Sequence
atgc intronic sequence ATGC exonic sequence...taatttataattgactattaagttagtgttcattagattacttaagagtatgtttgttagctttacatagtagtaatgaattgacattcttatttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
Basic information
species | Glycine max |
transcript | GLYMA03G27620.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 9
taatttataattgactattaagttagt-gttcattagattacttaag--agtatgtttgttagctttacatagtagtaatgaattgacattctt----atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
|||| | || | | ||| ||| |||||| | || || | | | || ||| || || | | || | | | || | ||||| | ||||| ||||| || || ||||| || ||||| || || ||| | || || || ||||||||||||||||| || ||||| |||||||||||||
--------gtttgatcttgaattccatagtttatttctttacttcaaccagaatctacttgggtttctcatggtc-tatttacttcatactacctgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01140.t01 (Vitis vinifera), 3'ss of exon 4
-taatttataattgactattaagttagtgttcattagattacttaagagtat-gtttgttagctttacatagtagtaatgaattgacattcttatttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
||| | | | | || || | || ||| || | | ||| | | || | | | | | || | | | || | |||| || ||||| |||| || ||||||| || ||||| || ||| ||| || ||||||||||||||||||| || ||||| |||||||||||||
ataaagaaatctcaagtgttgtctt-gaatttcttaaatcatctcttcttatcaaccatcattattttttgatgccacttgaaagagaat-taatcttgcagGTTAGGGACAATCCTTATGGTGATTTTAGAAGCATGTACAAACACATTTCTATGGGATCTTGGACATTCTCAGATCGGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 13
taatttataattgactattaagttagtgttcattagattacttaagagtatgtttgttagctttacatagtagtaatgaattgacattctt---atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
||| |||| | || | | || || | || |||| | | | || | || | | || |||| | || | ||| | | | ||||| | ||||| ||||| || || ||||| || ||||| || || ||| | ||||| || ||||||||||||||||| || ||||| |||||||||||||
--gtttgatcttgaattctattgtt-tatttctttgctttaacaagaatctactcgt--gtttctcttggtt-taattacttcatattacttgaaatatgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCATGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 9
taatttataattgactattaagt-tagtgttcattagattactt----aagagtatgtttgttagctttacatagtagtaatgaattgacattctt----atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
|||| | || | || |||| ||| |||||| |||| | | | || | || ||| || |||| | || | ||| | || | ||||| | ||||| ||||| || || ||||| |||||||| || || ||| | || || || ||||||||||| ||||| || ||||| |||||||||||||
--------gtttgatcttgaattctattgtttatttctttactttaacaagaatctactcgt--gtttctcatggtc-taattacttcatattacttgaaatcttgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGTATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCCGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 3'ss of exon 2
taatttataattgactattaagttagtgttcattagattacttaagagtatgtttgttagctttacatagtagtaatgaattgacattctt----atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
||| |||| || || ||| | | ||| | || ||| || | | || | ||| | || | ||||| | ||||| ||||| || || ||||| || |||||||| || ||| | ||||| || ||||||||||||||||| || ||||| |||||||||||||
---------------------gtttgtgtc--ttgactttaaccagaatctacttg--ggtttctcatggtc-catttgcttcatattgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 7
taatttataattgactattaagttagt-gttcattagattacttaag--agtatgtttgttagctttacatagtagtaatgaattgacattctt----atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
|||| | || | | ||| ||| |||||| | || || | | | || ||| || || | | || | | | || | ||||| | ||||| ||||| || || ||||| || ||||| || || ||| | || || || ||||||||||||||||| || ||||| |||||||||||||
--------gtttgatcttgaattccatcgtttatttctttacttcaaccagaatctacttgggtttctcatggtc-tatttacttcatactgcctgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 9
taatttataattgactattaagtt-agtgttcattagattacttaag--agtatgtttgttagctttacatagtagtaatgaattgacattctt----atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
|||| | || | | |||| || |||||| | || || | || | || ||| || | | | || ||| | || | ||||| | ||||| ||||| || || ||||| || ||||| || || ||| | ||||| || ||||||||||||||| | || ||||| |||||||||||||
--------gtttgatcttgaattccattgtttatggctttactttaaccagaatctactttggtttctcatggtc-catttacttcgtattgcttgaaatcttgaagGTCAAGGACAATCCTTCCGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATAAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 9
taatttataattgactattaagttagtgttcattagattacttaagagtatgtttgttagctttacatagtagtaatgaattgacattctt----atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
||| |||| || || ||| | | ||| | || ||| || || | || | ||| | || | ||||| | ||||| ||||| || || ||||| || |||||||| | ||| | |||| || ||||||||||||||||| || ||||| |||||||||||||
---------------------gtttgtgtc--ttgacttcaaccagaatctacttg--ggtttctcatggtc-tatttgcttcatattgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCAAAATTTCCCAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27620.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01340.t01 (Vitis vinifera), 3'ss of exon 2
taatttataattgactattaa-gttagtgttcattagattacttaagagtatgtttgttagctttacatagtagtaatgaattgacattctt----atttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
||| |||| | | ||| |||| || || ||| | | ||| | || ||| || || | | || | | | | || | ||||| | ||||| ||||| || || ||||| || |||||||| || ||| | ||||| || ||||||||||||||||| || ||||| |||||||||||||
--gtttgatcttgaattccattgtttgtgtc--ttgactttaaccagaatctacttg--ggtttctcatggtc-tatttacttcatactgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGTTCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtatgtttgttagctttacatagtagtaatgaattgacattcttatttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
aattgac putative branch site (score: 3)
ttcttatttc CT-rich tract
attcttatttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatttataattgactattaagttagtgttcattagattacttaagagtatgtttgttagctttacatagtagtaatgaattgacattcttatttcaaagGTGAGAGACAACCCTTCAGGAGATTTTAAGAGTATGTATCGTCATATTACTAAAGGGTCTTGGACATTCTCAGATCAAGACCATGGATGGCAAGTTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - -gttagtg
- - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacattc