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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag

Basic information

species Selaginella moellendorffii
transcript EFJ22352
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgac-ttctttattgtttgacag-----------------------------------
|||||||||||||||||||||||||||||| ||| ||||||||  | |||||||| ||||||||||||||||| || || |||||||||||||||||||||  ||    |  ||  |   |    |     | | |  | |||     ||    | ||||||                                      
ACAGGAAGAAGGACTACAAGGACGGGAGGTTCTCCCAGGTTGTCTCCAACGCGCTCGACATGAAGCTCAGGGATGATCTTGAGAGGCTCAAGAAGATCAGgtcagtacctcgtctgtcctatctcccccctgcttgccgaattagtactcaacctagtttgatgatggaaccgttttagattaagaactatttttttaat

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g07719.1 (Oryza sativa), 5'ss of exon 2
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctt-tcaatctcttggggatggatggattg-acttctttattgtttgacag----------------------------------
|||||||||||||||||||||| ||||||| ||| ||||||||  | ||||| |||||||||||||||||||| ||||| |||||||| ||||||||||||   |    |  || |||  ||   | |||  | |   |   ||| |  | |    || |  |||                                   
ACAGGAAGAAGGACTACAAGGATGGGAGGTTCTCCCAGGTTGTTTCTAACGCCCTGGACATGAAGCTCAGGGATGACCTTGAGAGGCTGAAGAAGATCAGgtttggttctgctcgcttaccacatttttgtagctttgtaacttgcatgtgtgaggtgctgtacatatacctttcatgcttttgttggattgatagaaat

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgc------------aagccgtttttccctttca-atctcttggggatggatggattgacttctttattgtttgacag-----------------------
|||||||||||||||||||||| ||||||| ||| ||||||||  | ||||| |||||||||||||||||||| ||||| |||||||| ||||||||||||             ||   ||  |  | |  || || | || ||  ||     | |  | ||| ||  ||     |                        
ACAGGAAGAAGGACTACAAGGATGGGAGGTTCTCCCAGGTTGTTTCTAACGCCCTGGACATGAAGCTCAGGGATGACCTTGAGAGGCTGAAGAAGATCAGgtttggttctgcttaatttgtgctcgcttaccacattttttaggcttgttgtaacttgcatctgtaaggtgctgtacatatactccctccgtccaaaaaa

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g07770.1 (Oryza sativa), 5'ss of exon 2
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag---------------------------------------
    |||||||||||||||||| ||||||| ||| ||||||||  | ||||| |||||||||||||||||||| ||||| |||||||| ||||||||||||  |    |  ||   ||    || | |        ||   ||   ||| |  |   |||   |                                       
----GAAGAAGGACTACAAGGATGGGAGGTTCTCTCAGGTTGTTTCTAACGCTCTGGACATGAAGCTCAGGGATGACCTTGAGAGGCTGAAGAAGATCAGgtgatttctgattaatttgtgctcacgtac---cacattttttaggttcatggtaacttgcatgtgtagggtagatttatcttttcatgcttttgttgcactg

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G178341_T02 (Zea mays), 5'ss of exon 2
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctct----------tggggatggatggattgacttctttattgtttgacag--------------------------
||||||||||||| ||||||||||| |||| ||| ||||| ||  | ||||| || ||||||||||||||||||||||||||||||||||||||||||||| |     ||| | |  |    || ||           ||   ||| |      | |   |||||  |||| |                           
ACAGGAAGAAGGATTACAAGGACGGAAGGTTCTCACAGGTCGTCTCCAACGCCCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgtatataatttatgctctgatgtccctgcattgctagaggcagtgggtaacagtaatagattattcgttgataaatgttgctattagatgatattcctat

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G130544_T02 (Zea mays), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag------------------------------------
||||||||||||| ||||||||||| |||| ||||||||| ||  | ||||| || || |||||||||||||||||||| |||||||||||||||||||||           | ||| |    |     |  ||||||    | ||| | |||||  |||| |                                     
ACAGGAAGAAGGATTACAAGGACGGCAGGTTCTCGCAGGTCGTCTCCAACGCCCTTGATATGAAGCTCAGGGACGACCTTGAGAGGCTCAAGAAGATCAGgtttttttcgcgttcctgtattgccagatgctatggataacatcactacattatttgttgagaaattatgcatttagatgatattcgtgcacttgtcatt

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G062911_T01 (Zea mays), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag------------------------------------
 ||  |||||||||||||| || || |||| ||| ||||||||  | || || || ||||||||||||||||| ||||| |||||||||||||||||  ||  || |  ||  |  | |   | | ||     ||  |   |     | | |||    |||||                                     
TCAACAAGAAGGACTACAAAGATGGTAGGTTCTCTCAGGTTGTTTCCAATGCCCTCGACATGAAGCTCAGGGATGACCTTGAGAGGCTCAAGAAGATTGGgtcagtctattaccattgtttttgtgttattattgattttctaatgctatatataagatgacatgcacacatatttgttgtcatggcattgctaaaaaca

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA20G30970.1 (Glycine max), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgacttctttattgt-ttgacag-----------------------------------
||||||||||||| |||||||| || | |||||| ||||||||| | || || || || |||||||||||||| ||| | ||||| || ||||||||||||  |  | ||   |  | | ||     |     |  || | |    |  |  ||| | ||  ||                                    
ACAGGAAGAAGGATTACAAGGATGGAAAGTACTCTCAGGTTGTGTCTAATGCTCTTGATATGAAGCTCAGGGATGACTTAGAGAGACTAAAGAAGATCAGgtcactcattaacctttgttaactgtctatcatttcatagttgagttgttcaattttgttatcaagtataatgtttggttgttcgaattgagaataagtt

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA10G36880.2 (Glycine max), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaa-gccgtttttccctttc---aatctcttgggga--tggatggat-tgacttctttattgtttgacag-----------------------------
|||| |||||||| |||||||| || |  ||||| || |||||| | || || || || |||||||||||||| || |||||||| |||||||| |||||| || |  | ||  |  ||||   | |    |||  |  ||  | ||| | |||  |  | |||||                                  
ACAGAAAGAAGGATTACAAGGATGGCAAATACTCTCAAGTTGTGTCTAATGCTCTTGATATGAAGCTCAGGGATGATCTCGAGAGACTCAAGAAAATCAGgtaatgaagattgacgttttctggattaatatggaaaaatgtttagatataactgatacactgttttgtgaaaatcaacctgtttaatcttgctgtgttt

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA10G36610.2 (Glycine max), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag------------------------------------
|||| |||||||| |||||||| || |  ||||| || |||||| | || || || || |||||||||||||| || || ||||| |||||||| ||||||     | ||   |  ||| ||     |    ||  || | ||    | ||| || ||    ||                                    
ACAGAAAGAAGGATTACAAGGATGGCAAATACTCTCAAGTTGTGTCTAATGCTCTTGATATGAAGCTCAGGGATGATCTTGAGAGACTCAAGAAAATCAGgtctatcattcaccttttttaactgtctatctattcattgttttgagttttttttattatcaagtccgatttttgtttgaatcatgctgactgctaaatc

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagcc-gtttttccctttcaatctcttgggga---tggatggat-tgact--tctttattgtttgacag-----------------------------
|||| ||||||||||||||||| || | ||| || ||||| ||| |||| || ||||| |||||| | ||||| ||| | ||||| || ||||| |||||| ||    | ||||   | |  || | |  ||||   ||  | ||| | |||  || | | |||||                                  
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagc-cgtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag-----------------------------------
|||||||||| ||| ||||||||||  | ||||| ||||||||  |||||||  ||||||||||||| ||||||||||||||| | || || || ||||||   |  |  |     ||| |  | |       |  | |||| | |    |||  || |  | |                                    
ACAGGAAGAAAGACCACAAGGACGGTCGCTACTCCCAGGTTGTTTCAAACGCCTTGGACATGAAGCTGAGGGACGACCTCGAGCGACTGAAAAAAATCAGgttggtacagtgcatgcttcctgttttgaccttagcgctggaatcaagctttttgtgatatatattttgttcttaaattcagaattcaatttcatgcaag

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagc-cgtttttccctttca--atctcttggggatggatggat-tgacttctttattgtttgacag--------------------------------
| |||||||| ||  ||||||| ||  | ||||| ||||||||  | |||||  ||||||||||||| ||||| ||||||||| | || ||||||||||||   ||   || ||  ||   |  || || |   ||||     |    |     | ||| |   | |                                 
ATAGGAAGAAAGATCACAAGGATGGTCGCTACTCCCAGGTTGTTTCGAACGCCTTGGACATGAAGCTGAGGGATGACCTCGAGCGCCTAAAGAAGATCAGgttcgcatattcttgtctcctagcatttcattatgatgctcaaacactagactctcattttccaaaatgcatgtcagcctttcaattctgaattcaattt

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagcc--gtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag-------------------------------------------------------------------------------------------------------
||||||| || ||| |||| |||||  | ||||| ||||||||  | || ||  ||||||||||||||||||| ||||| ||| | || ||||||||||||  ||     ||||   ||| || | | |     |||  |  ||| |  | | ||||     | |                                                                                                        
ACAGGAAAAAAGACCACAAAGACGGTCGCTACTCCCAGGTTGTATCTAATGCCTTGGACATGAAGCTCAGGGATGACCTTGAGCGTCTGAAGAAGATCAGgttagtgaaattttcttcttccagtttatgattaatgctt--attcaaatttatatttacaaatatagatcacttgtgatttgaactatgcagcactctattgcattgcgcctggctttaggcagtgctgattgccttgtgtcatgacggcttggtttgggggatgcag

upper sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 5'ss of exon 3
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatgg-attgacttctttattgtttgacag-------------------------------------
|||| ||||||||| ||||||| ||  | ||||| ||||||||  | |||||  ||||||||||||| |||||||| || ||| |  | ||||||||||||   |   |||    | ||  || |   |   ||  |||  ||| ||||     || | |   |                                      
ACAGAAAGAAGGACCACAAGGATGGTCGCTACTCCCAGGTTGTTTCCAACGCCTTGGACATGAAGCTGAGGGACGATCTTGAGCGCTTGAAGAAGATCAGgtgtg--atttaagacattttatttgacgtctatttatgatattaactttcgggttttgtatgaactctcgctttcaaatgtcaattcatgttggtagtatg

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169094756|gb|FE492933.1|FE492933
EST:     GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTTCGTCACTACTGGGGCCTGCGCGTCCGCGGGCAGCA
genomic: GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
EST: gi|169023844|gb|FE436395.1|FE436395
EST:     GCGCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
genomic: GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
EST: gi|169075906|gb|FE480966.1|FE480966
EST:     GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTTCGTCACTACTGGGGCCTGCGCGTCCGCGGGCAGCA
genomic: GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
EST: gi|70669635|gb|DN838212.1|DN838212
EST:     GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTTCGTCACTACTGGGGCCTGCGCGTCCGCGGGCAGCA
genomic: GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
EST: gi|169096504|gb|FE499208.1|FE499208
EST:     GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTTCGTCACTACTGGGGCCTGCGCGTCCGCGGGCAGCA
genomic: GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
EST: gi|169024190|gb|FE433036.1|FE433036
EST:     GCGCTCGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
genomic: GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA
EST: gi|169114528|gb|FE516598.1|FE516598
EST:     GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAG                         GAACCACCGTGGTCTTCGTCACTACTGGGGCCTGCGCGTCCGCGGGCAGCA
genomic: GCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCA

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: 89

ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtt ... tgtttgacagGAACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGGACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagccgtttttccctttcaatctcttggggatggatggattgacttctttattgtttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA