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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAGgttagtatgtgacctattctgaaatactattgtttttgtgatgttgactcag

Basic information

species Physcomitrella patens
transcript PP1S2_272V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA06G04230.1 (Glycine max), 5'ss of exon 13
GATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAGgttagtatgtgacctattctgaaatactattgtttttgtgatgttgactcag-------------------------------------------------
|||||  |||   | |||||||| || ||||||||||| ||||||||||| ||||||||||| ||||| |||||| |  |     | | |  |    | ||  || || | |  ||||  ||                                                    
GATGGAAAAGTTTTACCAGATGGTCCTGTTGTTATTTCCCCTGATGGACTTTTTCCCTCTCTATATCGAGAAGgtaacaactctgcttgtctttgttttctgctgcttct-tattgttccctttcttccaagttgtacaactttttttgtttttccttctttttttatccaggg

upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA04G04060.1 (Glycine max), 5'ss of exon 12
GATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAGgttagtatgtgacctattctgaaatactattgtttttgtgatgttgactcag-------------------------------------------------
|||||  |||   | |||||||| || ||||||||||| ||||||||||| ||||||||||| ||||| |||||| |  |     | | |  |    | ||  || || | |  ||||  ||                                                    
GATGGAAAAGTTTTACCAGATGGTCCTGTTGTTATTTCCCCTGATGGACTTTTTCCCTCTCTATATCGAGAAGgtaataactctgcttgtgtttcttttctgctgcttct-tattgttccctttcttccaatctaacacatcactgtgtcttcagttatccccccccccccccc

upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA17G36130.1 (Glycine max), 5'ss of exon 8
GATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAGgt----tagtatgtg---acctattctg-aaatactattgtttttgtgat---gttgactcag-------------------------------------
|||||  ||    | |||||||| || |||||||| || ||||||||||||||||| ||||| ||||| ||||||    |||| | |    |  |||| |   || |   |||    || ||    | |  | ||                                      
GATGGGAAACTTTTACCAGATGGCCCTGTTGTTATATCCCCTGATGGACTCTTTCCTTCTCTATATCGAGAAGgtaacttagtttttatttatttattgtatgaaaatggttgcggatgagaagaggctaccccatttcaagttcatgacatactataagcgttagtgatagg

upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA19G35930.1 (Glycine max), 5'ss of exon 9
GATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAGgttag--------tatgtgacctattctgaaatactattgtttttgtgatgttgactcag----------------------------------------
|||||  |  |  | ||  ||||||| ||||||||||| ||||||||| | |||||||||||||| || |||||| ||         ||||||       | |  |   |||| | |||  || ||   | |                                         
GATGGCAAGACCTTACCGAATGGACCTGTTGTTATTTCACCTGATGGATTATTTCCCTCTCTTTACCGAGAAGgtgagacacttttaatgtgagagtaattaaggttgaattggtattgcaattttagtttatgtagtcaattgtgagccatggatgatgataacgacttctc

upper sequence: PP1S2_272V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv18s0001g10680.t01 (Vitis vinifera), 5'ss of exon 9
GATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAGgt-----tagtatgtgacctattctgaaatactattgtttttgtgatgttgactcag-------------------------------------------
|||||  | ||  | |||||||| |||||||||||||| ||||||||||| ||||| ||||| | ||| ||||||       |||| ||  || ||    |   ||      |   |    || | | |                                            
GATGGAAAGGCTTTGCCAGATGGGCCAGTTGTTATTTCCCCTGATGGACTTTTTCCTTCTCTCTTTCGAGAAGgtatttggtgtatatgcactgtttctcagatctcacacataaattccatttatttatcaatctgccattaactttgtatggaaagggtttactgcttttt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGTGAAGCACTTCCAGATGGACCAGTTGTTATTTCTCCTGATGGACTCTTTCCCTCTCTTTATCGCGAAGgttagtatgtgacctattctgaaatactattgtttttgtgatgttgactcag

- - - - - - - - - - - - - - - - - - - - - GATGGA