Sequence
atgc intronic sequence ATGC exonic sequence...tgatcataattttcccaacatgctgttttggaaatcaagatgtccgatcagttatttgactgtttctttaacattttcaagttttccattcttattgcagCATTGAAATATACAAGCATAACAAAGAAGAAAGAGTTGCCAGAACATGGGGAACAACTGCTCCAGGATTACCTTATGTTGAAGAGGTAATTACTCCAGCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 1
tgatcataattttcccaacatgctgttttggaaatcaagatgtccgatcagttatttgactgtttctttaacattttcaagttttccattct-tattgcagCATTGAAATATACAAGCATAACAAAGAAGAAAGAGTTGCCAGAACATGGGGAACAACTGCTCCAGGATTACCTTATGTTGAAGAGGTAATTACTCCAGCT
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taatt-cgactactaaaacatgttaatttcttagcgtcaatttgagtcctgtttcttaatagaatattggatcctcatacgtacctttttgtatttcttagGGTGGAAATATACCCTCACAACAAAGAAGAAAGAATAGCAAGAACATGGGGGACAACCGCACCTGGTTTACCTTATGTAGATGAGGCAATAGCCCAAGCT
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 1
--tgatcata-attttcccaacatgctgttttggaaatcaagatgtccgatcagttatttgactgtttctttaacattttcaagttttccattcttattgcagCATTGAAATATACAAGCATAACAAAGAAGAAAGAGTTGCCAGAACATGGGGAACAACTGCTCCAGGATTACCTTATGTTGAAGAGGTAATTACTCCAGCT
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aatagtttcatgttagcaaagcatgacctttgtggtattact-tccgcatgcagct-cctgtgaaaatatttgatctttatgtgtat-ctatctggtgcacagAGTTGAAATATATCCCCACAATAAAGAAGAAAGAATCGCAAGAACATGGGGTACAACTGCACCTGGTTTACCCTATGTTGATGAGGCTATTGCGTCAGCT
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 1
tgatcataattttcccaacatgc-tgttttggaaatcaagatgtccgatcagttatttgact----gtttctttaacattttcaagttttccattcttattgcagCATTGAAATATACAAGCATAACAAAGAAGAAAGAGTTGCCAGAACATGGGGAACAACTGCTCCAGGATTACCTTATGTTGAAGAGGTAATTACTCCAGCT
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----tgttattttgaaaataaaagtattgaagtgaactggctatctaagtaaatttctgtcttggtgtctcgtggttttcattaaccattaagctcctat-gcagTATTGAAATCTACAAGCATAACAAGGAAGAAAGAATAGCTAGAACTTGGGGAACAACTGCTCCTGGATTGCCATATGTTGAGGAGGTGATTACTCCGGCA
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G05020.1 (Glycine max), 3'ss of exon 2
tgatcataattttcccaacatgctgttttggaaatcaagatgtccgatcagttatttgactgtttctttaacattttcaagttttccattcttattgcagCATTGAAATATACAAGCATAACAAAGAAGAAAGAGTTGCCAGAACATGGGGAACAACTGCTCCAGGATTACCTTATGTTGAAGAGGTAATTACTCCAGCT-------------------------------------------------
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------------------------------------------------tttttgtcttggtgtctcttggctttcattaaccattaagctcctac-gcagtattgaaatctacaagcataacaaggaagaaagaatagctagaacttagGGAACAACTGCTCCTGGATTGCCATATGTTGAGGAGGTGATTACTCCGGCAGGAAATTGGCTTATTGGAGGAGATTTGGAAGTGCTAAAACCTATCAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcagttatttgactgtttctttaacattttcaagttttccattcttattgcagCATTGAAATATACAAGCATAACAAAGAAGAAAGAGTTGCCAGAACATGGGGAACAACTGCTCCAGGATTACCTTATGTTGAAGAGGTAATTACTCCAGCT
ctttaac putative branch site (score: 3)
ttttccattcttatt putative PPT
tttctttaacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatcataattttcccaacatgctgttttggaaatcaagatgtccgatcagttatttgactgtttctttaacattttcaagttttccattcttattgcagCATTGAAATATACAAGCATAACAAAGAAGAAAGAGTTGCCAGAACATGGGGAACAACTGCTCCAGGATTACCTTATGTTGAAGAGGTAATTACTCCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - -cccaaca
- - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - -aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccatt