Sequence
atgc intronic sequence ATGC exonic sequence...ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os08g05870.1 (Oryza sativa), 3'ss of exon 4
ctcttctatcaattaagtcctgaattccttagc-aagatttatttttctctgagcattgt-catttcatcac--cccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
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----gacacttgcctccttttctatctgtgaactaaaatttaatatcttgatagtgtgaagcatttaattgcaacacattgcttttcgtcattttcatcactagGTTAGTCATCACCCCATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGGCAGTCAA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 5
ctcttctatcaattaa-gtcctgaattccttagcaagatt-tatttttctctgagcattgt-catttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
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taaaagtggcagacactgttctga--tgccaggcacattaatattcttctctacatttcacacaacatatgagttaatttgttagt-ttattcttgtcaccagGTTAGTCATCATCCGATGGTCATGGCATGCCATTGTGAAGGGAAAGGTTGGAAATTTTGGGGTGACAGCAATCTAAAGAGCAAATTTTGGGGGCAGTCCA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G402653_T03 (Zea mays), 3'ss of exon 4
---ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
| | | | | | | ||| | | | || ||| || | | | ||||||| | | || || | | || ||||||||||||| |||| || ||||||||||| |||||||| || || ||||||||||||| ||||| || || | | || |||||||||| ||||
tcgtttacatttttactgatcatccatttcttaattttgtggtactttgaattggagactttaatttcattgcattgctattcaacatt-tccacc--aatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G875564_T01 (Zea mays), 3'ss of exon 5
--ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctg-agcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
| | ||| || | || | || ||| | ||| | || | | | | || | || | ||| ||| | ||||||||||||| |||| |||| || || ||||||||||| |||||||||||||| |||| ||||| || || | || || ||||| | | |||
aatcagtatttcagttgaaa---aaaataaatattgctgtttcatgacctcagtagaaactatagctggagttcatgttatgatgctgtatttgttgcgatagGTTAGTCATCATCCAATGGTCATGGCTTGTCATTGTGAAGGAAAAGGGTGGAAATTTTGGGGAGACAGCAATGTAAAGAGCAAGTTCTGGGGGCAAACAA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 6
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtg-----ttgtttat---tgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
| | | | | | || ||| | | | || ||| | | || | || |||| || |||| |||||||||| ||||| || ||||| || |||||||||| |||||||||| ||| |||||||| ||||||||||||||| | || |||| ||||||||| | ||||
--------tttggtggggttttactgttttctcaaacaatgtgcaggtaagacaattaacctgccaatatttactgttttctcaaacaactgattatgtgtgaaacagGTGAGTCACCATCCAACTGTCGTTGCCTGCCACTGTGAAGGTAGAGGTTGGAAATTTTGGGCTGACAGTAACATTCGGTCAAAGTTTTGGGGAAGGTCAA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 5
ctcttctatca-attaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtgttgtttat---tgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
||| ||| | || || | ||| |||| || ||| | | | ||| | | || | | | || | |||| |||||||||| ||||| || ||||| |||||||||||||| || ||||||| ||| ||||| || ||||||||||| ||| | | |||| ||||||||| | ||||
--attcgatcttagtatgtattt--ttctctagctagtcttaatatgtgcaattcatcagcctgccaatatattcgatattcgctgacattatgtgtgaaacagGTCAGTCACCATCCAACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACAGCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 6
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtg-----ttgtttat---tgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
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--------gtggtcctatcatacgctcagttgcatacaatgtgcaggcatgacaattaacctgccaatatttactgttctctcaaacaactgattatgtgtgaaacagGTGAGTCACCATCCAACTGTCGTTGCCTGCCACTGTCAAGGTAGAGGTTGGAAGTTTTGGGCTGACAGTAACATTCGGTCAAAGTTTTGGGGAAGGTCAA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G03420.2 (Glycine max), 3'ss of exon 7
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcac----cccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
||| ||| || || | || |||| || ||| | | | ||| | | || | | | || | || | | | ||||||||| ||||| || || || |||||||||||||| || ||||||| ||| ||||| || |||||||||| ||| | | |||| ||||||||| | ||||
-aattcgatcttgtatgtattt--ttgtctagctagtcttaatatgtgcaattcatcaacctgccaatatatttcacgttccctgacattatgtgt-gaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G12460.1 (Arabidopsis thaliana), 3'ss of exon 5
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttg--tgttgt-ttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
|| | || | | | | | | || | |||| ||| | | | || || || || | | |||| | | || ||||||| || || |||||| | || ||||||||||| ||||||||||||||||| ||||||| |||| ||||| || | || |||||||| |||| |
gatttaaaaaaaatgaaacata---tggagaaaaaaaattatgagaatcttttcttaagaagtttggcatataattcgttagggtattgtactctcataatagGTTAGCCACCATCCAACAGTTATCGCCTGCCATTGCGAAGGTAAAGGGTGGAAGTTCTGGGGCGACACAAACCTCCGGTCGAAGTTTTGGGGGAGATCGA
upper sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 5
--ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
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gtatgtcacacaaattttaactcaaatttag-aatgtgatgaacataattgttagaatctttac--caagactagagaatatcattcttttggttataatagGTCAGTCACCATCCAACTGTTATCGCCTGCCACTGTGAAGGTAAAGGGTGGAAGTTTTGGGGTGACACTAACCTCAGGTCAAAGTTTTGGGGGAGGTCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctgagcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
tttattgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
- - -ctatcaa
- - - - - - - - -tcctgaa