Sequence
atgc intronic sequence ATGC exonic sequencegtagtaattatttgtaattttgaataagatcttttgtcctttattcttctctgatttaaatttgtttgcttgcaagAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g48820.1 (Oryza sativa), 3'ss of exon 12
gtagtaattatttgtaattttgaataagatcttttgtcctttattcttctctgatttaaatttgtttg-----cttgcaagAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
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---gta-tgccgaccacatccaaaaaagttcaattgtaacctgttgctatcttatt-gattttgtttattgatctcttcagAAATCTGGACTGAGAGACCTTACAACAAGCAAGACACCTGAGGCATCTATATCTGCTGCACTGTCAAGGGATTCAAAGCTTTTCGAAAGGACTGCACCTT
upper sequence: Vv10s0003g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g48180.1 (Oryza sativa), 3'ss of exon 11
------------------gtagtaatt-atttgtaattttgaataagatcttttgtcctttattcttctctgatttaaatttgtttgcttgcaagAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
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gtttgtttccacacagatatgctagctcaattttgctttgtgattttcttctttttgttctatagttgaatgaatttactcttttttatgtttagAAATCTGGATTGAGAGACCTCACAACAAGCAAGACGCCTGAGGCATCTATAGCTGCTGCCTTGTCAAGGGATACAAAACTTTTTGAGCGAACTGCTCCTT
upper sequence: Vv10s0003g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC196465.3_FGT006 (Zea mays), 3'ss of exon 6
gtagtaattatttgtaattttgaataagatcttttgtcctttat--------tcttctctgatttaaat---ttgtttgcttgca-agAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
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---gtacacatatatatcctgaacccccctcctcccgcccctaaagtggttatcttcaattttctaagctgattattttcctgttcagAAATCTGGATTGAGAGACCTCACAACAAGCAAGACACCTGAGGCATCCATAGCTGCTGCTTTGTCTAGGGATGCAAAACTTTTTGAGAGAACTGCTCCTT
upper sequence: Vv10s0003g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G159357_T01 (Zea mays), 3'ss of exon 12
gta---gtaattatttgtaattttgaataagat-cttttgtcctt----tattcttctctgattt---aaatt---tgtttgcttgca-agAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
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gtacatacacatatatgtatctttaatccctttacccttctccttaaagtggttatcttcaattttgtaagctgattattttcctgttcagAAATCTGGATTGAGAGACCTCACAACAAGCAAGACACCTGAGGCATCCATAGCTGCTGCCTTGTCTAGGGATACAAAGCTTTTTGAGAGAACTGCTCCTT
upper sequence: Vv10s0003g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G24370.1 (Glycine max), 3'ss of exon 12
gtagtaattatttgta-attttgaataagatcttttgtcctttattct--tctctgatttaaatttgtttgcttg-caagAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
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--gtgagttgcatgtccatattatgtaatcttttttattgtcaggtttagtcttaaattgttatgtctctgatcaatcagAAATCTGGTCTTCGAGACTTGACGACCAGCAAGACACCTGAGGCATCGATTTCTGTTGCTTTAACAAGAGATGCCAAGCTTTTTGAAAGGATAGCTCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaataagatcttttgtcctttattcttctctgatttaaatttgtttgcttgcaagAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
ctctgat putative branch site (score: 4)
tttgttt putative PPT
tgatttaaatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtaattatttgtaattttgaataagatcttttgtcctttattcttctctgatttaaatttgtttgcttgcaagAAATCTGGACTTCGAGACTTGACAAGAAGCAAGGCGCCTGAGGCATCCATATCTGCTGCTCTATCACGGGATGCAGCCCTATTTGAAAGAACAGCTCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC