Plant Circular RNA Database

Detail information of AT4G39420_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT4G39420_circ_g.7
					
						ID in PlantcircBase
						ath_circ_035690
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 18348217-18350228  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT4G39420						
					
						Parent gene annotation
						
							unknown protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G39420_circ_g.8 AT4G39420_circ_g.9 AT4G39420_circ_g.10 AT4G39420_circ_g.11 AT4G39420_circ_g.12 AT4G39420_circ_g.13 						
					
						Support reads
						1
					
						Tissues
						whole_plant
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						AT4G39420.4:5
AT4G39420.2:5
AT4G39420.3:5
AT4G39420.1:5

General Information
CircRNA Name	AT4G39420_circ_g.7
ID in PlantcircBase	ath_circ_035690
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 18348217-18350228 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT4G39420
Parent gene annotation	unknown protein
Parent gene strand	+
Alternative splicing	AT4G39420_circ_g.8 AT4G39420_circ_g.9 AT4G39420_circ_g.10 AT4G39420_circ_g.11 AT4G39420_circ_g.12 AT4G39420_circ_g.13
Support reads	1
Tissues	whole_plant
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	AT4G39420.4:5 AT4G39420.2:5 AT4G39420.3:5 AT4G39420.1:5

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							CGCAGTGCTTTGTGAACAACGCTTGTTTCTTCCTCTGCTAAAAGCTTTTGACTTGTTCCTCCCG
TCCTGCTCTCTACTGCCATTTTTCCGTGCTCTTCAGggaaccgagcttggacttgagcacttcc
tgcatcgtggacggccactcgcagcttttaatgcttttctggaacatagagttgaaaagttaaa
actggaag

									
								

					

						Assembled circRNA sequence  
						
							NA
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							NA						
					

						Genomic sequence
						
							GGAACCGAGCTTGGACTTGAGCACTTCCTGCATCGTGGACGGCCACTCGCAGCTTTTAATGCTT
TTCTGGAACATAGAGTTGAAAAGTTAAAACTGGAAGATCAATCTGGCTCTTCGATACATGGACA
AAGAAATATGCAGTCAGATGTTCCGATGCTACTTGCACCTCTGACGCAGAGTGATGAGTCACTT
CTTTCATCTGTACGTGCCGGTCACCTTACCATTACTAGCTTAAATTTCATTCGACATATCTGCA
TCGCTTTTATGCTGTCTATTTATGTCTGCATGACTGTTGCTTTACCTTCAGGTCATACCACTTG
CTATCACACACTTTGGGGATTCTGTGTTGGTGGCTTCGTGTGCCTTCCTTCTTGAGCTTTGTGG
TTTATCTGCTAGCATGCTTCGGATAGACGTTGCATCCTTGAGAAGAATATCATCCTTCTATAAA
TCAAATGGTAATGCGGATATGGCACATCAGAAATCGCTGAAGCGCTCAATGTTTCATAGTGTAT
CTAGTGAAGATGATCTAATGGGGTCACTAGCTAGGGCCCTTGCTAACGAATACGCTTATCCTGA
TATTTCAAGTGTCCCTAAGCAAAAACAGAATCCAAGTATTTCTGGTAGTCAACCCGGTCTTCCG
CTAATGCTTGTTCTTCATCATTTGGAACAAGCTAGTCTTCCAGAGATTGGAGTAGGTAGAAAAA
CAAGTGGATACTGGCTGTTAACAGGTGATGGTGATGGGTCTGAACTGCGGTCTCAACAGACATC
TGCTAGCTTGCATTGGAGTTTAGTTACTCTTTTTTGTCAGATGCATAAGATTCCTCTGAGCACC
AAATATCTTGCCATGCTAGCAAGAGACAATGATTGGGTATGCTTCATGATAATTCTTCTTACCT
TTTCGTTTCTTACCCTTGAGCTATTACTTGTCCTAATATACGTAAATATCAGGTTGGATTTTTA
TCTGAGGCGCAGCTTGGAGGATACCCATTTGATACAGTGCTCAATGTGGTACGTCTCTCACTCC
TTACTGGTTTCAGAAATCACAAACAGCAACTTAATGTGCTATGTTACAATTATATGACACATTT
TCATCTATCAGGCATCGAAGGAGTTTGGTGATCAACGTTTAAAAGCTCACATACTGACTGTTTT
GAGATATGCCAACTCAAAAAAGAAAGCCACCACATCGTTCTCAGATGACCCAAGCAGAGGACTT
TCATGTTCCCCCTCAGAGGGTGGAGCTTATGTCTCTGCTGAACTCTTTCGTGTTTTGGCATACT
CTGAGAAGCTAAAGAATCCTGGGGAATACCTTTTGTCAAAAGCTAAGGAATTCTCGTGGTCTAT
TTTGGCTCTCATAGCATCATGCTTTCCGGATGTTTCTCCTTTATCATGCCTAACAATTTGGTTG
GAAATTACCGCAGCCAGGTGTGACAAAATTTAATGAAATTCAATTGGGTTGGGTGTAATAGTAG
TAATTTACTATCTTAATGCAAGTCTATATAACATTGGGCGTTTTAAACTCTTTTTCTTGCATGT
TTTCTGGAATAAAAAGATGCATAACTTTTTTCTTAGCTCTAACAAAGATCATGCTTTTCAGGGA
AACGTCGTCTATCAAGGTGAACGATATAACGACTAAAATAGCTGAAAATATAGGAGCAGCTGTT
GTATCTACAAATTCCTTGCCGACGGATGCTAGAGGTGTCCAGTTTCATTACAATAGGAGGAATC
CCAAACGGAGACGACTTACTGCACATACATCTGTGGATTTATTGGCTTCAGCCAATAGTTTAAA
CATCTCTGCTGGTAAAACATTTTGTTCTCATAGAACAGAAGCTGCAGAAGATGAAAAAGCGGAA
GATAGCAGTGTTATTGATGATTCGTCTGATGAGCATGCGTCTCTATCAAAAATGGTCGCAGTGC
TTTGTGAACAACGCTTGTTTCTTCCTCTGCTAAAAGCTTTTGACTTGTTCCTCCCGTCCTGCTC
TCTACTGCCATTTTTCCGTGCTCTTCAG
						
					

			
		

Sequences
Splice junction sequence	CGCAGTGCTTTGTGAACAACGCTTGTTTCTTCCTCTGCTAAAAGCTTTTGACTTGTTCCTCCCG TCCTGCTCTCTACTGCCATTTTTCCGTGCTCTTCAGggaaccgagcttggacttgagcacttcc tgcatcgtggacggccactcgcagcttttaatgcttttctggaacatagagttgaaaagttaaa actggaag
Assembled circRNA sequence	NA The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	NA
Genomic sequence	GGAACCGAGCTTGGACTTGAGCACTTCCTGCATCGTGGACGGCCACTCGCAGCTTTTAATGCTT TTCTGGAACATAGAGTTGAAAAGTTAAAACTGGAAGATCAATCTGGCTCTTCGATACATGGACA AAGAAATATGCAGTCAGATGTTCCGATGCTACTTGCACCTCTGACGCAGAGTGATGAGTCACTT CTTTCATCTGTACGTGCCGGTCACCTTACCATTACTAGCTTAAATTTCATTCGACATATCTGCA TCGCTTTTATGCTGTCTATTTATGTCTGCATGACTGTTGCTTTACCTTCAGGTCATACCACTTG CTATCACACACTTTGGGGATTCTGTGTTGGTGGCTTCGTGTGCCTTCCTTCTTGAGCTTTGTGG TTTATCTGCTAGCATGCTTCGGATAGACGTTGCATCCTTGAGAAGAATATCATCCTTCTATAAA TCAAATGGTAATGCGGATATGGCACATCAGAAATCGCTGAAGCGCTCAATGTTTCATAGTGTAT CTAGTGAAGATGATCTAATGGGGTCACTAGCTAGGGCCCTTGCTAACGAATACGCTTATCCTGA TATTTCAAGTGTCCCTAAGCAAAAACAGAATCCAAGTATTTCTGGTAGTCAACCCGGTCTTCCG CTAATGCTTGTTCTTCATCATTTGGAACAAGCTAGTCTTCCAGAGATTGGAGTAGGTAGAAAAA CAAGTGGATACTGGCTGTTAACAGGTGATGGTGATGGGTCTGAACTGCGGTCTCAACAGACATC TGCTAGCTTGCATTGGAGTTTAGTTACTCTTTTTTGTCAGATGCATAAGATTCCTCTGAGCACC AAATATCTTGCCATGCTAGCAAGAGACAATGATTGGGTATGCTTCATGATAATTCTTCTTACCT TTTCGTTTCTTACCCTTGAGCTATTACTTGTCCTAATATACGTAAATATCAGGTTGGATTTTTA TCTGAGGCGCAGCTTGGAGGATACCCATTTGATACAGTGCTCAATGTGGTACGTCTCTCACTCC TTACTGGTTTCAGAAATCACAAACAGCAACTTAATGTGCTATGTTACAATTATATGACACATTT TCATCTATCAGGCATCGAAGGAGTTTGGTGATCAACGTTTAAAAGCTCACATACTGACTGTTTT GAGATATGCCAACTCAAAAAAGAAAGCCACCACATCGTTCTCAGATGACCCAAGCAGAGGACTT TCATGTTCCCCCTCAGAGGGTGGAGCTTATGTCTCTGCTGAACTCTTTCGTGTTTTGGCATACT CTGAGAAGCTAAAGAATCCTGGGGAATACCTTTTGTCAAAAGCTAAGGAATTCTCGTGGTCTAT TTTGGCTCTCATAGCATCATGCTTTCCGGATGTTTCTCCTTTATCATGCCTAACAATTTGGTTG GAAATTACCGCAGCCAGGTGTGACAAAATTTAATGAAATTCAATTGGGTTGGGTGTAATAGTAG TAATTTACTATCTTAATGCAAGTCTATATAACATTGGGCGTTTTAAACTCTTTTTCTTGCATGT TTTCTGGAATAAAAAGATGCATAACTTTTTTCTTAGCTCTAACAAAGATCATGCTTTTCAGGGA AACGTCGTCTATCAAGGTGAACGATATAACGACTAAAATAGCTGAAAATATAGGAGCAGCTGTT GTATCTACAAATTCCTTGCCGACGGATGCTAGAGGTGTCCAGTTTCATTACAATAGGAGGAATC CCAAACGGAGACGACTTACTGCACATACATCTGTGGATTTATTGGCTTCAGCCAATAGTTTAAA CATCTCTGCTGGTAAAACATTTTGTTCTCATAGAACAGAAGCTGCAGAAGATGAAAAAGCGGAA GATAGCAGTGTTATTGATGATTCGTCTGATGAGCATGCGTCTCTATCAAAAATGGTCGCAGTGC TTTGTGAACAACGCTTGTTTCTTCCTCTGCTAAAAGCTTTTGACTTGTTCCTCCCGTCCTGCTC TCTACTGCCATTTTTCCGTGCTCTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.178728517

Conservation Information
Conserved circRNAs	NA
PMCS	0.178728517

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							18348352-18350225(+)
						
					

						Potential amino acid sequence
						
							MQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLVASCAFLLELCGLSASMLRIDVASLRRI
SSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLARALANEYAYPDISSVPKQKQNPSISGS
QPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDGDGSELRSQQTSASLHWSLVTLFCQMHK
IPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNVASKEFGDQRLKAHILTVLRYANSKKKA
TTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKLKNPGEYLLSKAKEFSWSILALIASCFP
DVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIGAAVVSTNSLPTDARGVQFHYNRRNPKR
RRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDEKAEDSSVIDDSSDEHASLSKMVAVLCE
QRLFLPLLKAFDLFLPSCSLLPFFRALQGTELGLEHFLHRGRPLAAFNAFLEHRVEKLKLEDQS
GSSIHGQRNMQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLVASCAFLLELCGLSASMLR
IDVASLRRISSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLARALANEYAYPDISSVPKQ
KQNPSISGSQPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDGDGSELRSQQTSASLHWSL
VTLFCQMHKIPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNVASKEFGDQRLKAHILTVL
RYANSKKKATTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKLKNPGEYLLSKAKEFSWSI
LALIASCFPDVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIGAAVVSTNSLPTDARGVQF
HYNRRNPKRRRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDEKAEDSSVIDDSSDEHASL
SKMVAVLCEQRLFLPLLKAFDLFLPSCSLLPFFRALQGTELGLEHFLHRGRPLAAFNAFLEHRV
EKLKLEDQSGSSIHGQRNMQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLVASCAFLLEL
CGLSASMLRIDVASLRRISSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLARALANEYAY
PDISSVPKQKQNPSISGSQPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDGDGSELRSQQ
TSASLHWSLVTLFCQMHKIPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNVASKEFGDQR
LKAHILTVLRYANSKKKATTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKLKNPGEYLLS
KAKEFSWSILALIASCFPDVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIGAAVVSTNSL
PTDARGVQFHYNRRNPKRRRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDEKAEDSSVID
DSSDEHASLSKMVAVLCEQRLFLPLLKAFDLFLPSCSLLPFFRALQGTELGLEHFLHRGRPLAA
FNAFLEHRVEKLKLEDQSGSSIHGQRNMQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLV
ASCAFLLELCGLSASMLRIDVASLRRISSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLA
RALANEYAYPDISSVPKQKQNPSISGSQPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDG
DGSELRSQQTSASLHWSLVTLFCQMHKIPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNV
ASKEFGDQRLKAHILTVLRYANSKKKATTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKL
KNPGEYLLSKAKEFSWSILALIASCFPDVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIG
AAVVSTNSLPTDARGVQFHYNRRNPKRRRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDE
KAEDSSVIDDSSDEHASLSKMVAVLCEQRLFLPLLKAFDLFLPSCSLLPFFRALQ(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	18348352-18350225(+)
Potential amino acid sequence	MQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLVASCAFLLELCGLSASMLRIDVASLRRI SSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLARALANEYAYPDISSVPKQKQNPSISGS QPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDGDGSELRSQQTSASLHWSLVTLFCQMHK IPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNVASKEFGDQRLKAHILTVLRYANSKKKA TTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKLKNPGEYLLSKAKEFSWSILALIASCFP DVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIGAAVVSTNSLPTDARGVQFHYNRRNPKR RRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDEKAEDSSVIDDSSDEHASLSKMVAVLCE QRLFLPLLKAFDLFLPSCSLLPFFRALQGTELGLEHFLHRGRPLAAFNAFLEHRVEKLKLEDQS GSSIHGQRNMQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLVASCAFLLELCGLSASMLR IDVASLRRISSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLARALANEYAYPDISSVPKQ KQNPSISGSQPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDGDGSELRSQQTSASLHWSL VTLFCQMHKIPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNVASKEFGDQRLKAHILTVL RYANSKKKATTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKLKNPGEYLLSKAKEFSWSI LALIASCFPDVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIGAAVVSTNSLPTDARGVQF HYNRRNPKRRRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDEKAEDSSVIDDSSDEHASL SKMVAVLCEQRLFLPLLKAFDLFLPSCSLLPFFRALQGTELGLEHFLHRGRPLAAFNAFLEHRV EKLKLEDQSGSSIHGQRNMQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLVASCAFLLEL CGLSASMLRIDVASLRRISSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLARALANEYAY PDISSVPKQKQNPSISGSQPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDGDGSELRSQQ TSASLHWSLVTLFCQMHKIPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNVASKEFGDQR LKAHILTVLRYANSKKKATTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKLKNPGEYLLS KAKEFSWSILALIASCFPDVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIGAAVVSTNSL PTDARGVQFHYNRRNPKRRRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDEKAEDSSVID DSSDEHASLSKMVAVLCEQRLFLPLLKAFDLFLPSCSLLPFFRALQGTELGLEHFLHRGRPLAA FNAFLEHRVEKLKLEDQSGSSIHGQRNMQSDVPMLLAPLTQSDESLLSSVIPLAITHFGDSVLV ASCAFLLELCGLSASMLRIDVASLRRISSFYKSNGNADMAHQKSLKRSMFHSVSSEDDLMGSLA RALANEYAYPDISSVPKQKQNPSISGSQPGLPLMLVLHHLEQASLPEIGVGRKTSGYWLLTGDG DGSELRSQQTSASLHWSLVTLFCQMHKIPLSTKYLAMLARDNDWVGFLSEAQLGGYPFDTVLNV ASKEFGDQRLKAHILTVLRYANSKKKATTSFSDDPSRGLSCSPSEGGAYVSAELFRVLAYSEKL KNPGEYLLSKAKEFSWSILALIASCFPDVSPLSCLTIWLEITAARETSSIKVNDITTKIAENIG AAVVSTNSLPTDARGVQFHYNRRNPKRRRLTAHTSVDLLASANSLNISAGKTFCSHRTEAAEDE KAEDSSVIDDSSDEHASLSKMVAVLCEQRLFLPLLKAFDLFLPSCSLLPFFRALQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT4G39420_circ_g.7

Address

Any questions?

Supported by