Sequence
atgc intronic sequence ATGC exonic sequence...gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
Basic information
species | Glycine max |
transcript | GLYMA15G10870.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 3
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
| || | | | | | | || |||| | || | | | | | | | || || ||||||||||| |||||||| ||||||||||||||||| |||||||||||||||||| |||| ||| ||||| | |||||| |||||||||
--------------------gtaaattttcagtaatggataatgactattcagacaatatgtcacttctgtggggtactgagatcgcttaaattgaacagGTATTGTGTATGCTTGCATGTTGGGTTAAAGATCCAAATGGGGATTATTTCAAGAAGCATCTTGCTAGGATCCCATATTATATATGGGTTACAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 7
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaat----tttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
|| | | | | || | | | | || | || || || | ||| | || | | ||| || ||||||||| | |||||||| ||||||||||| |||||| |||||||||||| ||||| |||||||||||||| | |||||| ||||||||
------------------------gtaatttttctgcaatggataatgtctattcagacagtatatctcttctttggggtgctaatatggcttaaattgaatagGTGTTGTGTATGCTTTCATGTTGGGTTGAAGATCCAAACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01140.t01 (Vitis vinifera), 3'ss of exon 3
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaattttgtcaaaca-tgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
||| | | | ||| || | |||| | ||||| | | | || || | || | || | |||| || || |||||||||||||||||||| ||||||||| |||||||| ||||||||||||| ||||| || | || |||||| | ||| | |||||||||
-----------gtaacacg--attgtccgtgttatgagatgtttaaaagg---aaaaagaaactctaatcgaagaatgtctct--taaattgag----cagGTATTGTGTATGCTTGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTCCCGGATTATATATGGATGGCAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 7
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
| || | | | | || | ||| |||| | || | | || | || | || || || |||||||| | |||||||| |||||||||||||||||| |||||||||||| ||||| |||| ||||||| | | |||||| |||||||||
--------------------gtttttttctgcagtggataacttc-tatttagacaatatgtcagttctttaggatactgatatggcttaagttgaacagGCATTGTGTATGCTCACATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTTTATATGGGTTGCAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 5
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
|| | || || || | | | | | || | || || | | | | | || || ||| |||| || || |||||||| | |||||||| |||||||||||||||||| |||||||||||| ||||| |||| ||||||||| | |||||| |||||||||
---gtattttttcagtaatggataatgactat--tcagacaatatgtcactccttttggggtact------gatat-cccttaa---attgaa----cagGTATTGTGTATGCTCTCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 7
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaat----tttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
|| | | | | || | | | | || | || || || | ||| | || | | || | ||||||||| | |||||||| ||||||||||| ||| || |||||||||||| ||||| |||||||||||||| | |||||| ||||||||
------------------------gtaatttttctgcaatggataatgtctgttcagacagtatatcacttctttggggtgctaatatggcttaaattgaacagGTACTGTGTATGCTTTCATGTTGGGTTGAAGATCCAAACGGGAATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 7
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
| ||||| | | | | || |||| | || | | | || | | | || || |||||||| || |||||||| |||||||||||||||||| |||||||||||| ||||| |||| ||||||||| | |||||| |||||||||
-------------------gtattttttcagtaat-ggataatgactattcagacaatatgtcacttctttggggtactgatatcgcttaaattgaacagGTATTGTGTATGCTCGCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 11
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaat----tttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
| | | | | || | | | | || | || || || | ||| | || | | || || ||||||||| | |||||||| ||||||||| | |||||| |||||||||||| ||||| |||||||||||||| | |||||| ||||||||
------------------------gtattttttctgcaatggataatgtctgttcagacagtatatcacttctttggggtgctaatatggcttaaattgaacagGTATTGTGTATGCTTTCATGTTGGGTTGAAGATCCAGACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG
upper sequence: GLYMA15G10870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g01210.t01 (Vitis vinifera), 3'ss of exon 7
gagaaatgacaataataggagacaaaaaatgtaattaagcat-ttagtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
|| ||| | | ||| | | ||| || | | | ||| | | |||| || || |||||| ||||||||||||| ||||||||| |||||||| ||||||||||||| ||||| || | ||||||||| | ||| || |||||||||
-------------------------gtaacacgattgtccgtattatgaaatgtttaaaagaaactctaacgaactctttcttca---attgag----cagGTATTGTGTATGTTTGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTGCCAGATTATATATGGATTGCAGAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
cactaac putative branch site (score: 1)
atattggtatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagaaatgacaataataggagacaaaaaatgtaattaagcatttagtttttctacaaagagaattttgtcaaacatgccactaacatattggtattttagAGTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAATGGGGATGCTTTCAAGAAGCATCTTGCACGGATTCCAGATTATTTTTGGGTTTCAGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcca