Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgagaaatacacccagcttttaattgctttcatcctcagaaatagcaaaataatcttgattctaatgaatgtttgtttgatttacatctattgctatattttaaaccatggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgttgcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G065012_T03 (Zea mays), 3'ss of exon 8
gtaagcgagaaatacacccagcttttaattgctttcatcctcagaaatagcaaaataatcttgattctaatgaatgttt----gtttgatttacatctattgctatattttaaaccatggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgtt--gcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC
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------------------------------------------------------gtaattttcactcctttgttttatctgcagtttaatttgt-tctacaacaaaggtaaatctgttgtaaagtgttgtgtcgctcctttgctggtaatttctgcccccctccccttcaaacagACTAGCAGCGATTTCGATGCGAAGCCAATGGTCATGCTGTTGGGTCAATACTCCACGGGGAAAACAACATTCATAAAGCATTTACTAAAAACAAGTTATC
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 7
gtaagcgagaaatacacccagcttttaattgctttcatcctcagaaatagcaaaataatcttgattctaatgaatgtttgtttgatttaca-tctattgctatattttaaaccatggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgttgcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC
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gttagtaagtgattt------tatttatttggtttaattgagaaaacaagacaagctactttattttttgttt-catttgttaattcaataatctaatgac-cattatatataa-agagaaagatatacatttaggttatttattgattgttattcctttctcatttcagACAAATAGTGACTTTGATGCCAAACCTATGGTTTTGCTTTTGGGTCAATACTCAACTGGGAAAACAACATTTATTAAGCATATGCTTAAAAGCAGTTATC
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G46350.2 (Glycine max), 3'ss of exon 8
gtaagcgagaaatacacccagcttttaattgctttcatcctcagaaatagcaaaataatcttgattctaatgaatgtttgtttg---atttacatctattgctatattttaaaccatggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgttgcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC
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--------------------gtcagtaagttattttgt--ttagaaatgactagctactccagatttactatcacctttctttgtgcagtcatgt-tgttactatgttttaaat-atctacaaagatatacaattagtttctttattgattgtaattctttacatattgtagACAAATAGTGACTTTGATGCCAAACCAATGGTTATGCTTTTGGGTCAGTACTCAACTGGTAAAACAACATTTATCAAACATCTGCTTAAAAGTAGTTATC
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaagcgagaaatacacccagcttttaattgctttcatcctcagaaatagcaaaataatc-ttgattctaatgaatgtttgtttgatttacatctattgctatattttaaaccatggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgttgcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC
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------------------------------------------gtgagttgggcattgcttattggtgctcctatggcgttatttaagttccaaatactattgaattctaaactatatttgaccat------tgaactagttacttg-----------ttttttttcttagACTAACAGTGATTTCGATGCAAAACCTATGGTAATGCTTCTGGGTCAATACTCCACAGGAAAAACAACATTCATTAAGCATTTGCTTAAATCTACTTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgttgcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC
tgttgat putative branch site (score: 4)
atgatatataatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgagaaatacacccagcttttaattgctttcatcctcagaaatagcaaaataatcttgattctaatgaatgtttgtttgatttacatctattgctatattttaaaccatggacaatgatatataatgagcttatcacttgctgttgatgtgttatttgttgcagACAAATAGCGATTTTGATGCCAAACCTATGGTTATGCTTTTGGGTCAATACTCAACTGGAAAAACTACTTTCATTAAACATTTGCTGAAGAGTAGTTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA