Sequence
atgc intronic sequence ATGC exonic sequence...atgcttgtgtgggtgttcacttgcatgtgtgtgaaagacagagggctgtattcttgacgtgttttttcatctaattaacttgtttaagctgctcttctagGTGGTTGGGCAGGTTATTTCTCATATGACACTGTTCGTTATGTGGAAAAGAAAAAGCTACCATTTTCAAACGCTCCAGAGGATGACAGGAACCTTGCTGA
Basic information
species | Glycine max |
transcript | GLYMA18G03270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G03270.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g61120.1 (Oryza sativa), 3'ss of exon 3
atgcttgtgtgggtgttcacttgcatgtgtgtgaaagacagagggctgtattcttga--cgtgttttttcatctaattaacttgtttaagctgctcttctagGTGGTTGGGCAGGTTATTTCTCATATGACACTGTTCGTTATGTGGAAAAGAAAAAGCTACCATTTTCAAACGCTCCAGAGGATGACAGGAACCTTGCTGA
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ttgttgtctttttctttcagctaacaaagtg-gtcttgcaaatatattccctctaaagccatgataatttattctgttg-catcttgggatttattttacagGAGGATGGGTTGGATTCTTCTCTTACGACACAGTGCGTTATGTTGAAACAAAGAAGCTTCCATTTTCTAACGCGCCAGAGGATGATAGGAACCTTCCTGA
upper sequence: GLYMA18G03270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G05730.1 (Arabidopsis thaliana), 3'ss of exon 3
atgcttgtgtgggtgttcacttgcatgtgtgtgaa---agacagagggctgtattcttgacgtgttttttcatctaattaacttgtttaagctgctcttctagGTGGTTGGGCAGGTTATTTCTCATATGACACTGTTCGTTATGTGGAAAAGAAAAAGCTACCATTTTCAAACGCTCCAGAGGATGACAGGAACCTTGCTGA
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-tagatagaagattgattgccctta-gtgttttagtttactttttgtgctttatcttgttcatgaagtggtatctc-ttagtaagatttctttattatgatagGTGGGTGGGTTGGTTTTTTCTCGTACGACACTGTTCGTTATGTTGAGAAGAGGAAATTGCCATTTTCAAAGGCCCCTGAGGATGATAGGAACTTGCCAGA
upper sequence: GLYMA18G03270.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g00400.t01 (Vitis vinifera), 3'ss of exon 3
atgcttgtgtgggt---gttcacttgcatgtgtgtgaaagacagagggctgtattcttgacgtgttttttcat-ctaattaacttgtttaagctgctcttctagGTGGTTGGGCAGGTTATTTCTCATATGACACTGTTCGTTATGTGGAAAAGAAAAAGCTACCATTTTCAAACGCTCCAGAGGATGACAGGAACCTTGCTGA
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agagatatgtgggttatgttccttattgtattcttgatcaatactgg--ttcctttaaaatatgaaaatccatgcttagtaattaact--accgttttaaatagGTGGATGGGTTGGTTTTTTCTCATATGATACGGTTTGTTATGTGGAGAAGAAAAAGCTGCCATTCTCAAAAGCACAAGATGATGACAGAAATCTCGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtattcttgacgtgttttttcatctaattaacttgtttaagctgctcttctagGTGGTTGGGCAGGTTATTTCTCATATGACACTGTTCGTTATGTGGAAAAGAAAAAGCTACCATTTTCAAACGCTCCAGAGGATGACAGGAACCTTGCTGA
aattaac putative branch site (score: 2)
ctgctcttct putative PPT
ttttttcatctaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcttgtgtgggtgttcacttgcatgtgtgtgaaagacagagggctgtattcttgacgtgttttttcatctaattaacttgtttaagctgctcttctagGTGGTTGGGCAGGTTATTTCTCATATGACACTGTTCGTTATGTGGAAAAGAAAAAGCTACCATTTTCAAACGCTCCAGAGGATGACAGGAACCTTGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - gtgtggg
- - - - - - - - -cacttgc
- - - - - - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgacgtg