Sequence
atgc intronic sequence ATGC exonic sequencegtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g10380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g36700.1 (Oryza sativa), 3'ss of exon 1
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatga-aacaagcttcttattg--tttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
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-----------------------------------------------------gtacgccattacgttcgtgatcatggcgtctcgccattgatggaagcttgaagggtgtatggaatgacgaccgtgatggtgtgtcgcgtgcagGGGTTTAGGAAGGTCGTGCCGGAGAGGTGGGAGTTCGCCAACGAGTTCTTCAGGAAGGGCGAGAAGCAGCTGCTGTGCGAGATCCACCGGCGTAAGTCCG
upper sequence: Vv18s0001g10380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G04390.1 (Glycine max), 3'ss of exon 1
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
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------------------------------------------------gtattatattcacttacacac---tatatctagttcttcagttattcttataattaacatgg--ttaattttaaatgcatg--------aattagGGTTTTAGAAAGATTGTGCCAGACCGATGGGAGTTCGCCAACGAATTCTTCAAGAAGGGAGAGAAACACTTGCTGTGCGAGATCCATAGAAGAAAAACCG
upper sequence: Vv18s0001g10380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G04200.1 (Glycine max), 3'ss of exon 1
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttctt--attgtttttactgatttagattttgttttgcttgctt-gcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
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------------------------------------------------gtattatatttacttacacactgatacactatctctagttcttcaattattgttttcttttctttttatattctgacagttttaaatggatgaactagGGTTTTAGAAAGATTGTGCCAGACCGATGGGAGTTCGCGAACGAATTCTTCAAGAAGGGAGAGAAACACTTGCTGTGCGAGATCCATAGAAGAAAAACGG
upper sequence: Vv18s0001g10380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G35980.1 (Glycine max), 3'ss of exon 1
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactg-gttatatatatatatatgaaacaagcttcttat-tgtttttactgattta--gattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
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------------------------------------------tcccatttaacatacccatgttaatctcactttcaagatgttacatttttgcatgctcctattaattaactaacatggttttacattttttctt-----aaatagGGTTTTAGAAAGATTGTGCCTGATAGATGGGAGTTCGCGAATGAGTTCTTCAAGAAAGGAGCGAAGAACTTGCTGTGCGAGATCCACAGAAGGAAAACCC
upper sequence: Vv18s0001g10380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G09190.1 (Glycine max), 3'ss of exon 1
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttat-tgtttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
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------------------------------------aaattgtgatttaccatgttg-tggtaattagtccttcaagatgttacattttttgcatgctcccaattaacta-acttggctttgaat-tttgttt-----gaatagGGTTTTAGAAAGATTGTGCCTGATAGATGGGAGTTCGCGAATGAGTTCTTCAAGAAAGGAGAGAAGAACTTGTTGTGCGAGATTCACAGAAGAAAAACCC
upper sequence: Vv18s0001g10380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G46264.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
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----------------------------------ccaaaaa----cagaagaaaaaatgtgttcttgagatttggggtttttgagttttttgtcttcttctacaagaaatctgatgttatgatc-tttgattttg----ttagGGTTTCAGAAAGATTGTACCAGATCGATGGGAGTTCGCGAACGAGTTTTTCAAGAGAGGAGAGAAACATTTACTCTGCGAAATCCACCGCCGTAAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
tactgat putative branch site (score: 2)
cttgcttcc putative PPT
atttagattttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccttctctctcttcccccacttcccttcttcaaatcgtttctggagatgtaactggttatatatatatatatgaaacaagcttcttattgtttttactgatttagattttgttttgcttgcttgcttccggaaactagGGTTTTAGAAAGATTGTACCGGATAGATGGGAGTTTGCCAACGAGTTCTTCAAGAAAGGAGAGAAGCACTTACTCTGCGAGATCCATAGAAGAAAAACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA