Sequence
atgc intronic sequence ATGC exonic sequencegttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 9
gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttat---ttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
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------------------------------gt-atacaccgcttcattgtttgcatcaataatattgtcttactcaaattgatatatcttcttttttacaaaaactgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA
upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
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----------------------gtatacaccacttcgttgtttgcatcaataatattgtt-ttactcaaattgata------tatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 9
----gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
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gtatgttctcaaaacttat-gtttttctaatcagg--atgtgagcaaatataatccatttaggtcaggtagaaacagac------ttgctgtgtgtttccattt-ttgcagGACTTTGGTGATAGTATTCCGGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
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gtatgctctcaaaacttctgtttttgtaatcaggaagtga-gcaaatataatccatt-taggtataaaca-----gacttgctgtgt-----tcccattt-ttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG
upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 8
gttcactctggttattgttgacttagttaagtgatgctgatatgca-tggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
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-------------------------gtgggtttcagatgatattcagtataaaaccacaatatctatg-caacattgattcactgttaaatgttctccaaccttgcagGACTTTGGTGATAGTATTCCCGGACATGGCGGAATTACAGATAGAATGGATTGTCAG
upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 9
gttcactctggttattgttgacttagttaagtgatgctgatatgcatgga--aagcttcactgttgttgacactgttggttttttattt--ctttttccgat--------ttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
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---------------------gtcagt-aatcaatacctccaaatatgagccaagcttcactttccat-acgcatctaacctctaacaaaaccttgcttgacaaaaaccgtaatcgcagGACTTTGGTGATAGTATTCCAGGACATGGTGGAATCACAGATAGAATGGACTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
tgttgac putative branch site (score: 3)
ttttttatttcttttt putative PPT
ttttttatttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA