Sequence
atgc intronic sequence ATGC exonic sequencegtcaggttttaaacattggaattaaagctgtcttgtttgaaatagaattgagtaactagtaaattatgctggcaatctgttaaaatttgatcatctttctctttgagatttgggactgagaacccattttctttctaaatgttcgtcttcttgatcacagTTCTTAGAGTCTGGGATGTGCTTCTCTTTGAAGGAACTCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAACTATATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55020.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 9
gtcaggttttaaacattggaattaaagctgtcttgtttgaaatagaattgagtaactagtaaattatgctggcaatctgttaaaatttgatcatctttctctttgagatttgggactgagaacccattttctttctaaatgttcgtcttcttgatcacagTTCTTAGAGTCTGGGATGTGCTTCTCTTTGAAGGAACTCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAACTATATG
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gtcaggtttta--tgtt----------ctatctatttagtagtgtagcctagtc-ttacttcacaaagttgccaatgtg--aaa---tgagcatttgta-cgctattgtttgag----------cttccttctgatccattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
gtcaggttttaaacattggaattaaagctgtcttgtttgaaatagaattgagtaactagtaaattatgctggcaatctgttaaaatttgatcatctttctctttgagatttgggactgagaacccattttctttctaa---atgttcgtcttcttgatcacagTTCTTAGAGTCTGGGATGTGCTTCTCTTTGAAGGAACTCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAACTATATG
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-----------------------------gtcaggttttatgttctatctattgagtagcg---tagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 9
----------gtcaggttttaaacattggaattaaa-gctgtcttgt-ttgaaatagaattgagtaactagtaaattatgctggcaatctgttaa-------aatttgatcatctttctctttgagatttgggac-tgagaacccattttc---tttctaaatgtt-----cgtcttcttgatcacagTTCTTAGAGTCTGGGATGTGCTTCTCTTTGAAGGAACTCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAACTATATG
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gtcagtctccatcatggcttatata--gaaattagatgttatttggggcctacattgcatttaaaatctatttatatttctttgatttatggccatctcactaatcttagcattctcattgtcatgattgcattcataatgtcttggttacaagcttatgggttttgatggctttctcctgacttcagTTCTCCGGGTCTGGGATGTGCTTCTTTTTGAAGGAAACCGTGTCATGCTATTTAAAACAGCACTTGCTTTGATGGAGTTATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatttgggactgagaacccattttctttctaaatgttcgtcttcttgatcacagTTCTTAGAGTCTGGGATGTGCTTCTCTTTGAAGGAACTCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAACTATATG
ttcgtcttctt CT-rich tract
attttctttctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaggttttaaacattggaattaaagctgtcttgtttgaaatagaattgagtaactagtaaattatgctggcaatctgttaaaatttgatcatctttctctttgagatttgggactgagaacccattttctttctaaatgttcgtcttcttgatcacagTTCTTAGAGTCTGGGATGTGCTTCTCTTTGAAGGAACTCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAACTATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA