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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaacaacatcgttcttagttacctactcctgaccgttttttgttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ24508
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 12
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaacaacatc--gttcttagttacctactcctgaccgttttttgttgcag---------------------------------------------------------
 || || || ||||||| ||| ||||| || ||||||||||| || ||||||||||| || ||| | |||||||||||||||||||| ||||||||||||||   |      |   ||| || |||   | | | |  |  |||| |    | |                                                         
ATCTCGACTTGTTGTCAATCAGAACAAAAAGAACCTTTTGGAAAACTGGTTGGCTGAAGACAAATTGGAGTGCAGTGAAGAACTTGGAGATCTTGTCAAGgtaaaatgggtgttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 12
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaacaacatc--gttcttagttacctactcctgaccgttttttgttgcag---------------------------------------------------------
 || || || ||||||| ||| ||||| || ||||||||||| || ||||||||||| || ||| | |||||||||||||||||||| ||||||||||||||   |      |   ||| || |||   | | | |  |  |||| |    | |                                                         
ATCTCGACTTGTTGTCAATCAGAACAAAAAGAACCTTTTGGAAAACTGGTTGGCTGAAGACAAATTGGAGTGCAGTGAAGAACTTGGAGATCTTGTCAAGgtaaaatgggtcttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 10
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaacaacatcgttcttagttacctactcctgaccgttttttgttgcag-------------------------------------------------------
 || || || ||||||| ||| ||||| || |||||| |||| || ||||||||||| || ||||| ||||||||||||||||| || ||||||||||||||  ||         | ||   ||   |  |  | || || |||||||  |                                                        
ATCTCGACTTGTTGTCAATCAGAACAAAAAGAACCTTCTGGAAAACTGGTTGGCTGAAGACAAACTGGAGTGCAGTGAAGAACTAGGAGATCTTGTCAAGgtaagatgggtcctatgctgtttttattgatttt-actgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 12
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaacaacatc----gttcttagttac-ctactcctgaccgttt-tttgttgcag----------------------------------------------------------------------------------------------------------
 ||| | || ||||| |  || ||||||||||| |||||||||||||||||||| || ||||| || || |||||||| || || || |||||||| ||||| ||     |||      || | |   || |||  |    | |||| ||| ||||                                                                                                            
GTCAAGGCTGGTTGTGAACCAGAACAAGAAAAATCTTTTGGAGAATTGGTTGGCGGAGGATAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTTGTAAAGgt-tgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 12
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctga--------acaacatcgttcttagttacctactcctg-accgttttttgttgcag---------------------------------------------------------
 ||||| || ||||| |  || ||||||||||| |||||||||||||||||||| || || || || || |||||||| || || || |||||||| |||||  |         | ||  | | | ||  ||||||| |  |  ||   |  |||||| |                                                          
GTCACGGCTGGTTGTGAACCAGAACAAGAAAAATCTTTTGGAGAATTGGTTGGCAGAGGACAAGCTTGAATGCAGTGAGGAGCTAGGAGATCTTGTAAAGgttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 12
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtc---------tgaacaacatcgttc----ttagttacctactcctgaccgttttttgttgcag------------------
 || || || ||||| |  ||||||||||| |||||  |||| || |||||||| || |||||||| || ||||||||||||||||| || ||||| |||||          || || |  |  |||    |  || |  |    |  |  || | ||||  |                    
ATCTCGGCTGGTTGTGAACCAAAACAAGAAGAACCTCCTGGAAAACTGGTTGGCAGAGGATAAACTAGAATGCAGTGAAGAACTTGGAGACCTTGTGAAGgtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttgtgacgataaacctttctgttccag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 12
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgt---ctgaacaacatcgttcttagttacc-tactcctgaccgttttttgttgcag----------------------------
 || || || ||||| | ||||||||| || ||||| ||||| || |||||||| || |||||  | || |||||||||||||| || || |||||||| ||   || || |  | | || | | |||   |    |  |  |  || | | | |                             
ATCTCGGCTTGTTGTGAATCAAAACAAAAAGAACCTCTTGGAAAACTGGTTGGCAGAGGATAAGTTAGAATGCAGTGAAGAACTCGGAGACCTTGTCAAAgtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 12
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaa---caac-----atcgttcttagttacctactcctgaccgttttttgttgcag---------------------------------------------------------------------------------------------------
 ||||| || ||||| | ||| |||||||| || ||||||||||||||||| || || || || || ||||||||||| |||||||| ||||| || ||||| ||||   |||      ||  || ||  ||  | |||   |||  || || ||||                                                                                                      
ATCACGCCTGGTTGTGAATCAGAACAAGAAGAATCTTTTGGAGAATTGGTTAGCAGAGGACAAGCTGGAGTGCAGTGAGGAACTTGGGGATCTAGTGAAGgtttgaaatgcaattggagatgattattttttgtccacttaagacaattctt-gttgggatgctaatttgagtttattttattatttttatcctgctaatttaaatgatttttttttttaaatataattttgacattgaaaaccatgttttttttgtag

upper sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 13
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctga-acaacatcgttctt----agttacctactcctgacc----gttttttgttgcag---------------------------------------
||| ||  | ||||| | |||||||||||| |||||  | ||||| |||||||| || || ||||||||||||||||||||||| || |||||||||||||||||| |    ||  || ||    |||     | ||  || |     |||||   |  ||                                       
TTCCCGGTTGGTTGTTAATCAAAACAAGAAGAACCTACTTGAGAACTGGTTGGCGGAAGACAAACTCGAGTGCAGTGAAGAACTCGGAGATCTTGTCAAGgtctgatattgtatgcttattgagcagtgcatcagtctagatctactatttttcacttaagagctattgcaaatggatgtcaaggtctgagtctagctga

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: 24 (upstream exon), 25 (downstream exon)
Score: 5

TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaacaa ... tttgttgcagTCAGTTGATAATGATATGGCCTTAAAAATCTTCATCAAAGCAAGGGTTACACCAAAAGTGGTCGCGGCATTTGCAGAACGTGGAGAGTTCGATAAAATTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACGTCTCGTTGTCACTCAAAACAAGAAAAACCTTTTGGAGAATTGGTTGGCTGATGATAAACTCGAGTGCAGTGAAGAACTTGGTGATCTTGTCAAGgtctgaacaacatcgttcttagttacctactcctgaccgttttttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC