Sequence
atgc intronic sequence ATGC exonic sequencegttagaataggtagtcgatgtcagattacctccggtatattaaacctctgggcatcttaaacaagattttctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G47060.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 5
gttagaataggtagtcgatgtcagattacctccggtatattaaacctctgggcatcttaaacaag-attttctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
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----------gtaaccta---ctgtttgaggacaaaaatctagttttatgtgc---ttaaatgtgtgataactaattgcatttctt--tgtagATTGATGCTGTGGCAAAAAGCCGTGATGGCCGTTATCGTATCGTCAGTAATGATGAGCGAGAGCAGACACTAAATCAATTACTCACG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA0028S00210.2 (Glycine max), 3'ss of exon 5
gttagaataggtagtcgatgtcagattacctccggtatattaaacctctgggcatcttaaacaagattt-tctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
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gtataaaaatatattcttttgttgtgtgaaatcactttgttcaacatatat-tatttaatattaaactgatcaacatatcttttggtatgcagATAGATGCTGTGGCTAAAAGTCGTGATGGAAAATTTCGCATTGTCAGCAATGATGAACGAGAGCAAACCTTGAATCAGTTGCTCACT
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 5
--gttagaataggtagtcgatgtcagattacctccggtatattaaacctctgggcatcttaaacaagattt-tctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
| | |||| || || | | | | | || ||| | | || | | | | | | || | || | | ||||||||||||||||| ||||| |||||||| ||||| || || | ||||| |||||| | |||||||| || |||||||||||||||
gtataaaaatatatattcttttgttgtgtggaatcacttggttcaacatatat-tatttaatattaaactgatcagcatttcttttggtatgcagATAGATGCTGTGGCTAAAAGTCGTGATGGCAAATTTCGCATTGTCAGCAATGATGAACGAGAGCAAACCTTGAATCAGTTGCTCACT
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 6
gttagaataggtagtcgatgtcagattacctccggtatattaaacc-tctgggcatcttaaacaagattttctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
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gtaagaatgtgtattc----ttttattatgtaagatgtttgatttaatattgactattcaaccaag----taaactttcctttgata-tgcagATAGATGCTGTGGCTAAAAGTCGTGATGGTAAATTTCGCATTGTCAGCAATGATGAACGGGAACAAACCTTGAACCAGCTGCTCACT
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 6
gttagaataggtagtcgatgtcagattacctccggtatattaaacctctgggcatcttaaacaagattttctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
|| |||| ||| || | |||| | | || || | | | || ||| || | || ||| | | | ||||||||||||||||| ||||| |||||||||||||| || || | ||||| |||||| | || ||||| || || ||| ||||||||
gtatgaatgtgtattc----tttgattctattaag-atgtttgattta-atatttactattcaaccaattaaactttccttttgta-tgcagATAGATGCTGTGGCTAAAAGTCGTGATGGTAAATTTCGCATTGTCAGCAATGATGAACGAGAACAAACCTTGAACCAGCTGCTCACT
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 5
gttagaatag----gtagtcgatgtcagattacctccggtatattaaacctctgggcatcttaaacaagattttctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
||||||| | | | | ||| | | | | | || || | | || || || || || | ||| | | | ||||||||||||| ||||||||||||||||||| ||| || || | ||||| ||||| | |||||||| || || |||||||| |||
gttagaaccgtggaatttttgttgtgtattcatgttcagcattttgagcttcctggtgcgttg-------ttagtcatgtttttcttcttcgc-agATAGATGCTGTAGCAAAAAGCCGTGATGGTAGATTTCGCATTGTTAGCAATGATGAGCGAGAGCAAACCTTGAACCAGTTGCTTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattaaacctctgggcatcttaaacaagattttctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
ttttctatttgcctct CT-rich tract
ttaaacaagatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaataggtagtcgatgtcagattacctccggtatattaaacctctgggcatcttaaacaagattttctatttgcctctcatgctccagATAGATGCTGTGGCAAAAAGCCGTGATGGTAAATTCCGAATGGGGAGCAACGATGAAAGGGAGCAAACTTTAAATCAGTTGCTCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA