Sequence
atgc intronic sequence ATGC exonic sequence...atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
Basic information
species | Glycine max |
transcript | GLYMA08G24160.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttat---ctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||| |||| | | | | | | ||| || | | ||| | ||| || | || ||| | | ||| | | || || |||| || || |||||| ||| || |||||||| ||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||
--gtttgatcttgaattccatagtt-tatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactacc--tgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01140.t01 (Vitis vinifera), 3'ss of exon 4
atatttataattgattactaaattagtgtttgttagactattgaacaatat-gtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||| | | | | | | | ||| ||| | || ||| | || || | | | | | | | | | | || || |||| | || |||||| ||| ||||||| ||| ||||| || ||||||| ||||||||||||||||| |||| |||||||| |||||||||||||
ataaagaaatctcaagtgttgtcttgaatttcttaaatcatctcttcttatcaaccatcattattttttgatgccacttgaaagagaat-taatcttgcagGTTAGGGACAATCCTTATGGTGATTTTAGAAGCATGTACAAACACATTTCTATGGGATCTTGGACATTCTCAGATCGGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 13
atatttataattgattactaaat-tagtgtttgttagacta-ttgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt---attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||||| || | || ||||| || | || ||||| | | | || ||| ||| | |||| | | ||| | | | | |||| || || |||||| ||| || |||||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||
--------gtttgatcttgaattctattgtttatttctttgctttaacaagaatctactcgtgtttctcttggtttaattacttcatattacttgaaatatgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCATGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 6
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttat---ctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||| |||| | | | || | ||| || | | ||| | ||| || | || ||| | | |||| || || || |||| || | |||||| ||| || |||||||| ||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| || ||||||||||
--gtttgatcttgaattccatcttt-tatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactgc--ttgaaatcttgaagGTCAAGAACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGCCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaat-tagtgtttgttagacta-ttgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||||| || | || ||||| || || || ||||| | | | || ||| || | |||| | | ||| | || || |||| || || |||||| ||| || |||||||||||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||
--------gtttgatcttgaattctattgtttatttctttactttaacaagaatctactcgtgtttctcatggtctaattacttcatattacttgaaatcttgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGTATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCCGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 3'ss of exon 2
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
|| | ||| || | || || | | | ||| | || | | | ||| | || || |||| || || |||||| ||| || |||||||| |||||||| || ||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||
-------------------------gtttgtgtcttgactttaaccagaatctacttgggtttctcatggtc-catttgcttcatattgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 7
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttat---ctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||| |||| | | | | | ||| || | | ||| | ||| || | || ||| | | |||| | | || || |||| || || |||||| ||| || |||||||| ||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||
--gtttgatcttgaattccatcgtt-tatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactgcc--tgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 2
atatttataattgattactaaattagtgtttgttagactattgaacaatat-gtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
| | || | ||| | ||| || ||| | || || | | | | | | | | | | || |||| | || |||||| ||| ||||||| ||| |||||| | | |||| ||| |||||||||||||||| |||| |||||||| ||||||||||||
--------------gtgttgtctt-gaatttctcagatcatctcttcttatcacccatcattatttcttgatgccagttgaaagctaat-taagcttgcagGTTAGGGACAATCCTTCTGGTGATTTTAGAAGCATGTATAGATACATTTTTAAGGGATCTTGGACATTCTTAGATCGGGATCATGGTTGGCAAGTTTCTA
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||| |||| | | ||| | | | | ||| || | || || | ||| ||| | || | | | | | ||| | || || |||| || || |||||| || || |||||||| ||||| || || ||||| |||||||| ||||||||||| ||| | |||||||| |||||||||||||
--gtttgatcttga--attccattgtttatggctttact-ttaaccagaatctactttggtttctcatggtc-catttacttcgtattgcttgaaatcttgaagGTCAAGGACAATCCTTCCGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATAAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
|| | ||| | | || || | | | ||| | || || | | ||| | || || |||| || || |||||| ||| || |||||||| |||||||| | ||||| ||||||| ||||||||||| ||||| |||||||| |||||||||||||
-------------------------gtttgtgtcttgacttcaaccagaatctacttgggtttctcatggtc-tatttgcttcatattgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCAAAATTTCCCAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01340.t01 (Vitis vinifera), 3'ss of exon 2
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
||| |||| | | | | || | ||| || | || || | | | ||| | || || | | | | | | || || |||| || || |||||| ||| || |||||||| |||||||| || ||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||
--gtttgatcttgaattcca---ttgtttgtgtcttgactttaaccagaatctacttgggtttctcatggtc-tatttacttcatactgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGTTCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatgtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
ttcttatttt CT-rich tract
ttgtttttatctagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA