Sequence
atgc intronic sequence ATGC exonic sequence...aggacctgctttttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
aggacctgctttttcaatg-agcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatat--atgttccatcttaaaattgtggttgt-agAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
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atatgctacacctatgctggagcagttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctt----tttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
aggacctgctttttcaatg-agcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatat--atgttccatcttaaaattgtggttgt-agAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
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atatgctacacctatgctggaacagtttttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctt----tttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
---aggacctgctttttcaatgagc--attgcatgtagcctaacaacagcgtaaaat-tgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA-
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cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttga----cgcaacc--agAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
---aggacctgctttttcaatgagc--attgcatgtagcctaacaacagcgtaaaat-tgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
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cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtgcttctcatatttgtatgccctccttttga----cgcaacc--agAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 4
----aggacctgctttttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
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tcccgaagcttacatttt---tgtgttatttaaatttctgaacatcaa-accttgtgagattattaattgtaagaataattttatcacattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCATTTGCTTCGTTTAGA
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 5
---aggacctgctttttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaaca-atgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
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cccgaagcttacattttta-tgtgatttaaattt--ctgaacattaa-accttgtgagcttattaatgtgtaagaataattttatctcattttgtttgttgtagAGACCACAACTAGTAAAAGGAAACATGCAACTCTTCTCTGTGGATCAGCAACGTAGTCAGGCTCTTGAAGCACATGCTGCCTCGTTTGCTACATTTAGA
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 5
aggacctgctt-tttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
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ttaattttcttgcataaattaattggctaattatgtttttttgggggtgtgttaaatttcctatttgttgga-gtgatggaattttatttgttggttacagAGACCACAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAGCAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 5
aggacctgctttttcaatgagcattgcatgtagcctaacaacagcgtaa--aattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
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-ttttttatttttttttttttttttgggggggggggggggggggggttgttgttaaatttcctatttgttggagtgatgacattttatttgt-tggttacagAGACCGCAACTTGTAAAAGGAAATATGCAACTCTTCTCTGTGGATCAACAGAGGAGCCAGGCTCTTGAAGCACATGCTGCCTCATTTGCCACATTTAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaaattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
ttttaac putative branch site (score: 2)
attgattttttaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggacctgctttttcaatgagcattgcatgtagcctaacaacagcgtaaaattgattttttaacaatgatatatgttccatcttaaaattgtggttgtagAGGCCACAACTCGTCAAAGGGAATATGCAACTTTTCTCAGTGGATCAGCAACGTAGTCAGGCCCTTGAAGCACATGCTGCATCATTTGCCTCATTTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - cctgctt
- - - - - - - caatgag
- - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - aacaaca
- - - - - - - - - - - - - - - - - - - - - - - - aaattga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaatga