Sequence
atgc intronic sequence ATGC exonic sequence...ttgctaagacaagagctctttcttaataacattgatgagttttatttttttaatcactttagtgatgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGATACTGCAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0059g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g32890.1 (Oryza sativa), 3'ss of exon 3
ttgctaaga-caagagctctttcttaataaca-ttgatgagttttatttttttaatcactttagtgatgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGATACTGCAAAG
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-agccaaaatcaattgctgtataatcgtctcagcagaagatctgtgttgctttcttttattaaatgcagtttcatttaccttctccctacttatttgt-cagATCTTCCATGGAGCTGACAATGATGTTCTTTGGCTTCAGAGAGACTTTCATATTTATGTTGTGAATATGTTTGATACTGCCAAG
upper sequence: Vv12s0059g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G46220.1 (Glycine max), 3'ss of exon 3
-ttgctaagacaagagctc--tttcttaataacattgatga-gttttatttttttaatcactttagtgatgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGATACTGCAAAG
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tctgttgaaaaaatattttagtttattattgtcagtgtttttgtcatccaattctatttattacagtttttctctcac--tcaatggaaaatttgtggat--agGTGTTCCATGGGGCTGACAATGATATAGTCTGGCTACAGAGGGACTTCCATATATACGTTGTTAATCTATTTGATACTTCAAAG
upper sequence: Vv12s0059g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G10530.1 (Glycine max), 3'ss of exon 5
--ttgctaagacaagagctctttcttaataacattgatgagttttatttttttaatcactttagtg--atgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGAT--ACTGCAAAG
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attatctattgaaaaaatatttgtttattattgtcagtg--tttttgcatccaagtctatttattacagttttttcccactcaatggaaaatttgtggat--agGTGTTCCATGGGGCTGACAATGATATAGTCTGGCTACAGAGGGACTTCCATATATACGTTGTTAGTCTATTTGATATACTTCAAAG
upper sequence: Vv12s0059g00620.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G32415.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------ttgctaagacaagagctctttcttaataacat-----tgatgag----ttttatttttttaatcactttagtgatgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGATACTGCAAAG
|| | | ||| | | | | | || ||| || ||| | ||| || | || | || | || || ||| | || ||||||| || || ||||| || |||||| | ||||| || |||||||||||||||||||||||||| | ||||||||||| |||
gtatattgttcagtgttagaatcttgtaacttaatttgtttcaaatttttggaagaagtcttatgtagcacttgtatgtttctgacaagatgatttagtcccccaaatttctatgtgcattttggaaca-ttaatatgtgattggtgcatctagGTGTTTCACGGGGCTGACAACGATGTTATCTGGCTTCAAAGAGACTTCCATATATATGTTGTTAATATGTTTGATACTGCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttaatcactttagtgatgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGATACTGCAAAG
ttttaat putative branch site (score: 3)
tattttc putative PPT
tagaatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctaagacaagagctctttcttaataacattgatgagttttatttttttaatcactttagtgatgcagtaatagttggtagaatattttcggatgcagGTGTTCCATGGTGCTGATAATGATGTTTTGTGGCTGCAGAGAGACTTCCATATATATGTTGTTAACTTATTTGATACTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - -aagacaa
- - - - - - - - - - - - aataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagttgg