Sequence
atgc intronic sequence ATGC exonic sequencegtagttcaaactagatagcatttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 5
gtagttcaaactagatagcatttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactgacat-----ttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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-----------------------------------------gtgagcatggtgctattgaattttttttgttcatttaagttggagtaattctccaagctctaactcatctacacatgatgaacagGAACCAGTGATTCCTGGCTGCTACCTTAGAGCCAAGGCCATTGGCCTCATGCCTATGATTGATCAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 3
gtagttcaaactagatagcatttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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---------------------gtgaacagaattgacgcccttaattttctatatgactcacattttctgcatttgctaatttgtctaacgt--acaaccttgtgttg---ttcgcaaccagGAACCAGTTCTTCCTGGTTCATTCCTCCGAGCCAGGGCCATTGGTCTCATGCCTATGATTGACCAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 4
gtagttcaaactagatagcatttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgagtagattggaagtgtttttacaa-gctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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-----------------------------------gtgatcatccttcaactgta--tatgctgatgctgttataaattgtgcgataatcactgcaacacatgtccaaacgtttaattgcagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATGCCCATGATCGATCAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 5
-gtagttcaaactagatagc-atttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgag---tagattggaagtgtttttacaagctcaaactgacattt--ttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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gtcagcatgttcttacgacttgtttgtttcatcgatctagcccacttaattagtgtacttagatatatataggttaagccttcatcttctggggttaattattcactgactggcttacaaccaaatagGAACCGGTGATACCTGGCTGTTTTCTTCGGGCAAGGGCCATCGGCCTTATGCCCATGATTGATCAG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 4
----------------------------------gtagttcaaactagatagcatttaatcaataataagagctcgtctttg-ttttgcaact--aaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactg-----acatttttg-aacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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gtaaattagtaccattttcaaattcatatattttacaagaagcattaaatcctgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgttttaaattgttgaatagacaatgactatttaattaagaattttttctacattgttatgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCAAGGGCCATTGGACTGATGCCCATGATTGACGGG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 4
------------------------------------gtagttcaaactagatagcatttaatcaataataagagctcgtctttgttt-tgcaact--aaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactg-----acatt-tttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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gtaaattagtaccattttcaaattcatatattttacacaagaagcattaaatattgtttataatattctatagacatgtgtaaaattgtgtaaatgtagaatgccttaaattgttgaataggcaatggctatttaattaagaattgtttctgcattgttttgatagGAGCCAGTTCTTCCTGGATGTTTCCTGCGAGCCAGGGCCATTGTACTGATGCCCATGATTGACGGG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 5
gtagttcaaactagatagcatttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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--------------------gtaaatccagtgtacaa---tattctattttaattattgaataggcgataactatttatttaagaattttttt-----------ctgcattgttttgatagGAGCCTGTTCTTCCTGGATGTTTTCTGCGAGCCCGGGCCATTGGACTTATGCCCATGATTGACGGG
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 5
gtagttcaaactagatagcattt--aatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgag-tagattggaagtgtttttacaagctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
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--------------ataccattttagattagtaataa-atttgatgcgtatgtttgagctatata--tatcaacaaggttatccattagtaaatttacttaatta--ttgacaatgt-----agGAGCCAGTTCTTCCTGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgggcgagtagattggaagtgtttttacaagctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
aactgac putative branch site (score: 2)
cattttt CT-rich tract
tttttacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttcaaactagatagcatttaatcaataataagagctcgtctttgttttgcaactaaacagttgtgggcgagtagattggaagtgtttttacaagctcaaactgacatttttgaacagGAACCAGTTGTTCCTGGCTGTTTTCTTCGAGCCAGGGCCATTGGGCTGATGCCCATGATTGATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT