Sequence
atgc intronic sequence ATGC exonic sequence...tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacattttctctacattgataaaaatttattgttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g50330.1 (Oryza sativa), 3'ss of exon 2
-tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacattttctctacattgataaaaatttattgttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
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cagtgttgtcgtgacctttgcaaatccataaa-gctgtatgcgatctattacctttttgcattaaacagtacaataacttttttcctttcggcacatttagGATGAAAATGGCAGCAAGATGGTCAACCAATATGTCCACCTGGGGAAGATTGGTTCTGGAAGCTATGGCAAAGTG
upper sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G07340.1 (Glycine max), 3'ss of exon 3
tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacattttctctacattga--taaaaat-ttattg--ttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
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-----tattggaatgttatttgtattcaggaaacacttctctttgtattgaatatcttttccctcagaacttagaaatcttattgaacttttattttccttttagGATGAAAATGGGAACAAGATGATAAATGAGTATATTCGTGAGTATAAGATTGGTTCTGGTAGCTATGGGAAAGTG
upper sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G40190.1 (Glycine max), 3'ss of exon 3
-----tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacattttctctacattgataaaaatttattgttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
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aaacctatctgaatggtgtgatc--tgtattcag-gcaaagtttgtctactgtaataaatatctttttattttttttatcatcgcctttatttaaatatt--cagGATGAAAATGGGAACAAGATGATAAATGGATATGTTCGAGAGTATAAAATTGGTTCTGGAAGCTATGGCAAAGTG
upper sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G20690.1 (Glycine max), 3'ss of exon 2
tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacattttctctacattga--taaaaat-ttattg--ttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
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----atctgaatgttatt-ttgtattcaagaaacacttctctttgtgatgaatatcttttctctcagaacttagaagtcttgttgaacttttagtttcctttcagGATGAAAATGGGAACAAGATGATAAATGAGTATATTCGTGAGTGTAAAATTGGTTCTGGTAGCTATGGGAAAGTG
upper sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G29640.4 (Glycine max), 3'ss of exon 1
tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacat-tttctctacattgataa-aaatttatt--gttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
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-atctgaatggtgtgatc--tgtattcag-gcaaagtttgtctgctgtaacgaatatctttttttattatcattgcctttatttaaatattttcatcccttcagGATGAAAATGGGAACAAGATGATAAATGAATATGTTCGAGAGTATAAAATTGGTTGCGGAAGCTATGGCAAAGTG
upper sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G60550.1 (Arabidopsis thaliana), 3'ss of exon 3
tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacattttctc-tacattgataaaaattt-attgttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
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----gtaagtga-cttctggtgc-ctgtctctcagattattgcttctttgaatatcccatggcgtgtctataccaattttgttgttttttga---tatttagGATGAAAATGGTGACAAGACAATCAATGAGTATGTTCGCGTGTGTAAAATTGGATCCGGTAGCTATGGTAAAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttaaacattttctctacattgataaaaatttattgttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
cattgat putative branch site (score: 4)
attttctctacattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttttaggggaacaattgttgcgttagatgtagaatttgttatttgttaaacattttctctacattgataaaaatttattgttttctgaatgctgtcagGATGAAAATGGGAATAAGACGATCAATGAGTATGTTCGTGAGTACAAGATTGGTTCTGGAAGCTATGGCAAAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - -ggaacaa
- - - - - - - - ttgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa