Sequence
atgc intronic sequence ATGC exonic sequencegtaattgtttcttcattttttttaattggtttaatttttatttgttcttaatgcagcagtgttagctcatgtcattttaatgattctttcattcaaatgtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g15120.1 (Oryza sativa), 3'ss of exon 6
gtaattgtttcttcattttttttaattggtttaatttttatttgttcttaatgcagcagtgttagctcatgtcattttaatgattctttcattcaaatgtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
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------------------------------------------------------------gtaagctt-tgtatcgccaaatgttttagcgtc--aatgca---acttccattct--------cgcccttcttattgccttaaaatttc-cagGTCATTGCATGTCTTGATGTTCGGTCAAATGATAGTGGGGATCTTGTGGTAACAAAAGGTGACCAGTATGATGTAAGAGACCATAGTAGTAGCAAAGAG
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G12920.1 (Glycine max), 3'ss of exon 9
gtaattgtttcttcattttttttaattggtttaatttttatttgttcttaatgcagcagtgttagctcatgtcattttaatgattctttcattcaaatgtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
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-------------------------------------gtaatagtcatggaaatcctcttgt-gctttaaattagttaatgtgttcttcgcctctagggtgc--attcattattttga-----tttcctgacaaa--acattgtttat-taagGTGATTGCTTGTCTTGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G10460.1 (Glycine max), 3'ss of exon 9
gtaattgtttcttcattttttttaattggtttaatttttatttgttcttaatgcagcagtgttagctcatgtcattttaatgattctttcattcaaatgtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
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-------------------------------------gtaatagtcatggaaatcctcttgt-gctttaaattagttaatgtgttcttcgcctctggggtgc--attcattattttga-----tttcctgacaaa--acattgtttat-taagGTGATTGCTTGTCTCGATGTGAGAACAAATGATAAGGGGGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAACATACAAAAGAGAATGAG
upper sequence: Vv19s0090g00810.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G26900.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaattgtttcttcattttttttaattggtttaatttttatttgttcttaatgcagcagtgttagctcatgtcattttaatgattctttcattcaaatgtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
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---------------------------gtaagaagtttgtcctgttattattgaaagtctgcctcctt-tgcaacattgct-atctttgctcttaactattctggtaggcagtttt-------tctaatgatattttgt----tttcctttagGTGATTGCTTGTCTTGATGTGAGGACGAATGATAAAGGAGATCTCGTAGTTACTAAAGGGGATCAGTATGATGTGAGAGAGCAATCTAATGAAAACGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
tgctaaa putative branch site (score: 2)
ttgtttctctc putative PPT
tattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgtttcttcattttttttaattggtttaatttttatttgttcttaatgcagcagtgttagctcatgtcattttaatgattctttcattcaaatgtatttgtttgctgtctagagaaggcatcatgctaaatggtattgtttctctcagGTAATTGCTTGTCTTGATGTGAGGACAAATGATAAAGGAGACCTTGTTGTAACCAAAGGAGACCAGTATGATGTAAGAGAAAATACAGGAGAGAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA