Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatttaaatctagcttctcagttacatttgctgattttttatgattccttaactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT

Basic information

species Physcomitrella patens
transcript PP1S270_53V6.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
gtaaaaatttaa--atctagcttctcagttacatttgc--tgattttttatgattccttaactcatgctgtactttccacgtgtat------acagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT
|| |  |||| |   |  |  |    |   ||||||||  |     |  |||  | ||||||| |  |  |   |||  | || ||        ||| | | || |||||  | || ||||  ||||| || |||||||| ||| |  | ||||| || ||||  ||||||||||||||||| ||||||||||| |
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatg-ctgcttaact-actcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT

upper sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
gtaaaaatttaaatctagcttctcagttacatttgctgattttttatgattccttaactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT
||     | |     | |||| | |  |  ||      |    ||    ||   ||  |  |  | || | |  || | | |  |||  || ||||| |||||||| || |||||||| || || ||||| || ||| | |||||||| || |  |||||||||||||| || |||||||||||||
gttcttttattttctttgctt-taatctgtatccatgaaacaattggtgttatatagttttttttttaatatttac-tatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT

upper sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 14
-----------------gtaaaaatttaaatctagcttctcagttacatttgctgattttttatgattccttaactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT
                 |    ||| |  ||| |    |  | |    ||   |  |||| | |  ||  |  | |  |  |  | | |  || | | |  |||  || ||||| |||||||| || |||||||| || || ||||| || ||| | |||||||| || |  |||||||||||||| || |||||||||||||
gttctcttactttctttgctgtaatctctatccatgagccaattggtgttatatagttttgttttgtttttatattttt--ttaaatatttac-tatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT

upper sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 16
gtaaaaatttaaatctagcttctca---gttacatttgctgattttttatgattcctt-----aactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT
       | |     | | ||||||   ||||       |    | | |  |||| ||     ||||  | |  |  | |  |    | | ||||   | || || ||||| || ||||| || || || || ||||| || ||| |||||||||| ||||  ||||||||||||||||| ||||| |||||||
----gtgtgtggcctttgtttctcatccgttatgggcattctactctgaaaattctttctttgaactgttacgatcttgtgaattgctgttcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAGCTTT

upper sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 16
gtaaaaatttaaatctagcttctca---gttacatttgctgattttttatgattcctt-----aactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT
       | |     | | ||||||   ||||       |    | | |  |||| ||     || |  | |  |  | |  |    | | ||||   | || || ||||| || ||||| || || || || ||||| || ||| |||||||||| ||||  ||||||||||||||||| ||||| || ||||
------gtgtggcctttgtttctcatctgttatgggcattttactctgaaaattctttctttgaagtgttacgatgttgtgaatcactgttcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctgattttttatgattccttaactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT
                    ccttaac  putative branch site (score: 3)
     tgattttttatgatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatttaaatctagcttctcagttacatttgctgattttttatgattccttaactcatgctgtactttccacgtgtatacagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT