Sequence
atgc intronic sequence ATGC exonic sequence...actttggttatgatgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g38970.1 (Oryza sativa), 3'ss of exon 3
actttggttatgatgtagacatgcccacatgcagcttatggtctaacaa---tatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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----------gtatgttgatctatcttctggggatgcatcattcagtaaacttatttgatttttgtgttataactcttgttatacaaaatt---atttggcagGTTCGCAAATTCAGTAAACACTGCAGAAGTTGTGACAAATGTGTTGATGGATTTGATCATCATTGTCGG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g44230.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------actttggttatgatgtag-----acatgcccacatgcagcttatggtctaacaatatttccttttg--ggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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gtaagcttgtatatgtgctcaacgttggaactgcataatgatttttgtctcagtttcaggcaaaatatatcatttattttcctctgtaataactttgtaaaagcgaaaacttctgttgtcagatgttgctaattacaaaggcaaaatttt------cagGTTCGCAAATTCAGTAAACATTGCAGAAGTTGTGATAAATGTGTGGATGGTTTTGATCATCACTGTCGG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G321767_T01 (Zea mays), 3'ss of exon 3
actttggttatgatgtagacatgcccacatgcagcttatggtctaacaatatttcct--tttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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------------------gtatgtcgattt--agcttttcaccaggcttcactatctagcttgtgttgttcatctttgtttcacaaaagta--atttctcagGTTCGCAAATTCAGCAAACACTGCAGGAGTTGTGACAAGTGTGTGGATGGATTTGATCATCATTGTCGG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G149442_T01 (Zea mays), 3'ss of exon 3
----actttggtta-tgatgtagacatgcc-cacatgcagcttatggtctaacaa--tatttcct-------tttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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gtacgttctgttcaacgttgcaaccatgtagcatatttttttcctaagtcagcaggttatatcctgtcttaacttgtgttgtcatcacttccaattaagaaagatgatttttcagGTTCGCAAATTCAGTAAACACTGCAGAAGTTGTGACAAGTGTGTGGATGGATTTGATCATCACTGTCGG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
---actttggttatg-atgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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acatttctggttgcatgagtcagtagaggcattttagagaagtagctt--ccacctctcacttagtatgtatattctgtgccttgta--tttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
actttggttatgatgtagacatgcccacatgcagcttatggtc-taaca-atatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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-atctggttgc-atgcagctatcagtagaggcattttagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtatttcctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G22180.1 (Arabidopsis thaliana), 3'ss of exon 3
-actttggt---tatgatgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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tttcttggtctttatcttctagaatctgctttaagaagtctttagg--gaaagcaatttggttcagattttagatgtgtactcaatta--tgtatgtttcacagGTACGCAAGTTCAGCAAGCATTGTCGAAGTTGTGATAAATGTGTTGATTGTTTTGATCACCATTGCAAG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
actttggttatgatgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatt-taccaagaa----aatttttcatg--ttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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------gttgtattggtca-atgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ36891 (Selaginella moellendorffii), 3'ss of exon 3
actttggttatgatgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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---------------------------------gtttgagttctttccgtgagtatgtcgaca-----ttgatttgataagtttggtttatctcacgcagGTTCATAAGTTCAGCAAACATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGT
upper sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ33542 (Selaginella moellendorffii), 3'ss of exon 3
actttggttatgatgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
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---------------------------------gtttgagttctttccgtgagtatgtcgaca-----ttgatttgataagtttggtttatctcacgcagGTTCATAAGTTCAGCAAGCATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
gtctaac putative branch site (score: 2)
tttttcat putative PPT
tttttttatttaccaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actttggttatgatgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - gcccaca
- - - - - - - - - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa