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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag

Basic information

species Physcomitrella patens
transcript PP1S148_87V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag----------------------------------------------------------------------
                    ||    ||||||||| | |||||||||||||| ||||| || || || ||||||||||| ||||| || ||  | ||||| || ||| | |||||||||||  |     || ||| ||                                                                       
-------------------GTACTTTGCATATCAACGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTATGAGATGGTTAACCACCAGGGCATTACATTTCTTGCTGAGCAGgttggtgatatgaatgtcattgcagatatcttgaatggagacagctttgtcaacaaattttgctaattatgcatacccttattttgtcag

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA18G39880.1 (Glycine max), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag-------------------------------------------------------------------------------
                  | ||    || |||||| | ||||||||||| |||||||| ||||| || ||||||||||||||||| || |||  |||||| || ||| |  | ||||||||||| | ||| || |                                                                                   
------------------TCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCATTACATTTATATCAGAGCAggtgagttacgtttaaggtgctgtttatttttaacaaaatcaagaaaattcccatgtttcttatgccttttttattttttttgggggggtgggagggtgc

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA12G06690.1 (Glycine max), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag--------------------------------------------------------------------------------
                    ||    ||||| ||| | || ||||||||||| |||||||| || || ||||||||||||||||| || |||  ||| || || ||| | ||||| |||||    ||   |||||  |                                                                                 
-------------------GTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAATTACATTTCTTGCTGAACAGgtatcttttcagtatgtgattctcatggaaactctctggtgcaggattttctacactactttctctccttctctgcatgtctttgaaatattgtgttctt

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA07G15930.3 (Glycine max), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag--------------------------------------------------------------------------------
                    ||    || |||||| | || |||||||| |||||||| ||||| || ||||||||||||||||| || |||  |||||| || ||| |  | |||||||| || | ||| || |                                                                                    
-------------------CTACTATGCCTATCAACGAACGTGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCATTACATTTATATCAGAGCAGgtaagttacgtttaaggtgctgtttatttttaaccatggtggtgagacttatgtctttttttattttttttgggggcggttgcttggcttcccttgatat

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GLYMA11G14770.1 (Glycine max), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag--------------------------------------------------------------------------------
                    ||    || || ||| | || ||||||||||| |||||||| || || ||||||||||||||||| || |||  ||| || || ||| | ||||| |||||    ||   |||||  |                                                                                 
-------------------GTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAATTACATTTCTTGCTGAACAGgtatcttttcagtatgtgattctcatggaaactctctggtgcatgatttctactcactttctctcctctgcgtgtctttgaaatattctgttctctcttg

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtg-agcttcgtgtatgacag---------------------------------------------------------------------------------
                   |||    || |  ||| | || ||||||||||||||||||||||| |||||||| ||||| ||||| || |||  ||| ||  | ||| |  |||||||||||  |||     | | |  |                                                                                 
-------------------TTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGATTTCTTTTATTTCTGAGCAGgtgcggctatacatctcattgttactcacatagtggataatgactaattcgcaataagtcatatatttgtttcatttataataagttactgtaatttttcag

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT5G02100.1 (Arabidopsis thaliana), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagc--ttcgtgtatgacag--------------------------------------------------------------------
                    |||  ||| || ||  | || |||||||| |||||||| |||||||| ||||||||||| |||   || |||||||| ||||  ||| | ||||| ||||||||   ||  | ||  ||                                                                      
-------------------GTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGATCAATTTTATAGCTGAACAGgtgagtgatttctttacaactcatattccaatgtgacttgggaaaaattatgagttcttagttgacatatgtcaatgttttgttcctcag

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag--------------------------------------------------------------------------------
                    |||   || || ||| | || ||||||||||| ||||| ||||| || ||||||||||||||||  || |||  ||| || || ||| |  | ||||| ||  | ||  ||     |                                                                                  
-------------------CTATTATGCCTACCAACGAACTTGGAAGCCTTTTAATCCCATTCTTGGTGAGACTTATGAAATGGCTAATCATGGTGGAATAACATTTATTTCAGAGCAAgtaggttttttgagcaccttttattttattttatttattttttaggtttttaaatttcagttttatttatatatcgttttaagtgtgctctttttttatc

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ08612 (Selaginella moellendorffii), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgta-tgacag-----------------------------------
                    |||   || ||  |  || | |||||||||||||||||||||||||||||||| |||||||||||||| |||| |||||| |||||  | || |||||||||   ||  | |  |  |                                     
-------------------ATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCATAACGTTCCTCGCCGAGCAGgtgcttttgatctcctcgcttttgtggctggtcttctataagtttttgttctgtag

upper sequence: PP1S148_87V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ19778 (Selaginella moellendorffii), 5'ss of exon 5
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgta-tgacag-----------------------------------
                    |||   || ||  || |  | |||||||| ||||||||||||||||||||||| |||||||||||||| |||| |||||| |||||  | || |||||||||   ||  | |  |  |                                     
-------------------ATATTATGCTTACGAACGTGCGTGGAAGCCATTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCATAACGTTCCTCGCCGAGCAGgtgcttttgatctcctcgcttttgtggctggtcttctataagtttttgttctgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATGgtgaagcataatggcatcacgtttttggctgagcaggtgagcttcgtgtatgacag

- - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - -  TGGAAG