Sequence
atgc intronic sequence ATGC exonic sequence...ttatagccgtattatgataatgtgtttttgccatgctttttccaaagtgggtttcaattttgttgttctatttggtagccacttttgtttgattgcgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
Basic information
species | Glycine max |
transcript | GLYMA12G23220.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 4
---ttatagccgtattatgataatgtgtttttgccatgctttttccaaagtgggtttcaattttgttgttctatttggtagccacttttgtttgattg----cgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
||||| |||||| | || | || || ||| || || | || | | |||| | | | |||| | | ||||||||||||||| |||||||| |||| ||||||||||||| || |||| || ||||||||||| | || ||| | || ||||||||||
gctttataa----attatggc--tttggatatgtcaaaatttatcttt-gttgtttctatatggattgtatgaagtaattattgggattgtcttggcgggattgcagATTCAAAGGCTAAGTGGAGTGGATTATGATTTTGCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTT--GATTTATACTATGGAAGAG----
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 4
---ttatag-ccgta-ttatgataatgt--gtttttgccatgctttttccaaagtgggtttcaattttgttgttctatttggtagccacttttgtttgattgcgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
||||| | | || |||| ||| | | ||||| | | ||| || | || || | |||| || | | ||||| |||||||| ||||| |||||||| |||||||||||||||||| || |||| || ||||||||||| | || ||| | || ||||||||||
gctttataaattatggctttggatatgtcaaaatttatctttgttttttctatatggattgta----tgaagtaattattgg-gattgtcttggctggattg--cagATTCAGAGGCTAAGTGGAGTGGATTCTGATTTTGCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTT--GATTTATACTATGGAAGAG----
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 3
---ttatagccgtattatgataatgtgtt----tttgccatgctttttccaaagtgggtttcaattttgttgttctatttggtagccacttttgtttgattgcgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
||||| | | || ||| ||| | || || | | ||| || | || || | |||| || | | ||||| |||||||| ||||| |||||||| |||||||||||| ||||| || |||| || ||||||||||| | || ||| | || ||||||||||
gctttataaattttggctttggatatgtcaaaatttatatttgttgtttctatatggattgta----tgaagtaattattgg-gattgtcttggctagattg--cagATTCAGAGGCTAAGTGGAGTGGATTCTGATTTTTCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTT--GATTTATACTATGGAAGAG----
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 3
---ttatagccgtattatgataatgtgtttttgccatgctttttccaaagtgggtttcaattttgttgttctatttggtagccacttttgtt-tgattg---cgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
||||| |||||| | || | || || ||| | || | || | | |||| | | | |||| || ||| ||||||||| ||||| |||||||| |||||||||||| ||||| || |||| || ||||||||||| | || ||| | || ||||||||||
gctttataa----attatggc--tttggatatgtcaaaatttatattt-gttgtttctatatggattgtatgaagtaattattgggattgtcatggttggattgcagATTCAGAGGCTAAGTGGAGTGGATTCTGATTTTTCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTT--GATTTATACTATGGAAGAG----
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 4
---ttatagccgtattatgataatgtgtttttgccatgctttttccaaagtgggtttcaattttgttgttctatttggtagccacttttgt-ttgattg---cgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
||||| |||||| | || | || || ||| || || | || | | ||| | | | |||| ||| || |||||| || ||||| |||||||| |||||||||||||||||| || |||| || ||||||||||| | || ||| | || ||||||||||
gctttataa----attatggc--tttggatatgtcaaaatttatcttt-gttgtttctatatggactgtatgaagtaattattgggattgtcttggctggattgcagATCCAGAGGCTAAGTGGAGTGGATTCTGATTTTGCTCCACTTTTGCAACATGCAGGGGTTCCTTCTGTT--GATTTATACTATGGAAGAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgggtttcaattttgttgttctatttggtagccacttttgtttgattgcgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
gtttgat putative branch site (score: 5)
tttcaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatagccgtattatgataatgtgtttttgccatgctttttccaaagtgggtttcaattttgttgttctatttggtagccacttttgtttgattgcgcagATTCAAAGGCTCAGTGGAGTTGATTCTGATTTTGCTCCATTTGTGCAGCACGCAGGGGTTCCATTCATTTTGATATGTATTATGGAAGAGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - ccatgct
- - - - - - - - - - - - - - - - - - - - - - - gtgggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt