thaliana), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcgggaactcaaaagttc-----ggtttttccattcttccag---------------------------------
| | ||||| ||| | || ||||||||||| || ||  |||| || || ||||||| ||| || || ||||| || |||||| |||| |||||||||||||||||  |    |  ||  | |||  |   ||| || ||  ||     | |   |     |||   |                                 
TAGACATGGGGATCTCCTTAACAAGTATCTTTATCTGTCTGGTCGGGTAGACATGAGGCAGATTGAAAAGACTATTCAGTACCTGATTGGTTCTGGAATGgtaagctctgctaactttcttttttgctttaacccataatctcctaaagttgcatttgcgctttaggaagtgactggggatggggatacaatcgttacat

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv00s0499g00030.t01 (Vitis vinifera), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagttt-cttctttctcgggaactcaaaagttcggtttttccattcttccag-------------------------------------
| | ||||||||  | |||||||||||||| |||||  |||||||||| |||||||||||||| |||||||| || |||||  | || || || |||||||||||| || |     | ||| |||  | | | |    |   ||      |  || ||   ||                                     
TAGGCATGGTGACCTTCTCAACAAGTATCTTTACCTTTCTGGACGAGTAGACATGAAGCAAATTGAGAAGACAATTCAGTATCTCATAGGATCAGGAATGgtaagatcctaattcctacttatttggctgcatccactatcatcataaactatatactatgagtcttgtttcacagagaatgtaggaaaattttgccatt

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00580.t01 (Vitis vinifera), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccag--agtttcttctttctcgggaactcaaaagttcggtttttc-cattcttc--cag--------------------------------------
  | || |||||  | || || ||||||||||| ||  ||||| |||| |||||||| ||||||||||||||||| ||||| ||||| ||  |||||||||| |||  |  |  |  | ||| ||| |       |      |   ||   || || |||||   ||                                      
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgctttttttttttttttttttttctgtagtcaatcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00550.t01 (Vitis vinifera), 5'ss of exon 1
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaaga------------gcccagagtttcttctttctcgggaac---tcaaaagttcggtttttccattcttccag-------------------------
  |  | |||||  | || || ||||||||||| ||  ||||| |||| |||||||| ||||||||||||||||| ||||| ||||| ||  |||||||||| |||            ||||    ||| || ||| || | |     ||| ||  |    |  | | |     ||                          
CAGGGACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGAGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatgcccttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00730.t01 (Vitis vinifera), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccaga-----gtttcttctttctcgggaactcaaaagttcggtttttccattcttccag---------------------------------
  | || |||||  | || || ||||||||||| ||  ||||| |||| |||||||| ||||| ||||||||||||||||| |||||  |  |||||||||| |||  |  |        || ||   | |        |||||   |  | |    |    |   |                                 
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATTGAGAAGACGATCCAGTATTTGATTAGGGCTGGAATGgtgagattcttgctgcatacttttttactgttttatctccaaaaccacaatatagtgacagattttggtaagacgtaaggtggatttgaaattgatacac

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00650.t01 (Vitis vinifera), 5'ss of exon 5
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcc----cagagtttcttctttctcgggaactcaaaagttcggt-----ttttccattcttccag--------------------------------
  | || |||||  | || || ||||||||||| ||  ||||| |||| |||||||| ||||||| ||||||||| ||||| ||||| ||  |||||||||| |||  |     | |    ||| ||| |       |       || ||     | |||  |  |||  |                                
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGACATGAAACAAATCGCGAAGACGATTCAGTATTTGATTGGGGCTGGAATGgtgagattcttgctacatcccctttttttttttttttttctgtagtcagtcacaatcttcactagttcttgaactcaagttcttcttctccatcttttcatag

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00750.t01 (Vitis vinifera), 5'ss of exon 2
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagccc--------------agagtttcttctttctcgggaactcaaa--agttcggtttttccattcttccag----------------------
  | ||||||||  | ||||||||||| || || ||  |||||||||| |||||||  ||||| |||||||| || || || ||||| || || |||||||||||  ||                 |   | || | |||     |||  ||  ||||    ||| | |  |||                          
CAGGCATGGTGACCTTCTCAACAAGTACCTATATCTGTCTGGACGAGTAGACATGAGACAAATTGAGAAGACAATTCAATATTTGATTGGATCAGGAATGgtaagttccttcacatgaacatttgaaaggttttatctctaaactactttaagcagttaaactttgcaaaacttttgaaatgaggaaatgatgggaggct

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv05s0094g00740.t01 (Vitis vinifera), 5'ss of exon 3
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccaga-----gtttcttctttctcgggaactcaaaagttcggtttttccattcttccag---------------------------------
  | || |||||  | || || ||||||||||| ||  ||||| |||| || ||||| ||||| |||||||| |||||||| |||||  |  |||||||||| |||  |  |        || ||   | |        |||||   |  | |    |    |   |                                 
CAGGCACGGTGACCTTCTTAATAAGTATCTCTATCTGTCTGGAAGAGTAGATATGAAACAAATTGAGAAGACAATCCAGTATTTGATTAGGGCTGGAATGgtgagattcttgctgcatacttttttactgttttatctccaaaaccacaatatagtgacagattttggtaagacgtaaggtggatttgaaattgatagac

upper sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S157_50V6.1 (Physcomitrella patens), 5'ss of exon 3
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcgggaactcaaaagttcggtttttccattcttccag------------------------------------------
 || || || ||  | || ||||||||  | ||| | || || ||||| |||||||  |||||||||||||| || ||||||||||| || ||||| |||||||||  |||   | | |||   ||    || |   | | ||| |   |   | || ||||                                          
CCGTCACGGAGACCTGCTGAACAAGTACTTGTACTTGACAGGGCGAGTGGACATGAGACAAATCGAGAAGACAATTCAGTACTTGATTGGATCTGGGATGgtaagaagcca---tgttttcaccctaaaaaattatgatgctcgctgaatgtgt-ctgccagctactgtatctacgcaaattaaattgcgtacggaagttcgaa

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), 33 (downstream exon)
Score: 13

TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagccc ... attcttccagGATCCCCAGACCGAGAACAATCCATATCTCGGGTTCATCTACACGTCCTTCCAGGAGCGAGCCACCGCCATCTCTCATGGCAACACTGCTCGCCACGCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaagagcccagagtttcttctttctcgggaactcaaaagttcggtttttccattcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA