Sequence
atgc intronic sequence ATGC exonic sequencegtagttcttttgcttcttgttggttatcctgcgtcctattatagtggcaacgataatgttttatatgaatactttttcttcagacttcagttgataaatcaagcgtagtaactactttttcctgtgtatttccggctttccttttgatagACTGTCAGCAGACATGTGTGGAGCCTCTCACTTCAACTCCCTTTGGTTCACCTTGTGGTTGTGTCTTCCCCATGAAAGTTCAGCTTCTACTAAGTGTCGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20300.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G32640.1 (Glycine max), 3'ss of exon 4
gtagttcttttgcttcttgttggttatcctgcgtcctattatagtggcaacgataatgttttatatgaatactttttcttcagacttcagttgataaatcaagcgtagtaactactttttcctgtgtatttccggctttccttttgatagACTGTCAGCAGACATGTGTGGAGCCTCTCACTTCAACTCCCTTTGGTTCACCTTGTGGTTGTGTCTTCCCCATGAAAGTTCAGCTTCTACTAAGTGTCGC
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----gtgaccaaatctgtactgatccgctcacatcaactccctttggt-----tcaccttgtggttgtgta-tttcccatgaaaatcagACT--TACACTGGATATAG------CTCCTTATGCTGTTTTTCCGGTAATGACTGAGTTAGAG----AATGAAATTGCGTTGGGCACTTATTTAGAGCAGAGTCAGGTGAAG-------------------------------------------------
upper sequence: AT2G20300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G35390.1 (Glycine max), 3'ss of exon 4
gtagttcttttgcttcttgttggttatcctgcgtcctattatagtggcaacgataatgttttatatgaatactttttcttcagactt-cagttgataaatcaagcgtagtaactactttttcctgtgtatt---tccggctttccttttgatagACTGTCAGCAGACATGTGTGGAGCCTCTCACTTCAACTCCCTTTGGTTCACCTTGTGGTTGTGTCTTCCCCATGAAAGTTCAGCTTCTACTAAGTGTCGC
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----------------------------------------------------ttgctgattgat-tggatttctgaacttaacatttgctattttttggtcctcc-cagttagtgtctcatactgtatactcatttatactgaatttctggcagCTTGTGACCAAACCTGTACTGATCCGCTCACATCAAGTCCCTTTGGTTCACCTTGTGGTTGTGTATTTCCCATGAAAATCAGACTTACACTGGATGTAGC
upper sequence: AT2G20300.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G19030.1 (Glycine max), 3'ss of exon 2
gtagttcttttgcttcttgttggttatcctgcgtcctattatagtggcaacgataatgttttatatgaatactttttcttcagacttcagttgataaatcaagcgtagta-actactttttcctgtgt--atttccggctttccttttgatagACTGTCAGCAGACATGTGTGGAGCCTCTCACTTCAACTCCCTTTGGTTCACCTTGTGGTTGTGTCTTCCCCATGAAAGTTCAGCTTCTACTAAGTGTCGC
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----------------------------------------------------acggaattatgcg-aaatagcatttccccccgccttgttatctaatgtagttatactatattataataccatacactcattacgtaaaaaatttctggcagCTTGTAGCCAAATCTGTACAGATCCATTAACTGCAACTCCTTTTGGTTCACCCTGTGGTTGTGTATTTCCCATGAAAATCAGACTAGTACTGGATGTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcaagcgtagtaactactttttcctgtgtatttccggctttccttttgatagACTGTCAGCAGACATGTGTGGAGCCTCTCACTTCAACTCCCTTTGGTTCACCTTGTGGTTGTGTCTTCCCCATGAAAGTTCAGCTTCTACTAAGTGTCGC
tagtaac putative branch site (score: 1)
tttccggctttccttt putative PPT
tacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttcttttgcttcttgttggttatcctgcgtcctattatagtggcaacgataatgttttatatgaatactttttcttcagacttcagttgataaatcaagcgtagtaactactttttcctgtgtatttccggctttccttttgatagACTGTCAGCAGACATGTGTGGAGCCTCTCACTTCAACTCCCTTTGGTTCACCTTGTGGTTGTGTCTTCCCCATGAAAGTTCAGCTTCTACTAAGTGTCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT