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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag

Basic information

species Selaginella moellendorffii
transcript EFJ05720
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgt-----acagtgacaaatctgtatcttatgttttaacttattcctgcag-----------------------------------------------------
|| |  |  |||| || || ||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||| | ||||| ||||     | | |    | ||  |||  ||   |||||    |  || |||                                                     
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 7
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag-------------------------------------------------------
|| |  | |||||||| || || || || ||||| || ||||| || ||||| ||||| || |||||||| || || |||||||||||| |||||||||||||   | |    |    || || |   |     | || |||                                                          
TGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCAAgta--attattccttgtcattttttcgctagtaatgtttctgttctgcttaataaacgaatgctgactgaattccttttgggcctttttcattcacttag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 10
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgac-aaatctgtatcttatgttttaacttattcctgcag----------------------------------------
| |  || |||||||| || ||||| || ||||||||||| ||||||||||| |||||||| ||||| ||||| || ||||| ||||||||||| ||||||||      | |||    | || |    ||      | |     ||                                        
TATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCAAgtatgtcttctaaacagatttcctcaagttatgtacactgtccaagtctatgcatacctaaacatattttcacccaactcttgcag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 10
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctg--tatcttatgtttta-acttattcctgcag-----------------------------------------
||| ||| |||||||| || ||||| || ||||||||||| ||||| ||||| |||||||| ||||| || || || ||||| ||||||||||| ||||||||      | ||   |  |  || | | | ||  |  | |     ||                                         
TGTCCTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGGATTGTCATGTCTCATTATACCTGGCATAATGTGACTGAGAGTTCAAGAATCACTACCAAgtatgtcttctaaatagatttcctcaagatatacgcacactgtccaagtctatgcatacctaaacatatttttcatccaactcttgcag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag--------------------------------------------------------
| |  || |||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| ||||| || || || |||||||| ||||| || |||||||| |    | || |    |  |      |||  |||   || |                                                         
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 9
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagt-----gacaaatctgtatct----tatgttttaacttattcctgcag------------------------------------------------
| |  || |||||||| || || || || ||||| ||||| ||||||||||| |||||||| ||||| || || || |||||||| ||||| || |||||||| |       ||||    |  | ||    ||| | |  |  ||||   |  |                                                
TATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctagacattcttcaagctaagttatatatggatctatttgggttgggggtagtaacactgtctaatttgatttattaaaacttgttgttacag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 5'ss of exon 10
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgac----aaatctgtatcttatgttttaacttattcctgcag----------------------------------------
| ||| || |||| || |||||||| || || || ||||| ||||| ||||| ||||| ||||||||||| || ||||||||||||||||| ||||| |||||     ||       |||    ||| || |   | | |  | | |                                          
TTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAAAgtatgcaaactttagtttctccgccttttgctgagattaacactttctacctcccaatgattatcttatgatttttttcgatgaaacag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 5'ss of exon 6
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag--------------------------------------------------
| |||  | ||||||| ||||| || || || || ||||| ||||| ||||| ||||| || |||||||| ||||| |||||||||||||| || ||||||||   ||||    ||  || || | ||  ||   | | |    |                                                  
TATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCAAgtaatatgac----ctccattttctcttgaaaacaaattcaaatgttttccatcttcaatacttacttactttctatgcatttacgatgagacag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: Vv14s0128g00020.t01 (Vitis vinifera), 5'ss of exon 9
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgt-tttaacttattcctgcag------------------------------------------------------
| || |  |||||||||||  | ||||| ||||| ||||||||||| ||||| ||||| |||||||| || || || || |||||  |||| ||||||||||    | |  | | ||  | |    |   ||   || |  ||  |                                                      
TTTTATCTCTGAGTGGGATTTTAACAGTTTTCTTCTGTGGCATTGTCATGTCGCATTACACATGGCATAATGTTACCGAAAGCTCGCGAATAACAACCAAgtgagtttatgattttgagtataggatacatatagtacttgtgtggtgatacttatgaacagtgaattgttttcatccacagcctgtagaaatgattaag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatg-ttttaacttattcctgcag-------------------------------------------------------
| |||||||||||||| || || || |||||||||||||||||||| |||||||| || || ||||| |||||||| || |||||| || | || ||||||||  |   |   ||| |   ||  | | |    ||  ||   |||                                                       
TTTTCTACCTGAGTGGAATTCTTACCGTCTTCTTTTGTGGCATTGTAATGTCACACTACACCTGGCATAACGTCACTGAAAGCTCACGAGTAACTACCAAgta-ggcatctcttctttcagttgggatgtccttttcatctaacagaatttttatctgttgaataggccacgtacaagcagctcaagatttagtctatttg

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 9
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag--------------------------------------------------------------------------------------------------------------------------
| |||||| ||||||| || ||| |||| |||||||| |||||||| ||||| ||||| || ||||| |||||||||||||  ||  ||||||||| |||||||  |    |||  ||| || |  || ||  |   |  ||||                                                                                                                           
TTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCAAgtacgttttataat--gtacctcagtttcta--tgggtgttgcaaattagtatttgtttatgtcgaatatttttggaacagatgtagaatttcctcggaactagacccattattcaatgctgatactaagcgtcaatgttatgttgatacgttttggttaattgcag

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: PP1S207_23V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatct-----------gtatcttatgttttaacttattcctgcag--------------------------------------------
| |||||| |||||||||| || || |||||||||||||||||||| ||||| || ||||| ||||| || || || || |||||  |||| || |||| ||| |    ||  |||            | || | |  || ||   |   |   ||                                            
TTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCAGgtaaacaaccatctcttctgaatcggaatgtcctgtcattcaatggaacacctaagttgtttaaattatagtcatatattaatatcctttgtcttaacac

upper sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 5'ss of exon 8
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag-----------------------------------------------------------------------------------------------------------------
| |||||| ||||||| || ||| |||| ||||||||||||||||| ||||| ||||| || ||||| || |||||||| |  ||  ||| |||||||| ||||  |     ||   | |    |    |    ||| |  ||                                                                                                                   
TTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCAGgtacgttccttcatgcctcttagcttcgatgttctatactagcgaacgaatggcaacatcaaatattcttgagactgatgcgtaatttcttggaggttggagttatgatactgatgcttgtcatcaacgtgacattaatgcactttggtgattcacag

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: 29 (upstream exon), 22 (downstream exon)
Score: 6

TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgac ... attcctgcagGCACACCTTTGCAACTATGTCCTTCATCGCTGAGACATTTATCTTTTTATACGTTGGAATGGACGCACTGGACCTGGAGAAATGGAGGCTGGCAGATAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgtacagtgacaaatctgtatcttatgttttaacttattcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA