Sequence
atgc intronic sequence ATGC exonic sequencegtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaatcttttgaagtgagtttaagtggtggtttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 6
gtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaatcttttgaagtgagtttaagtggtgg-----tttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
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-----gaccaaatagaccaaattaactatcaatatccatatttcatatacgttagctactaggcattgtgttaagctatggaactgattttgtttgttttaacagTTTCCCAATCGATGACCAAATGAACATGAAATCTGTCGTAGAGTATTTCAAGGAAATGTATGGCTTCACCATTCAGCATCCCCATCTTCCCTGCCTTCAG
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 5
gtactgatattttgtattttgccttcttttaattgtcct--ttttttttttttttaatcttttgaagtgagtttaagtggtggtttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
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-tctaagtcaccttagcagtgaatacattcgacaattaaaagtatatgatgatcaagggttgttaaatcaccttagcctg-atttttatctaattttcacagTTTCCCAATTGATGAACAAATGAATATGAAATCTGTCGTGGAGTACTTCAAGGAAATGTATGGTTTCACCATTCAGCATCCTCATCTTCCTTGCCTTCAG
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 6
gtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaatcttttgaagtgagtttaagtggtggtttcttctcat--tccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
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-----------gtatgtcttttttaactttagaaggttgaacttttacatttta--cacatgccctcttttgaaatgattgtctcttttccccattgaacagTTTCCCTCTTGATGACCAAATGAACATGAAATCAGTAGTTGATTATTTTCAAGAAATGTATGGATTTACAATCAAATATTCTCATCTACCTTGCCTTCAA
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 6
gtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaatcttttgaagtgagtttaagtggtggtttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
||| || || | | ||||| || | || |||||| | | | | ||| || | || | |||| || | | ||||||||||| || |||||| ||||||||||||||||||| ||||| |||||||| || |||||||||| ||| || ||||||||||||||| ||||| |||
gta-tggctttgtaaactttgcattacaaaatgaactctaaattttttagatatgacctctcaag-------aaattgt--tctcttttcctcctaacagTTTCCCCGTCGATGAGAAAATGAACATGAAATCAGTAGTTGATTACTTTCAAGAAATGTATGGATATACAATCATATATTCTCATCTACCCTGCCTTCAA
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 6
gtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaat-cttttgaagtgagtttaagtggtggtttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
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gta-tggctttgtaaattttgcattacaa-aatggacctcaatttttttagataggacctctcaag-------aaatgat--tctcttttcctcctaacagTTTCCCCGTCGATGAGAAAATGAACATGAAATCAGTAGTTGATTACTTTCAAGAAATGTATGGATATACAATCATATATTCTCATCTACCCTGCCTTCAA
upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G21450.1 (Glycine max), 3'ss of exon 7
gtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaa----tcttttgaagtgagtttaagtggtggtttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
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---------gtatgtcttttaactttagctggctgaacttttacaatttacacaaatcctcctttgaaatgattttctcttctttttttctccccattgaacagTTTCCCTCTCGATGAGCAAATGAACATGAAATCAGTAGTTGATTATTTTCAAGAAACGTATGGATTTACTATCAAATATTCTCATCTGCCTTGTCTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttaatcttttgaagtgagtttaagtggtggtttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
ttttaat putative branch site (score: 3)
tttcttctcattcc putative PPT
tttaatcttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgatattttgtattttgccttcttttaattgtcctttttttttttttttaatcttttgaagtgagtttaagtggtggtttcttctcattccaacagTTTCCCAGTTGATGAGCAAATGAACATGAAATCAGTTGTTGAGTACTTTCAGGAGATGTATGGATTTACCATTCGATATTCTCATCTACCTTGCCTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG