Sequence
atgc intronic sequence ATGC exonic sequence...attactatattgaactggtttgttgctagttcaatctagtggcttaacaccaagttaagttgtgttttccaagttttcaaactagtattttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
attactatattgaactggtttgttgctagttcaatctagtggcttaacaccaagttaagttgtgttttccaagttttcaaactagta--ttttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT------
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gcttttgtatgttgtctgtttgcaatt--ttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTG------CAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
attactatattgaactggtttgttgctagttcaatctagtggcttaacaccaagttaagttgtgttt--tccaagttttcaaactagtattttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT------
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gcttttgtatgtagtctgtttgcaatt--ttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTG------CAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
---attactatatt-gaactggtttg--ttgcta--gttcaatctagtggcttaacaccaagttaagttgtgttttccaagttttcaaactagt-attttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT------
||| ||| ||| | | ||| || | | || ||| | | | | | ||| |||| | ||| | | || | | || ||||||||| ||| || | | || | | ||| | ||| |||||||||||||| |||||||| || ||||||||||| || |||||||||||||||||
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaataactccagGTTACAATGACCCTG------CCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------attactatattgaactggtttgttgctagttcaatctagtggcttaacacca-agttaagttgtgttttccaagttttcaaactagtattt--------tcaatggca-gGTTACAGTG-ATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT------
| | | | | | ||| | | |||||| ||| | || | | | || | || || ||||| || || | || ||||| | | ||||||| |||||| || || || || || || ||||||||||| |||||||| ||||||||||| || ||||||||||| |||||
gtcagtaacaaatttctctcatttttcataccatttttgtcatgtggctgatctgtagttctgtcttctacacaaatattttggatggcatgcttgaataaaaattggtaactaacgttgatattctgtctttaacacaaatacagGGTACACAGATCCAGCTAAACCAGACCTTCCACGTCTACACGAATGGCATTTCAGATCTGGACTTGATCGCTACATATGGATCATCGGCATGATATATGC
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S5_239V6.1 (Physcomitrella patens), 3'ss of exon 8
attactatattgaact-ggtttgttgctagttcaatctagtggcttaacacca--agttaagttgtgttttccaagttttcaaactagtattttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTC----CCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT---
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--------aggaaacttagtactgtgtaattctagaaaattgggttgtctttgtcattccagcacaaatgtgcaa-tttatgtatgatggtttttggttgtttgt-gcagCGTATCAAAACCCCTCGCATGCGACCCCGCAGCCCTTGCTTCATGAATGGCATTTTAGATCAGGACTGGATCGATATATTTGGATCGTCGGCATGCTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaccaagttaagttgtgttttccaagttttcaaactagtattttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT
gcttaac putative branch site (score: 3)
tattttc putative PPT
tattttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attactatattgaactggtttgttgctagttcaatctagtggcttaacaccaagttaagttgtgttttccaagttttcaaactagtattttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT
- - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - -tggctta
- - - - - - - - - - - - - - - - - - - - - - - acaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaact