Sequence
atgc intronic sequence ATGC exonic sequencegtatcatgaaatcattttcatgtttccatcctgttactaaaatttaatcaagcactgctgttcttttagatgtcttcgcttatcttcttctcctatttctccccatatctgttgattatttgaggttctgtgaaatcaaatgcagtttttagtaacttgttgtgtactcgttctcagTCTGGACCTGATGAAAGGAGCATTCCTGGAAATACCATTGCAGTTAATGCAGAGATGCCATTCAATGGACTGACAACTTTTGGAGGGGCATTTTTATCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0516g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G01310.1 (Glycine max), 3'ss of exon 10
gtatcatgaaatcattttcatgtttccatcctgttactaaaatttaatcaagcactgctgttcttttagatgtcttcgcttatcttcttctcctatttctccccatatctgttgattatttgaggttctgtgaaatcaaatgcagtttttagtaacttgttgtgtactcgttctcagTCTGGACCTGATGAAAGGAGCATTCCTGGAAATACCATTGCAGTTAATGCAGAGATGCCATTCAATGGACTGACAACTTTTGGAGGGGCATTTTTATCAA
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---------------------------------gtaccataatcttcttttttctagtactggctttgaaaattgt----taatttgttcccttgttgttttc---atttgtgctttgcttgtgctcatggaggttcaaatctgaattt-----actttt-----acttgt----agTCTGGTCCTGATGAAAGGAGCATTCCTGGAAATACAATAGCTGTTGATGCTGATATGCCTTTTAGTGGACTTACAACTTTTGGTGGTTCATTTTTGTCGA
upper sequence: Vv00s0516g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G11970.1 (Glycine max), 3'ss of exon 9
---------gtatcatgaaatcattttcatgtttccatcctgttactaaaatttaatcaagc----actgctgttcttttagatgtcttcgcttatcttcttctcctatttctccccatatctgttgattatttgaggttctgtgaaatcaaatgcagtttttagtaa-----cttgttgtgta-ctcgttct---cagTCTGGACCTGATGAAAGGAGCATTCCTGGAAATACCATTGCAGTTAATGCAGAGATGCCATTCAATGGACTGACAACTTTTGGAGGGGCATTTTTATCAA
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gtataagaagtttcattc--ctgttctagtattgctgtattgcctctggaagtcaataaaatccaaatagaaaagtatttatgtgtgataaatagttgaaatcatgatgttattgttaccattttttttctttctaaattctgtcaatttgtgttctgatcgtgctcatggtgcttgctgcaaaactctttttatttagTCTGGACCTGATGAGAGAAGTATTCCTGGAAATACTATTGCTGTTGATGCTGACATGCCTTTTGGTGGCCTGACAACATTTGGAGGTTCATTTTTATCAA
upper sequence: Vv00s0516g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G39450.1 (Glycine max), 3'ss of exon 10
gtatcatgaaatcattttcatgtttccatcctgttactaaaatttaatcaagcactgctgttcttttagatgtcttcgcttatcttcttctcctatttctccccatatctgttgattatttgaggttctgtgaaatcaaatgcagtttttagtaacttgttgtgtactcgttctcagTCTGGACCTGATGAAAGGAGCATTCCTGGAAATACCATTGCAGTTAATGCAGAGATGCCATTCAATGGACTGACAACTTTTGGAGGGGCATTTTTATCAA
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-------------------------------------------------gtaccataatcttcttttttctagtactggctttgaaaattgttaatttgttcccttgttgttt--tcatttgtgctt-tgcttgcgctcatggaggttcaa--agctgaatataattttacttgtagTCTGGTCCTGATGAAAGGAGTATTCCTGGAAATACAATAGCTGTTGATGCTGATATGCCGTTTAGTGGCCTTACAACTTTTGGTGGTTCATTTTTGTCGA
upper sequence: Vv00s0516g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G01160.1 (Glycine max), 3'ss of exon 8
gtatcatgaaatcattttcatgtttccatcctgttactaaaatttaatcaagcactgctgttcttttagatgtcttcgcttatc--ttcttctcctatttctccccatatctgttgattatttgaggttctgtgaaatca------aatgcagtttttagtaacttgttgtgtactcgttc---tcagTCTGGACCTGATGAAAGGAGCATTCCTGGAAATACCATTGCAGTTAATGCAGAGATGCCATTCAATGGACTGACAACTTTTGGAGGGGCATTTTTATCAA
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gtaaaa-gaagtttcattcttgttctcatattgcctctggaagtcaataaagtccaaatagaaaaatatttatgtgtgataaatagtagaaatcatgatgttattgttaccatttttttcttctaaattctgtcaagttgtgttttgattgtgctcatggtgcttgcttcaaaactctttttatttagTCTGGACCTGATGAGAGAAGTATTCCTGGAAATACTATTGCTGTCGATGCTGACATGCCTTTTGGTGGCCTGACAACATTTGGAGGTTCATTTTTATCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggttctgtgaaatcaaatgcagtttttagtaacttgttgtgtactcgttctcagTCTGGACCTGATGAAAGGAGCATTCCTGGAAATACCATTGCAGTTAATGCAGAGATGCCATTCAATGGACTGACAACTTTTGGAGGGGCATTTTTATCAA
tagtaac putative branch site (score: 1)
ctcgttctc putative PPT
tttttagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcatgaaatcattttcatgtttccatcctgttactaaaatttaatcaagcactgctgttcttttagatgtcttcgcttatcttcttctcctatttctccccatatctgttgattatttgaggttctgtgaaatcaaatgcagtttttagtaacttgttgtgtactcgttctcagTCTGGACCTGATGAAAGGAGCATTCCTGGAAATACCATTGCAGTTAATGCAGAGATGCCATTCAATGGACTGACAACTTTTGGAGGGGCATTTTTATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG