Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttatctggtttcatggccatatgttctctgattgtgatgtgttggttctggacttaaagcatattactcacttatctcttaaatgatagcagttctccatgcattttttctgattttctttggataaatagtatctcttactttgagtttttatctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g54170.1 (Oryza sativa), 3'ss of exon 2
gtaatgttatctggtttcatggccatatgttctctgattgtgatgtgttggttctggacttaaagcatattactcacttatctcttaaa--------tgatagcagttctccatgcattttttctgattttctttggataaatagtatctcttactttgagtttttatctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
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gtatgctttttccaatatatctctttcttttcctagtttgtcttatctta--tgtaatctacgcaccaatgatttggtggcatcgcagaaagccagttcaagctaaatgtgtgtgtaccatattaattcctctatgcttttacaatgactaa-agtttatgttcacgaactgcagGAAACCAAACAATTGAGAGGCTTCAACAAATATTTTCTTCATCAAGCCAAACATATGGTGGCTTGACACTGGATTTACATTGTAATCGATTTGGTCCAAC
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g54280.1 (Oryza sativa), 3'ss of exon 12
gtaatgttatctggtttcatggccatatgttctctgattgtgatgtgttggttctggacttaaagcatattactcacttatctcttaaatgatagc-agttctccatgcattttttctgattttctttggataaatagtatctcttactttgagtttttatctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
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gtatgctttttccagtatatctgtttcttctcctagtttgtcttatgtaatctatgcaccaatgatttggcgacatcacagaaagccagttcaagctaaatgtgtgtgtatcatattaattcctctatgctcttacaatgactaa-agtttatgttcacgaactgcagGAAACCAAACAATTGAGAGGCTTCAACAAATATTTTCTTCATCAAGCCAAACATATGGTGGCTTGACACTGGATTTACATTGTAATCGATTTGGTCCAAC
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G15560.1 (Glycine max), 3'ss of exon 12
gtaatgttatctggtttcatggccatatgttctctgattgtgatgtgttggttctggacttaaagcatattactcacttatctcttaaatgatagcagttctccatgcattttttctgattttctttggataaatagtatctcttactttgagttttta-tctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
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----------------------------------------------------------tttgaaaactaaaacc-----atgaaaagaattaaaatagataaaaatataatgtg---ggaatctattgaatagttttagcctttta--ttgagttgataatattttagGAAATGGAACAATCGAGAAACTGCAAAAGGTGTTCACAGCATCAGGACAATCTTATGGTGGCTTAACTCTGGATTTGCATTGCAATCGATTTGGCCCAAC
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G32290.1 (Glycine max), 3'ss of exon 12
gtaatgttatctggtttcatggccatatgttctctgattgtgatgtgttggttctggacttaaagcatattactcacttatctcttaaatgatagcagttctccatgcattttttctgattttctttggataaatagtatctcttactttgagttttta-tctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
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-------------------------------------------------gtttgaaaactaaaaccatgaaaagaattaa------aatagataaaaaataacgagggaatctattaaatagttttag-----------cctttta--ttgagttgataatattttagGAAATGGAACAATCGAAAAACTTCAAAAGGTGTTCACAGCATCAGGACAATCTTATGGTGGGTTAACTCTGGATTTGCATTGCAATCGATTTGGCCCAAC
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G18730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatgttatctggtttcatggccatatgttctctgattgtgatgtgttggttctgg-acttaaagcatattactcacttatctcttaaatgatagcagttctccatgcattttttctgattttctttgga--taaatagtatct-cttactttgagtttttatctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
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---------------------------------------gtgaaa-gttgcctctgacgtcttacttaatttaatgagctgacc--taagtga-gttagttggttatgcatagg----gaactactaggaaattcagaagtgttaatttccatcgtctcattggttgttagGGAATGGAACAATGGAGAAATTGAAACAACTTTTTGCCTCATCAAGCCAGATGTATGGTGCTTTAACTTTGGATTTGCACTGCAATCGATTTGGTCCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctgattttctttggataaatagtatctcttactttgagtttttatctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
ctcttac putative branch site (score: 3)
tttttatctccc putative PPT
ataaatagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttatctggtttcatggccatatgttctctgattgtgatgtgttggttctggacttaaagcatattactcacttatctcttaaatgatagcagttctccatgcattttttctgattttctttggataaatagtatctcttactttgagtttttatctcccagGGAATGGAACAATGGAGAAACTTCAACAAGTATTCATATCATCAGGCCAAAAATATGGTGGCTTGGCTTTGGATTTGCACTGCAATCGATTTGGTCCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG