Sequence
atgc intronic sequence ATGC exonic sequence...cttgctcattctaaatacaaattgtgaaagtgaatatgtgaattcaactaattggatggttctgattgtaacatattgagttcattttctctacactcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g14790.1 (Oryza sativa), 3'ss of exon 5
cttgctcattctaaatacaa-attgtgaaagtgaatatgtgaattcaactaattggatggttctgattgtaacatattgagttcatt----ttctctacactcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
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-tcagaaatccaagcttcattattctgcccggaaaccttt---tttttttccctgtacaact-taataatgttttgtggtaatcattatgcttcattttgtttagAATGAAGGCTTGGGGAAGCGACTTGCTCATGGATACCCATTTTTGGAGGCTGAAGTAGCATACTGTGCTCGCCACGAGTACTGTGAATCTGCTGTGGACT
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G446108_T03 (Zea mays), 3'ss of exon 5
cttgctcattctaaatacaaattgtgaaagtgaatatgtgaat-tcaactaattggatggttctgattgtaacatattgagttcattttctctaca-----ctcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
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--tgcttgt-ctaaa---aaaatgtgatacctattttttggccaccaatatatctgattgcacatgatatgtcgtcttcatagtatttgtacttcaatgtttttagAACGAAGGCTTGGGAAAGCGCCTTGCTCATGGATACCCATTTTTGGAAGCTGAAGTAGCATACTGTGCTCGTTATGAGTACTGTGAATCTGCCGTGGATT
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G28000.1 (Glycine max), 3'ss of exon 5
cttgctcattctaaatac-aaattgtgaaagtgaatatgtgaattcaactaattggatggttctgattgtaacata-ttgagttcattttctctacactcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
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-tttttctatctgaacactgtgcttttgcaatttatacaagt-tttagtcagtttcatggtttcatcaatgccaaggtttatattatatattttgtatgcagAATGAAAATTTGGGCAAGCGACTTGCCCATGGTTACCCTTTTTTGGAGGCTGAGGTGGCCTACTGTGCCCGTCATGAATATTGTGAATCTGCGATTGACT
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G32390.1 (Glycine max), 3'ss of exon 5
cttgctcattctaaatacaaattgtgaaagtgaatatgtgaattca-actaattggatggttctgattgtaacatattgagttcattttctctacactcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
| | || || || || | ||| | || | | | | | | |||| | || || |||| | | | || ||||| || | || || || |||||||| || ||||||| ||| ||||| |||||||| |||||||| |||||||| || |||||||||||| | ||||
-gttaagaggcttcatgcatgttctaggagttctagtctgcttcagtatttcgtaagtattaagaattgattctgttttttttttttttttttctgtttagAATGAAAATTTGGGTAAACGACTTGCCCACGGTTACCCTTATCTGGAGGCAGAAGTGGCGTACTGTGCTCGTAATGAATATTGTGAATCTGCTATTGATT
upper sequence: Vv13s0019g04730.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G35170.1 (Glycine max), 3'ss of exon 5
--cttgctcatt--ctaaatacaaattgtgaaagtgaatatgtgaattcaactaattggatggttctgattgtaacatattgagttcattttctctacactcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
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tctatgttaagaggcttcatgcatgttctaggagttctagtctgc-ttcagc--atttcaca-tcacaactattaaaaattgattctgtattttttctgtttagAATGAAAATTTGGGTAAACGACTTGCCCACGGTTACCCTTATCTGGAGGCAGAAGTGGCCTACTGTGCTCGTAATGAATATTGTGAATCTGCTATCGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactaattggatggttctgattgtaacatattgagttcattttctctacactcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
ttgtaac putative branch site (score: 2)
ttcattttctctac putative PPT
taacatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgctcattctaaatacaaattgtgaaagtgaatatgtgaattcaactaattggatggttctgattgtaacatattgagttcattttctctacactcagGATGAACATCTAGGGAAGCGGCTTGCCCATGGATACCCTTTTCTAGAGGCTGAAGTGGCATACTGTGCCCGTAATGAGTACTGTGAATCTGCTGTAGATT
cttgctc
- - - - - - - atacaaa
- - - - - - - - - - - - - aaagtga
- - - - - - - - - - - - - - - - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - tggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg