Sequence
atgc intronic sequence ATGC exonic sequencegtgatctttctttttctacttaccaaagagaaagttttgtgctctgaatctttgtacaactatctctttcacccagtcgccatgcttgattgcttctgtttgttcttcttgttgcagCAAGATTTACCTTGGCCAAACTATATGAAAAGATTGGCTTCAACAAGGAAACTATATCTAGAGGAAAATATGCTGAGCTTCTGGGGGCTGAGGAAAGACC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73990.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 10
gtgatctttctttttctact-taccaaagagaaagttttgtgctctgaatctttgtacaactatctctttcacccagtcgccatgcttgattgcttctgtttgttcttcttgttgcagCAAGATTTACCTTGGCCAAACTATATGAAAAGATTGGCTTCAACAAGGAAACTATATCTAGAGGAAAATATGCTGAGCTTCTGGGGGCTGAGGAAAGACC
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-----------atataaattgtaatatcatgaacagcctgtgctctatatattctt-caattttgtaatctgttaattgatgaca-ttatttacataacattggt-----tattgtagGAAAATTTAACCTGGGGAAACTGTATGAGAAGATTGGCTTTAACAAAGAAATTTTATCAAGGGGAAAATATGCTGAGCTCCTTGCTGCTGAACAACGTCC
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G09020.2 (Glycine max), 3'ss of exon 2
gtgatctttctttttctacttaccaaagagaaagttttgtgctctgaatctttgtacaactatctctttcacccagtcgccatgcttgattgcttctgtttgttcttcttgttgcagCAAGATTTACCTTGGCCAAACTATATGAAAAGATTGGCTTCAACAAGGAAACTATATCTAGAGGAAAATATGCTGAGCTTCTGGGGGCTGAGGAAAGACC
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-------aagacattgtaatt-tcataaacaa---tcagctccccagatatt-gtcc--ttaggttttgtaatatattaatttgatggtataacactataacatatttttgt---agGAAAATTTAACCTTGGGAAACTTTATGAGAAGATTGGCTTCAACAAAGAAATCATATCAAGGGGTAGATATGCTGAGCTCCGTGCAGCTGAACAGCGTTC
upper sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 5
gtgatctttctttttctacttaccaaagagaaagttttgtgctctgaatctttgtacaactatctctttcacccagtcgccatgcttgattgcttct-gtttgttcttcttg--ttgcagCAAGATTTACCTTGGCCAAACTATATGAAAAGATTGGCTTCAACAAGGAAACTATATCTAGAGGAAAATATGCTGAGCTTCTGGGGGCTGAGGAAAGACC
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-----------------aagaaaaatggttagaacttttttctcaggttatactcaacataacctattcta---atttttcttagttgtgtgttaatagattgatattctttgcttgtagGGAAGTTCAATTTGGGGACACTATATGAAAAAATTGGCTTCAATAAGGAGATTATATCAAGGGGAAGATTTGCTGAGCTCACAGCAGCTGAACAGCGGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctttcacccagtcgccatgcttgattgcttctgtttgttcttcttgttgcagCAAGATTTACCTTGGCCAAACTATATGAAAAGATTGGCTTCAACAAGGAAACTATATCTAGAGGAAAATATGCTGAGCTTCTGGGGGCTGAGGAAAGACC
gcttgat putative branch site (score: 5)
ttgcttctgtttgttc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatctttctttttctacttaccaaagagaaagttttgtgctctgaatctttgtacaactatctctttcacccagtcgccatgcttgattgcttctgtttgttcttcttgttgcagCAAGATTTACCTTGGCCAAACTATATGAAAAGATTGGCTTCAACAAGGAAACTATATCTAGAGGAAAATATGCTGAGCTTCTGGGGGCTGAGGAAAGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT