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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactagttcttttccaaagtgtccgcgttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG

Basic information

species Glycine max
transcript GLYMA0041S00200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 3
---ta-ctagttcttttccaaagtgtccgcgttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
   || || | |   | |||        |   ||    ||     | |  ||||   |||     |||||||| |||  ||||    |      |   ||  |||||| ||||| ||||| ||||| ||||| ||||| ||||||||||| || |||||||| ||||| ||||| || ||||| |||||||||
gtgtatcttggtgagtaccagtacacaagtacttgggatgaattgattagtttttggaaacaaagatttgatt-gtga-gattgcaatgtaacctttgct--agGTGGGTATGACATGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCTGCGCTCAAGTACTGGGGCCCTTCCACGCACATCAACTTCCCG

upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 2
-----tactagttcttttccaaagtgtccgcgtt-ttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttgt---gaactga--agGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
     |  || | | || |  | |||    | ||     ||    ||  | |  |    ||| |  ||  | | ||       || ||||  ||||    |   |||  |||||| ||||| ||||| |||||||| || || || ||||| || ||||| |||||||||||||| ||||| |||||||| |||||||||
gtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattagGTGGGTATGACATGGAGGAGAAAGCGGCGAGAGCGTATGACCTGGCGGCGCTCAAGTATTGGGGCCCTTCCACACACATCAACTTCCCG

upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 4
-tactagttcttttccaaagtgtccgcgttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
 ||   |||       | | | ||   ||| ||| ||  | ||  |||| ||     |||| |  |                |||| || |||  |   |||||||||||| |  ||||| |||||||| |||||||||||||| || || || || || ||||| |  || || || ||||| ||||||
gtaactgttgccccttacaatttctttgttctcattgtacttatattttgtatctgttgctgacct----------------ttttcttcgtgttcgttagGTGGTTATGACACTGAAGATAAAGCTGCGAGGGCTTATGATCTGGCTGCGCTGAAATACTGGGGGCTATCTACGCATATAAATTTCCCG

upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
-----tac-tagttcttttccaaagtgtccgcgttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttg--tgaactga----agGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
     |||  | |||  |    | |  | |  | ||||    |||| | ||| |     ||||  | ||    || |   |  || ||||||||||  | ||        ||| |||||||||||||| |||||||||||  | || ||||||||||| || |||||||| ||||| || || || ||||  || ||| | 
gtaagtacacacttcaatcttcatggattcatgatttcccc-ctca-aatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT

upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
tactagttcttttccaaagtgtccgcgttttcagtgctcatacttttttt-actaaatgctaatt-tgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
    ||  |  ||      | |    | |   | ||   | ||  | | | | || || ||  |  || |||    | |||  || |     ||   |  ||| || |||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| || || || |||||||||
-gtaagcccccttt-----tctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG

upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
tactagttcttttccaaagtgtccgcg--ttttcagtgctcatactt----tttttactaaatgctaatttgattagtggtgattttttttgtttgtgaac-tgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
 |   |   ||| ||   |||   |    | ||   || || | |||    |||||  |   | || |||| ||       | || ||   |    ||||   | ||| |||||||| |  ||||||||||| ||  | || |||||||| ||||| |||||||||||||||||| | ||   ||| ||||| || 
aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgcttgaagttttttttcgttcctcatttaat-------gtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT

upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 3
tactagttcttttccaaagtgtccgcg--ttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttgtgaac-tgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
 |   |   ||| ||   |||   |    | ||   || || | |||    |  |   |  |   |   ||| ||    || ||   |    ||||   | ||| |||||||| | |||||||||||| ||  | || |||||||| ||||| |||||||||||||||||| | ||   ||| ||||| || 
aatgcgcagtttacctgggtgagtgtcactctttgttgttcgtgcttgaagtgttttttcgttcctcatttaatg---tttcttgccgggaatgaatgcgcagGGGGTTATGACAAGGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttactaaatgctaatttgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG
                                ttttttttgtttgt  CT-rich tract
                             tgattttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactagttcttttccaaagtgtccgcgttttcagtgctcatactttttttactaaatgctaatttgattagtggtgattttttttgtttgtgaactgaagGTGGTTATGATATGGAAGAGAAAGCTGCAAGGGCTTATGATCTTGCGGCTCTCAAGTATTGGGGACCTTCAACACACATAAACTTCCCG

- - - - - - - - - - - - - - - tcagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - taaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtggtg