Sequence
atgc intronic sequence ATGC exonic sequencegttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 1
gttaggagtatcttatatttttc-ttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
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---------gtgtgagatcatgcatcataattcagagcattctagactattg--tttccagaactaattgactaacttc--attattttacccagGCTGTGTATCATATGCCAACCACCGAAAATGATATGCCATCTGGGAGTATTCCGTTGGCATTGCAGAGCCTTTTCTACAAGCTCCAGTATAGTGACAATA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 5
gttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatg-tatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
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----------------gtgaggctaa--atttgtaa--attctcttaaatgaat-cctatgatgcgaggc--tgatacagagaatgatattttagGCTGTATACCATATGCCAACTACAGAGAATGATACACCTTGCGGGAGCATCCCTTTGGCTTTGCAAAGTCTTTTCTGCAAACTTCAGCATAGTGACAATA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 5
gttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
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---------gtctgagatcattactttttcctagt-ctacatgatttgttaagtacctgaacttaaga---ctaattgaaatttc--atcttagGCTGTATATCATATGCCAACTACTGAGAATGACATGCCATCTGGGAGTATTCCTTTAGCCCTGCAGAGCCTTTTTTACAAGCTCCAATACAGCGACAATA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 1
gttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
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---------gtggggcaacatttctattttttattactgtt-----------gtttcttaagtgtggtgc-tgatactgaaattaatattttagGCTGTATATCATATGCCTACTACAGAGAATGATACGCCTTCAGGGAACATTCCATTGGCTTTGCAAAGCCTTTTTTATAAACTTCAGCATAGTGATAACA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 5
gttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
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-----------gtgaaatcaatc--attgttctgttctacatgtttctctaagcacctgaattttga-accatttattgaaatgttttcat-agGCTGTATATCATATGCCAACAACTGAGAATGACATGCCATCTGGGAGTATCCCTTTAGCCCTGCAGAGCCTGTTTTACAAGCTACAGTATAGTGACAACA
upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 5
gttaggag--tatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttatt--ttggactatgtatgtc----agGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
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gttggatgcttgttttgttttctttttctatttgcttaatcatgagttcgcaaaat-tctagagaaagacatttgagtaatgcacccatcctttccttgtagGCTGTTTACCACATGCCAACGACTGAAAATGATGCACCTACCGCTAGTATCCCATTGGCGCTCCAGAGTTTATTTTACAAGCTTCAGTATAATGATACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
atctaaa putative branch site (score: 3)
aaataccttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcagGCTGTGTACCATATGCCAACTACAGAGAATGATATGCCTTCAGGAAGCATTCCATTGGCTCTGCAGAGTTTATTTTATAAGCTCCAGTATAATGACAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG