Sequence
atgc intronic sequence ATGC exonic sequence...gcttctgaaaacatttttttttcaacttccattgatctttcattgcatcaactttgcacttgaacactatctgattagtactgtcagtataaattttcagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0030g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 3
------gcttctgaaaacatttttttttcaacttccattgatctt--tcat-tgcatcaactttgcacttgaacactat---ctgattagt--actgtcagtataaatttt------cagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAG
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gttatgtcatctgttca-gtttcatgcctaactactattgtgcccgatcatctttattctgttcgtgtaagaatgcaaagcactgcaccgttgacttacagtatgtaattcacataccagGTTTCATCTTTACAAGGAGAACAAGGACACCCAAGAGGCACTAGGAAAGATAGGCAAGATGCTAGGGCTTCAG
upper sequence: Vv14s0030g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 4
----gcttctgaaaacatttttttttcaacttccattgatctttcattgcatcaactttgcacttgaacactatctgattagtactgtcagtataaattttcagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAG
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agccagtcatttttgcattttttatttggt---catgtcattttcctgttttttatattgtatttgtttgtcaactgaatgtttctgccaatgtaa-tttctagGTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAG
upper sequence: Vv14s0030g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 4
-gcttctgaaaacatttttttttcaacttccattgatctttcattgcatcaactttgcacttgaacactatctgattagtactgtcagtataaattttcagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAG
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gtagccagtcattgttgcatttttatttggtcatggtattttcctgtttttatattgtatttgtttgtcaactgaatgtttcttccaatgtaa-tttctagGTTTCATCTTTACAAGGAGAACAAAGATACACATGAAGCCTTGGGGGTTATTGGAAATATGCTCAGCATCCAG
upper sequence: Vv14s0030g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 4
-gcttctgaaaacatttttttttcaacttccattgatctttcattgcatc--aactttgcacttgaacactatctgattagtactgtcagtataaattttcagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAG
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tattttatacatcataatctctgtag-tgcttttattttattaatgcatttggacgttcaacctatgtgtcatttgatt--tatgagtcgtttaagttaatagGTTCCATCTTTACAAGGAGAACAAAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcaactttgcacttgaacactatctgattagtactgtcagtataaattttcagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAG
atctgat putative branch site (score: 4)
ttttc putative PPT
tcagtataaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttctgaaaacatttttttttcaacttccattgatctttcattgcatcaactttgcacttgaacactatctgattagtactgtcagtataaattttcagGTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - gaaaaca
- - - - - - - - - - - caacttc
- - - - - - - - - - - - - - - - - - - - - - -catcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgtc