Sequence
atgc intronic sequence ATGC exonic sequence...atgtgtaacttatttaccggttgaaatggtgagttttcatttgagttcttaatttctgttttgtctcatgcttcctgtggcaaaatcttgtctattccagGATGATACTGCATTTGAGAAACAAAGTGCCTTGTTTGCTTTGGCAATATCAGACATTGTGCTGATAAACAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g41170.1 (Oryza sativa), 3'ss of exon 3
atgtg---taacttat-ttaccggttgaaatgg--tgagttttcatttgagttcttaatttctgttttgtctcatgcttcctgtggcaaaatcttgtctattccagGATGATACTGCATTTGAGAAACAAAGTGCCTTGTTTGCTTTGGCAATATCAGACATTGTGCTGATAAACAT
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atgtgcctttacatgtattacgagtttaagcaacttgagggat-acatgagttgtt--tcttcagttccttttctgatacctgtgtct---tctgccccattttagGACGACACTGCATTTGAGAAGCAAAGTTCGTTGTTTGCTCTTGCAATTTCAGACATAGTTCTAATTAACAT
upper sequence: Vv10s0116g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 3
-------atgtgtaacttatttac-cggttgaaatggtgagttttcatttgagttcttaatttctgttttgtctcatgcttcctgtggcaaaatcttgtctattccagGATGATACTGCATTTGAGAAACAAAGTGCCTTGTTTGCTTTGGCAATATCAGACATTGTGCTGATAAACAT
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atttttactggcaaatgtacctgttctctttctttgttgtatgtacattagaactcactattgccttgctttctttttcttttttaaatataactct--------cagGATGACACTGCTTTTGAGAAACAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACAT
upper sequence: Vv10s0116g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G13380.2 (Glycine max), 3'ss of exon 3
atgtgta---acttatttaccggttgaaatggtgagttttcatttgagttcttaatttctgttttgtctcatgcttcctgtggcaaaatcttgtctattccagGATGATACTGCATTTGAGAAACAAAGTGCCTTGTTTGCTTTGGCAATATCAGACATTGTGCTGATAAACAT
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atttttaccgacaaatgcacctgttctctttctttgttgt-atgtacattagaactcactattgccttgctttctttttcttttttaattataactct--cagGATGACACTGCTTTCGAGAAACAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACAT
upper sequence: Vv10s0116g00810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G45160.1 (Arabidopsis thaliana), 3'ss of exon 4
-atgtgtaacttatttaccggttgaaatggtgagttttcatt-tgagttcttaatttctgttttgtctcatgcttcctgtggcaaaatcttgtctattccagGATGATACTGCATTTGAGAAACAAAGTGCCTTGTTTGCTTTGGCAATATCAGACATTGTGCTGATAAACAT
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tatctttccgatacttatacatatacttgatccttttactttatgtgtgtctagcatttttcttatt--attctttttgtcaatggctcatgtgtttttcagGATGACACTACATTTGAGAAACAAAGTGCCCTGTTTGCTATAGCTGTTGCCGATATTGTACTGATAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttaatttctgttttgtctcatgcttcctgtggcaaaatcttgtctattccagGATGATACTGCATTTGAGAAACAAAGTGCCTTGTTTGCTTTGGCAATATCAGACATTGTGCTGATAAACAT
tcttaat putative branch site (score: 3)
tcttgtct putative PPT
aaaatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtgtaacttatttaccggttgaaatggtgagttttcatttgagttcttaatttctgttttgtctcatgcttcctgtggcaaaatcttgtctattccagGATGATACTGCATTTGAGAAACAAAGTGCCTTGTTTGCTTTGGCAATATCAGACATTGTGCTGATAAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - tggtgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaaaa