Sequence
atgc intronic sequence ATGC exonic sequencegtagaatctatctgccagtgactcagctggtggaatccaaaaatgatgggggttcagtttgtctctccccttctctattcttgttacaagtattttgtcatacatttatctgtcattatgcaactctaattgtttcatgtagGTTGGGCCAGATGAGGAAGGAATAACCCATTACTGTTTAACCAGTACCGTTATGCTGTCATTGACTACAAATGATCAGTCATCAGGCACATTCAGTTTGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g01970.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G36400.1 (Glycine max), 3'ss of exon 5
-------------------------------------gtagaatctatctgccagtgactcagctggtggaatccaaaaatgatgggggttcagtttgtctctccccttctctattcttgttacaagtattttgtcatacatttatctgtcattatgcaactctaattgtttcatgtagGTTGGGCCAGATGAGGAAGGAATAACCCATTACTGTTTAACCAGTACCGTTATGCTGTCATTGACTACAAATGATCAGTCATCAGGCACATTCAGTTTGT
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gtaaagtatcattccatttataagactaaacatgataaatgcagatgtataatagtgact--atcaatagattgggaaactaa-aatatctctgtttagttctaatttttctgattcttttcttgcaagtttattt---cattaattcttagtcctctcattttttttgtta-atttagGTGGGACCAGAGGAAGAAGAAAACACCAATTATCGGTTAACCAGTACAGTTATGCTGACTCTGACTACAAATAATGAGTCATCAGGAACTTTCAGTTTAT
upper sequence: Vv18s0001g01970.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G15910.1 (Glycine max), 3'ss of exon 5
-------------------------gtagaatctatctgccagtgactcagctggtggaatccaaaaatgatgggggttcagtttgtctctccccttctctattcttgttacaagtattttgtcatacatttatct-gtcattatgcaactctaattgtttc-----atgtagGTTGGGCCAGATGAGGAAGGAATAACCCATTACTGTTTAACCAGTACCGTTATGCTGTCATTGACTACAAATGATCAGTCATCAGGCACATTCAGTTTGT
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gtaaagtatcattccatttataggactaaacatgataaatgcatatgtataatagtgactttcaatag-attgggaaactaaaatatctgtatttagttctaatttttttg--attcttttcttgcaagtttatttcattaattcatagtcctcattttttttgttaatttagGTGGGACCAGAGGAAGAAGAAAACACCAATTATCGGTTAACCAGTACAGTTATGCTGACTCTGACTACAAATAATGAGTCATCAGGAACTTTCAGTTTAT
upper sequence: Vv18s0001g01970.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G31170.1 (Glycine max), 3'ss of exon 5
--gtagaatctatctgccagtgactcagctggtggaatccaaa--aatgatggggg--ttcagtttgtc------tctccccttctctattcttgttacaagtattttg--tcatacatttatctgtcattatgcaa-----ctctaattgtttc----atgtagGTTGGGCCAGATGAGGAAGGAATAACCCATTACTGTTTAACCAGTACCGTTATGCTGTCATTGACTACAAATGATCAGTCATCAGGCACATTCAGTTTGT
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gtaaagtatcattccatttaagactaaacatgataaatgcagatgtataatagtaacttttaatacattgggaaacttaaacatctctatt-tagttctattttttctgattcttgcaagtttatttcattaattcatagtcctcccatttttttgttaatttagGTGGGACCAGAGGAAGAAGAAAACACCAATTATCGTTTAACCAGTACAGTTATGCTGACTCTGACTACAAATAATGAGTCATCCGGAACTTTCAGTTTAT
upper sequence: Vv18s0001g01970.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G08740.1 (Glycine max), 3'ss of exon 2
---------------------------gtagaatctatctgccagtgactcagctggtggaatccaaaaatgatgggggttcagtttgtctctccccttctctattcttgttacaagtattttgtcatacatttatct-gtcattatgcaactctaattgtttc-----atgtagGTTGGGCCAGATGAGGAAGGAATAACCCATTACTGTTTAACCAGTACCGTTATGCTGTCATTGACTACAAATGATCAGTCATCAGGCACATTCAGTTTGT
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gtaaagtatcattccatttataagactaaacatgataaatgcagatgtataa--tagtgactttcaatag-attgggaaactaaaatatctgtatttagttctaatttttctg--attcttttctagcaagtttatttcattaattcttagtcctcattttttttgttaatttagGTGGGACCAGAGGAAGAAGAAAACACCAATCATCAGTTAACCAGTACAGTTATGCTGACTCTGACTACAAATAATGAGTCATCAAGAACTTTCAGTTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtattttgtcatacatttatctgtcattatgcaactctaattgtttcatgtagGTTGGGCCAGATGAGGAAGGAATAACCCATTACTGTTTAACCAGTACCGTTATGCTGTCATTGACTACAAATGATCAGTCATCAGGCACATTCAGTTTGT
ctctaat putative branch site (score: 3)
ttgtttc CT-rich tract
atacatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagaatctatctgccagtgactcagctggtggaatccaaaaatgatgggggttcagtttgtctctccccttctctattcttgttacaagtattttgtcatacatttatctgtcattatgcaactctaattgtttcatgtagGTTGGGCCAGATGAGGAAGGAATAACCCATTACTGTTTAACCAGTACCGTTATGCTGTCATTGACTACAAATGATCAGTCATCAGGCACATTCAGTTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG