Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattactaacacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

Basic information

species Glycine max
transcript GLYMA20G03120.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattactaacacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
             ||  ||||| |     |||| |  |  | || | | |  | ||   || | |   |      ||||    | |   |||  |||||||||||| |||||||||||||||||||| ||||||||||||||||| || ||||||||||| || ||||||||||||||||||||| |||| |||||||||
----------gtaatgcatatgttt-caagcatagcatagactgttcaagccttttaaaagattgttatggcctgatttgagaaatga-aacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG

upper sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 4
tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattacta-acacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
    || | |   |         |    ||| |  |   | |   ||   | | ||| | |    ||| | |||| | | |   | |||      |   ||||| || |||||||| |||||||| ||||| ||||||||||| || || ||||| |||||||| ||||| |||||||||||||| ||||||||||| || 
--gtaagattttgagttgaggttttggatgcctgtgggacgtgcttt---tcttttggcggggttcgtaactgac-tgtgcgattgactgcgtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGACACATTGAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAACTA

upper sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------tcccaacactcctatcaatatgatca--tctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattacta-acacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                                                             ||    | ||  || |||| |  | | |  | |     |   || |   |  |    | | ||     | | | | |  || |  ||   | ||||||||| || |||||||| |||||||| || |||||||| || || ||| | || || |||||||||||||| |||||||||||||| |||||||||||| ||
gtaagattgtggtagttgattatgcggtgaagcagatgagagtgattgaaccgtctattggacggggccattgat-tgatgaagttttcggtagcatgctgaatttgtgcttatctgggtttgcaccggtaataatcaggtagtggtatggaattacagGGCATGCCATTTGGCGAAGCAAGCATTTGATGAGGCTATCGCTGAGCTGGATACGTTGAGTGAAGAGTCGTACAAGGACAGCACATTGATCATGCAGTTG

upper sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattactaacacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                 |    ||    || |   |  | |   | || |  |||   ||  | ||| ||         ||| | |  ||||   |   |   | | ||  |  |||||| || |||||||| || ||||| || || ||||| ||||| ||||| || || || ||||| ||||| |||||||||||||| |||||||||||||| 
gtatgaattttggtcagtagagacttagctgttggttggttttacggcgt--gttttttttttcagggattgaatatattggagcttgtgac---tgaatgccattgactgtggcagGGCATGCCATTTGGCGAAACAAGCATTTGACGAGGCGATTGCTGAGTTGGATACGTTAAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAGCTA

upper sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S348_15V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacc-tattactaacac-ttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                                                                           |        |  |||  ||  | ||    ||     | | ||     |  ||   |   ||  |  ||| |       |  |  |   |  || ||| || || |||||||| |||||||| || |||||||| || || ||| | || || ||||| || ||||| |||||||||||||| |||||||||||||| 
gtaagagtggctgtgtggcatgcggcgaagcggttgagggtgattgtggaggcgtggatggaacgtgggcgtgggatggatgggtggatagcat-gtgtgtgggggcgtggtggattcatggttgtggtggtccgcaatgctgaaacggggtgtggtggtgtgagatttcagAGCATGCCATTTGGCGAAGCAAGCGTTTGATGAGGCGATCGCGGAGCTGGATACGTTGAGCGAGGAGTCGTACAAGGACAGCACGTTGATCATGCAGCTA

upper sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36243 (Selaginella moellendorffii), 3'ss of exon 4
tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattactaacacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                  |  || |  || | |    |   | | ||       ||  || ||| | ||  || | ||       |  |       |||| || || ||  | || ||||||||||| || || || || || ||| | |||||  | || ||||| || ||||||||||||||||||||||||||||| 
-----------------gtgagagcgcct-cgtcctctttttagttttctccactt--caactgac-tttgtggctttgtttcgctgttg----caacagCGCTTGCCAGCTAGCCAAGCAAGCTTTTGACGATGCGATCGCGGAGCTGGACACGCTCAGCGAAGAATCCTACAAGGACAGCACTTTGATCATGCAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaggtatgttgccagctggcgttaatgacatttacctattactaacacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                                        tactaac  putative branch site (score: 0)
                                     tattactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattactaacacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- ccaacac
- - - - - - - - - - - - catctgc
- - - - - - - - - - - - - - - - - - - ccattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctggcg