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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatcttgctcatttgttgcaattttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC

Basic information

species Glycine max
transcript GLYMA07G40300.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
----------------gtaacaatgctgtgctgt-aagttacatgtaacttg-gtttgttttttagaaat-tatcttgctcatttgttgcaattttc---agATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
                 ||    | || | || |  |||| || ||   | | |||| || || |   || |   |     || | |      ||||   || |  | ||||| |||      || |||||    || ||||||||  | ||||| ||||| |||||||| |||||||||||||| || ||||||||||| |
gtatcacctagctattttagagtttctttcctttcgagtttcacgttggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 11
---------------gtaacaatgctgtgctgtaagttacatgtaacttg-gtttgttttttagaaattatcttgctcatttgttgcaattttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
                |  ||      | |  |   ||  |  |  |||     || ||  |    |  |  |  | |||    |    | |  || | || | ||||||||     ||  | || |  || |||| |||  | ||||| ||||| |||||||| ||||||||||||||||| ||||| || || |
gtaccactttgttctatttcaccaacttacaatgcattctacttccctttcacctgcttcctgagcacaacat--cccatcatctcttttctgaagGTCGTTGAAATTGCAACCAATGCATTGGATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCAC

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaat-tatcttgctcattt---gttgcaattttca--------------gATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
||| ||    |    | | |   |  | |  ||   | || || ||   | | | |  ||  | |||   | || || ||| |              | |||| ||||| |||      ||  | ||| | || ||||| ||  ||||||| ||||| ||||| || ||||||||||| ||||| |||||||||||||
gtatcaccttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
------gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatcttgctcatttgttgcaattttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
       |     | |||  || | |||| ||| |   || || |   |  |||   ||   || || |  |  | |      ||| |||| || || |||||| | || || || | ||| || |||||| | || || ||||| |||||| ||||||||||||||||||||||||| || || |
gtaattatgcttttactgctctttcagttgcattt---ttcgtcttactaatagctgtttcttttcttaaataat-cgtcaaccagGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 11
---gtaacaatgctgtgctg-taagttacatgtaacttggtttgttttttagaaattatcttgctcatttgttgcaattttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
    |||  ||  | || || |   ||   |   | ||  |   ||   ||  | ||||     ||        ||     ||| |||| || || |||||| |||| || || |  || || |||||| |||| ||||||||||||||||||||||||||||| || || ||||| || || |
gtaataatgattttttggtgctttattcagtaatattttatcatttcggtaacagttattcctttctgactaatcatcaaccagGTTGTAGCTATAGCAAGTGCAGCACTTGATGGTTTCAAGAATGAAGCCAAGAAAATGGTGGTTGCACTAGTTGATATGGAACGCGCTTTTGTACCACCTC

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------------gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatcttgctcatttgttgcaatttt------cagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
                                                       ||    |  | || | |   | |  |  || || ||| | ||||      |  |    |||| ||||   || |||      ||| ||||||||||||||  | | || || || |  ||||| |||||  | || |||||||| |||||||| |||||||||||||||||||||||||| || |
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggctttt-----gtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S33_163V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------------gtaacaa-tgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatct--tgctcatttgttgcaat----tttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
                       |||  |  ||||  | |  | ||   |  | |  | || ||||      |||||||    || |  ||||  || ||    || |||||||| || ||||| |||||||| || || | ||  |    |||||| || |||||||| ||||| || ||||| ||||||||||||||| | || || |
gtttgtacaatttcggttccttcgtagtatctgcttcgataaatgtggtacatta--tagtgtgttgggctaaaattattcaatgattctttgaggctatgcgtttgcagATTGTTGCCATTGCCAGTTCAGCGCTGGACGAATACAGGGTTGAATCAAAGAAAATGGTTGTTGCTCTTGTTGACATGGAGCGTGCATTTATCCCACCTC

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------------------------gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatc--ttgctcatttgttgcaatttt-cagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
                                                                    || | ||  | | |  | | || ||   ||  || || |  ||  || | | |    || |||  | |||  |||  | |||||||| || ||||| | | | || || || |  | || |   ||| | || |||||||| ||||| || ||||||||||||||||||||| |||| || |
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggt-gttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaacttggtttgttttttagaaattatcttgctcatttgttgcaattttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
 atgtaac  putative branch site (score: 3)
                                                ttttc  putative PPT
           tttgttttttagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatcttgctcatttgttgcaattttcagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG