Sequence
atgc intronic sequence ATGC exonic sequencegtatcttgttctctgcagctctgatctcctatttccttaattcatagatgccccatcagaattgtgaattacatctcgtgtccattccttttactgatgggttcctcatgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 4
gtatcttgttctctgcagctctgatctcctatttccttaattcatagatgccccatcagaattgtgaattacatctcgtgtccattccttttactga-tgggttcctcatgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA
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----------gtattgatgtttgaactaaaattaccttaa---------gttcctttagattttccaattg------gtcgccgtcctatttgctgagcatattttatatgcagGATGAATTTGATGAAGAAGATGAGATGAACATGTACCGTGTACAAGGAACTCTTAGAGAGTGGGTCACAAGAGATGAAGTCCGCCGCTTTATCGCAAAGA
upper sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 3
gtatcttgttctctgcagctctgatctcctatttccttaattcatagatgccccatcagaattgtgaattacatctcgtgtccattccttttactgatgggttcctcatgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA------
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gtactatctactttgtgatttt--tttcctttttcttttgttaat--------tatctactttgtgatttttaaagtttcaccattgattttatta----------cataaaatgtag-
upper sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 3
gtatcttgttctctgcagctctgatctcctatttccttaattcatagatgccccatcagaattgtgaattacatctcgtgtccattccttttactgatgggttcctcatgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA------
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gtattatctactttgtgattttttttttctttttaaatattttaaagtttcgtcattg--attttatttcacaattaacatgggtac---------atgga------atgtagGATGATTTTGATGATGG------ATACGAGATGTATCATGTTCAAGGTACACTTAGAGAGTGGGTTACAAGAGATGAAGTGCGCCGCTTCATAGCCAGGAAATTCA
upper sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatcttgttctctgcagctctgatctcctatttccttaattcatagatgccccatcagaattgtgaattacatctcgtgtccattccttttactgatgggttcctca-tgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA
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------------------gtatgagtatgaatctttctgcgtcatgg------tgctag----gtgtattactactagtgtctaatggtt-----ggtgaatttcttaatatagGATGATAATGATGATGAAGCAGAGTTTGAGATGTATAGGATTCAAGGAACTCTGAGGGAATGGGTTATGAGAGATGAAGTGAGACGGTTTATTGCTAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattgtgaattacatctcgtgtccattccttttactgatgggttcctcatgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA
tactgat putative branch site (score: 2)
ttcctcat putative PPT
aattacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttgttctctgcagctctgatctcctatttccttaattcatagatgccccatcagaattgtgaattacatctcgtgtccattccttttactgatgggttcctcatgcagGATGATGATGATGATGATGGTGAGTTCGAGATGTACCGTGTTCAAGGAACGCTAAGGGAATGGGTTACTAGAGATGAAGTGCGCCGCTTCATTGCAAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG