Sequence
atgc intronic sequence ATGC exonic sequencegtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttctagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
Basic information
species | Glycine max |
transcript | GLYMA08G24160.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttc--tagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
|| | | | | || | | || | | | | | || | | | ||| | || || || |||| || ||||||||||| |||||||| |||||||||| || ||| |||||||||||||||||| ||||||||| |||| |||||||| | |||||||
-------------------------------------------gtaaattttcagtaatggataatgactattcagacaatatgt-cacttctgtggggtactgagatcgcttaaattgaacagGTATTGTGTATGCTTGCATGTTGGGTTAAAGATCCAAATGGGGATTATTTCAAGAAGCATCTTGCTAGGATCCCATATTATATATGGGTTACAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttc--tagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
|| | | | | | || | || || | | || | || ||| | | |||| ||| || || ||||| || ||||||||| | |||||||| |||||||||||||| ||| |||||||||||| ||||| ||||| |||||||| |||||||| |||||||
-------------------------------------------gtaatttttctgcaatggataatgtctattcagacagtatatctcttctt-tggggtgctaatatggcttaaattgaatagGTGTTGTGTATGCTTTCATGTTGGGTTGAAGATCCAAACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01140.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattca-ttcaaatatgacactaacatgcatttttttctagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
|| | ||| | | |||| |||||| | ||| | || ||| | | | | | || | |||| || |||||||||||||||||||| ||||||||| | || ||| ||||||||||||| ||||| ||| |||| ||||| ||||| | | |||||||
-------------------------------------------gtaacacgattgtccgtgttatgagatgtttaaaaggaaaaagaaactctaatcgaagaatgtctcttaaattgagc-agGTATTGTGTATGCTTGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTCCCGGATTATATATGGATGGCAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttc--tagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
|||||| ||| ||| ||| |||| | | | | ||| || || ||| | ||| || || ||| || |||||||| | |||||||| ||||||||||| || ||| |||||||||||| ||||| ||||||||||||| |||||||| | |||||||
------------------------------gtttttttctgcagtggataa--------------cttctatttagacaatatgtcagttctt-taggatactgatatggcttaagttgaacagGCATTGTGTATGCTCACATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTTTATATGGGTTGCAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 5
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttc--tagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
||| || | ||||| | | || | | || | | | | | | | | | ||| | || | || || |||| || |||||||| | |||||||| ||||||||||| || ||| |||||||||||| ||||| |||||||||||||| |||||||| | |||||||
-----------------------------------gtattttt-tcagtaa--tgga-----taatgactattcagacaatatgtcactccttttggggtactgatatcccttaaattgaacagGTATTGTGTATGCTCTCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttc--tagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
|| | | | | | || | || || | | || | || || | | | |||| ||| || || |||| | ||||||||| | |||||||| |||||||||||||| || |||||||||||| ||||| ||||| |||||||| |||||||| |||||||
-------------------------------------------gtaatttttctgcaatggataatgtctgttcagacagtatat-cacttctttggggtgctaatatggcttaaattgaacagGTACTGTGTATGCTTTCATGTTGGGTTGAAGATCCAAACGGGAATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttc--tagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
||| || | ||||| | | || | | || | | | | | || | | | ||| | || || || |||| || |||||||| || |||||||| ||||||||||| || ||| |||||||||||| ||||| |||||||||||||| |||||||| | |||||||
-----------------------------------gtattttt-tcagtaa--tgga-----taatgactattcagacaatatgt-cacttctttggggtactgatatcgcttaaattgaacagGTATTGTGTATGCTCGCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 11
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttc--tagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
|| | | | | || | || || | | || | || || | | | |||| ||| || || |||| || ||||||||| | |||||||| ||||||||| |||| ||| |||||||||||| ||||| ||||| |||||||| |||||||| |||||||
-------------------------------------------gtattttttctgcaatggataatgtctgttcagacagtatat-cacttctttggggtgctaatatggcttaaattgaacagGTATTGTGTATGCTTTCATGTTGGGTTGAAGATCCAGACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG
upper sequence: GLYMA08G24160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01210.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttctagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
|| | ||| | | |||| |||||| || || | | || | | | || || |||| || |||||| ||||||||||||| ||||||||| | || ||| ||||||||||||| ||||| ||| | |||||||| ||||| || | |||||||
-------------------------------------------gtaacacgattgtccgtattatgaaatgtttaaa-agaaactctaacgaactctttcttcaa---------ttgagcagGTATTGTGTATGTTTGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTGCCAGATTATATATGGATTGCAGAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttctagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
cactaac putative branch site (score: 1)
catttttttct putative PPT
aaattcattcaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtgtcacaacaataatgcatattgattttttttatccttgtgagtaaattaaactttttattttccttttaaagaggaaattcattcaaatatgacactaacatgcatttttttctagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGATCCCAGATTACTTATGGGTTTCTGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG