Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
--------gtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
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attttaatttgaattgtctagggtctgaaatagttcaagccccta----atgactagagttgattattgatc-ttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 5
gtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatg----tatttatattgcaaatatt--ttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
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-aaaaaacataaagcagacagtg--cctggagtagttcctgcatcttagcttggtgactcatctgcttctgatgaccttactaaagtggcaaatcttgtttagGTACCCAAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAAGCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
gtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatat------tttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
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-aaaacattgctacaataggagagtctggaggtagt-tactgcatctttgcttg-gtgactccagcttctcatgaccttgctaaactgatatatcttgtttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG
upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5
gtaagtatctcacccttttgtttttcttaaaatccta-taaaaagtctaaacttgtatagtattcatttctaatgtatttatatt-gcaaat--attttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
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---------------------gtaagtgaaagttcaactacattgattctcatggttcattacctgcaccatggttcttaatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA
upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 5
gtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
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----gtaagtgaaagttcaacgacattgattgtcatatggttcatt---acctgcac--cacgggttcttaatatttgcaaatc-----cacttcagGTACCCTAATTTGAAGAGTGTAAAAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAA
upper sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 5
gtaagtat-ctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
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----gtatgtttacttccctgccatactta---tttaattatgattataggtttttata------actgctaatgagacttc--tgcttttgttttagATACCCAAATCTTAAGAGTGTGAGAGAACTTATTTACAAGAGAGGGTATGGAAAGCTAAACAAGCAGAGGACTGCTCTAACTGACAACTCCATCATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtctaaacttgtatagtattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
ttctaat putative branch site (score: 2)
tattcatttctaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA