Sequence
atgc intronic sequence ATGC exonic sequence...cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgttgaatctgattgtggactggtttttgtttgtaattgtatttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0100g00690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G32090.1 (Glycine max), 3'ss of exon 2
cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgt-tgaat--ctgattgtggactggtttttgtttgtaattgtatttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
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tgttgctttccttttatg--catgtttatgatgcactga-ttcagaaatcagaatatggcttactaaatgagattttggtttgttttgattcttgatttgaagACTGCTTTGATGCAAGCTTGTAGATATGGTCATTGGGAAGTTGTGCAGACCCTTCTGCTCTTCAGATGCAAT
upper sequence: Vv16s0100g00690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G38270.1 (Glycine max), 3'ss of exon 2
cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgttgaat---ctgatt--gtggactggtttttgtttgtaattgtatttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
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---tcaatggatctgat-gtaaattcaatagaagcatgataaaatgaagctttattagctatactaatttgataatatggtttgcattgacccttg-atttgaagACGGCGTTGATGCAAGCTTGTAGATATGGGCATTGGGAGGTTGTACAAACACTTCTACTCTTCAGATGCAAT
upper sequence: Vv16s0100g00690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G26560.1 (Glycine max), 3'ss of exon 2
cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgttgaatctga-ttgtggactg--gtttttgtttg---taattgt--atttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
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-------atg-catgttgctttgcttttttatgcatgtgtatgatgcactgattcagaatatggcttactaaatgagattttggtttgctttgatccttgatttgaagACCGCTTTGATGCAAGCTTGTAGATATGGACATTGGGAAGTTGTACAGACCCTTCTGCTCTTCAAATGCAAT
upper sequence: Vv16s0100g00690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G29590.1 (Glycine max), 3'ss of exon 2
cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgttgaat---ctgatt--gtggactggtttttgtttgtaattgtatttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
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---tcaatggatctgat-gtcaattcaatagaagcatgataacatgaagctttattagctatactaatttgataatatggtttgcattgatccttg-atttgaagACCGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAGGTTGCACAGACACTTTTACTCTTCAGATGCAAT
upper sequence: Vv16s0100g00690.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 2
cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgttgaatctg-----attgtggactggtttttgtttgtaattg--tat-ttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
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------tgaaatctgacttagattactaatggttacaaattcgatt--cctacactgaatctattaaaatccaggaatatgctaagtttgcaattaatcatgtttcagACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatctgtgttgaatctgattgtggactggtttttgtttgtaattgtatttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
atctgat putative branch site (score: 4)
tttttgtttgtaattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgttgaatctgattgtggactggtttttgtttgtaattgtatttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - gaaataa
- - - - - - ctgattg
- - - - - - - - -tgtcttc
- - - - - - - - - - - - - - - - -caaagaa
- - - - - - - - - - - - - - - - - - - - -tgatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggactgg