Sequence
atgc intronic sequence ATGC exonic sequence...tttaaattggacgacgaatttagtgttcattagattattgattaatatgtaatttgctagctttacatagcagtaatgaactaacactcttatttcacagGTGAAGGATGACCCTTTAGGAGATTTTAAGAGTATGTATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGATCAGGGATGGCAAGTTTCTG
Basic information
species | Glycine max |
transcript | GLYMA03G27660.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 13
tttaaattggacgacgaatt-tagtgttcattagattattgattaatatgtaatttgctagc-tttacatagcagtaatgaactaacactctt---atttcacagGTGAAGGATGACCCTTTAGGAGATTTTAAGAGTATGTATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGATCAGGGATGGCAAGTTTCTG
|| || ||||| || |||| ||| || | |||| | | ||| | || | ||| | | |||| | | | | | | | | |||| ||||| | |||| || || ||||| || ||||| || || ||||| ||||| || ||||||||||| ||||| ||||| || |||||||||||||
-----gtttgatcttgaattctattgtttatttctttgct--ttaacaag-aatctactcgtgtttctcttggtttaattacttcatattacttgaaatatgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCATGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 9
tttaaattggacgacgaatt-tagtgttcattagattattgattaatatgtaatttgctagctttacata-gcagtaatgaactaacactctt----atttcacagGTGAAGGATGACCCTTTAGGAGATTTTAAGAGTATGTATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGATCAGGGATGGCAAGTTTCTG
|| || ||||| || |||| ||| ||| | |||| | | ||| | || | || | | | |||| | | | | | | || | |||| ||||| | |||| || || ||||| |||||||| || || ||||| || || || ||||||||||| ||||| ||||| || |||||||||||||
-----gtttgatcttgaattctattgtttatttctttact--ttaacaag-aatctactcgtgtttctcatggtctaattacttcatattacttgaaatcttgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGTATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCCGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 3'ss of exon 2
tttaaattggacgacgaatttagtgttcattagattattgattaatatgtaatttgctagctttacatagcagtaatgaactaacactctt----atttcacagGTGAAGGATGACCCTTTAGGAGATTTTAAGAGTATGTATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGATCAGGGATGGCAAGTTTCTG
|| | | || | | || || || | | || ||| | | | | | | | | || | |||| ||||| | |||| || || ||||| || |||||||| || ||||| ||||| || ||||||||||| ||||| ||||| || |||||||||||||
----------------------gtttgtgtcttgactttaaccagaatctacttgg---gtttctcatggtc-catttgcttcatattgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG
upper sequence: GLYMA03G27660.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0054g01340.t01 (Vitis vinifera), 3'ss of exon 2
tttaaattggacgacgaatttagtgttcattagattattgattaatatgtaatttgct--agctttacatagcagtaatgaactaacactctt----atttcacagGTGAAGGATGACCCTTTAGGAGATTTTAAGAGTATGTATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGATCAGGGATGGCAAGTTTCTG
|| || ||||| || || | | || | ||| | || | || ||| | || | | | | ||| | || | |||| ||||| | |||| || || ||||| || |||||||| || ||||| ||||| || ||||||||||| ||||| ||||| || |||||||||||||
-----gtttgatcttgaattc--cattgtttgtgtcttgactttaaccagaatctacttgggtttctcatggtc-tatttacttcatactgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGTTCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtaatttgctagctttacatagcagtaatgaactaacactcttatttcacagGTGAAGGATGACCCTTTAGGAGATTTTAAGAGTATGTATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGATCAGGGATGGCAAGTTTCTG
aactaac putative branch site (score: 1)
ctcttatttc CT-rich tract
tttacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaaattggacgacgaatttagtgttcattagattattgattaatatgtaatttgctagctttacatagcagtaatgaactaacactcttatttcacagGTGAAGGATGACCCTTTAGGAGATTTTAAGAGTATGTATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGATCAGGGATGGCAAGTTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - -agtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgctagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaacac