Plant Circular RNA Database

Detail information of AT4G00060_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G00060_circ_g.3
					
						ID in PlantcircBase
						ath_circ_029024
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 25294-26752  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						MapSplice
					
						Parent gene
						
							AT4G00060						
					
						Parent gene annotation
						
							Nucleotidyltransferase family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G00060_circ_g.2 AT4G00060_circ_g.4 AT4G00060_circ_g.5 AT4G00060_circ_g.6 AT4G00060_circ_g.7 AT4G00060_circ_g.8 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						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
						AT4G00060.1:5
AT4G00060.3:5
AT4G00060.4:5

General Information
CircRNA Name	AT4G00060_circ_g.3
ID in PlantcircBase	ath_circ_029024
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 25294-26752 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	MapSplice
Parent gene	AT4G00060
Parent gene annotation	Nucleotidyltransferase family protein
Parent gene strand	+
Alternative splicing	AT4G00060_circ_g.2 AT4G00060_circ_g.4 AT4G00060_circ_g.5 AT4G00060_circ_g.6 AT4G00060_circ_g.7 AT4G00060_circ_g.8
Support reads	NA
Tissues	leaf
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	AT4G00060.1:5 AT4G00060.3:5 AT4G00060.4:5

			
						 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  
						
							TTTGCCAACAAACACTGGAAACTTGGCAATTGCAAAATCTGTCCGTCTTGACATCAGTTTCAAA
ACTCCATCCCATACGGGTCTTCAAACCACGCAGCTGcctgatgtggccttccctctgcaaccac
ccgagttattgaactgtccaatgcaaggggaatctctctcactgatccacggtattcttaatga
cgagatag

									
								

					

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 687
Transcript exons: 25294-25410,25559-25741,25818-25880,26339-26410,26501-26
752
CCTGATGTGGCCTTCCCTCTGCAACCACCCGAGTTATTGAACTGTCCAATGCAAGGGGAATCTC
TCTCACTGATCCACGGTATTCTTAATGACGAGATAGATTCTTTCTGCAAGCAGGTTGCTGCAGA
GAATATGGCCCGCAAACCTTATATCAATTGGGCAATCAAGCGGGTTACCCGATCTCTCCAAGTT
CTGTGGCCCAGGTCTAGGACGAACATATTTGGTTCATCTGCAACTGGTTTGTCTCTCCCTTCTA
GTGATGTGGATCTTGTGGTTTGTCTTCCTCCAGTGAGAAATTTAGAACCTATCAAAGAGGCAGG
AATTTTGGAGGGTCGCAATGGTATAAAGGAGACTTGCCTTCAGCATGCAGCCAGGTATCTCGCG
AATCAAGAGTGGGTAAAAACTGACTCCCTGAAGACAGTTGAAAACACAGCTATACCAATTATCA
TGCTTGTTGTGGAAGTCCCTTGTGATCTGATATGCAGTATACAGTCACCAAAAGATGGTCCAGA
CTGTATCACCGTTGACCAGGATAGCAATGGTAACACTGAAATGGTTGGATTTGAAGACTCTGCA
GCAGCAAACTCTTTGCCAACAAACACTGGAAACTTGGCAATTGCAAAATCTGTCCGTCTTGACA
TCAGTTTCAAAACTCCATCCCATACGGGTCTTCAAACCACGCAGCTG
						
					

						Genomic sequence
						
							CCTGATGTGGCCTTCCCTCTGCAACCACCCGAGTTATTGAACTGTCCAATGCAAGGGGAATCTC
TCTCACTGATCCACGGTATTCTTAATGACGAGATAGATTCTTTCTGCAAGCAGGTAATCACAAT
ACCTCTTTTTTTTCTCCATATGCTTTAGTAACTGCCTTTAGTTTGCAGAGAACTATATGAGCAT
CTTTGAAGTGTGTATTTACTTTTCTTGGGATGGCGTTTCTTCTAATCCTTTGAATTATATACTG
CTCGCGAAGGTTGCTGCAGAGAATATGGCCCGCAAACCTTATATCAATTGGGCAATCAAGCGGG
TTACCCGATCTCTCCAAGTTCTGTGGCCCAGGTCTAGGACGAACATATTTGGTTCATCTGCAAC
TGGTTTGTCTCTCCCTTCTAGTGATGTGGATCTTGTGGTTTGTCTTCCTCCAGTGAGAAATTTA
GTAAGCAAACCCAAAATCATTCCTCGTGTGCATTACTTGTTGAACTGGAAGATCTGATATATAA
TACCCGCCTCAGGAACCTATCAAAGAGGCAGGAATTTTGGAGGGTCGCAATGGTATAAAGGAGA
CTTGCCTTCAGGTATGGTTAGTGGCGCAAGTCATGTTGCAACTGTTGAATGTCTTTGGGCTTGG
CAGATCTTGTTCTTAAAATCTATATTTCGTTACTCTTGAAATGGGTAGTAGTATACAATCAAGA
TTCTGTTCTTAAGTTTTACATTTACTTTATTTTGATGATGAATACGTGCTTGTATATTTTTGTA
TTAGGCGCTAGTCTAATTATTCCATATATGGTTCTATTTTTCTTAATATGTGGTTGCTCAGGTC
ATGTTATATATGAGGTAACGAGAATTGCTTTAGTATTGTGTAAGCATTGTAATTTACTAATTTG
AATAATGCTTGAGCCGACATTCAACTCTACTTCTTTTTCTTTCTTAGAACTGTTTTTATCCTGT
TAAGTAAATAAGAGTCCTATATCTGACAGTTCACGTGCTGCATTTTATAACTGAATCCACTTTG
CTACATGTTTTTGCTATTCAGCATGCAGCCAGGTATCTCGCGAATCAAGAGTGGGTAAAAACTG
ACTCCCTGAAGACAGTTGAAAACACAGCTGTAATGCGTCACTTATTGATGTTTTTCTTTATCCA
CGATTGCTAGTACTTATCATGCTTTTGTTGATATGATCCCTTTATGCTTGTGTAGATACCAATT
ATCATGCTTGTTGTGGAAGTCCCTTGTGATCTGATATGCAGTATACAGTCACCAAAAGATGGTC
CAGACTGTATCACCGTTGACCAGGATAGCAATGGTAACACTGAAATGGTTGGATTTGAAGACTC
TGCAGCAGCAAACTCTTTGCCAACAAACACTGGAAACTTGGCAATTGCAAAATCTGTCCGTCTT
GACATCAGTTTCAAAACTCCATCCCATACGGGTCTTCAAACCACGCAGCTG
						
					

			
		

Sequences
Splice junction sequence	TTTGCCAACAAACACTGGAAACTTGGCAATTGCAAAATCTGTCCGTCTTGACATCAGTTTCAAA ACTCCATCCCATACGGGTCTTCAAACCACGCAGCTGcctgatgtggccttccctctgcaaccac ccgagttattgaactgtccaatgcaaggggaatctctctcactgatccacggtattcttaatga cgagatag
Assembled circRNA sequence	Yes 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	Transcript length: 687 Transcript exons: 25294-25410,25559-25741,25818-25880,26339-26410,26501-26 752 CCTGATGTGGCCTTCCCTCTGCAACCACCCGAGTTATTGAACTGTCCAATGCAAGGGGAATCTC TCTCACTGATCCACGGTATTCTTAATGACGAGATAGATTCTTTCTGCAAGCAGGTTGCTGCAGA GAATATGGCCCGCAAACCTTATATCAATTGGGCAATCAAGCGGGTTACCCGATCTCTCCAAGTT CTGTGGCCCAGGTCTAGGACGAACATATTTGGTTCATCTGCAACTGGTTTGTCTCTCCCTTCTA GTGATGTGGATCTTGTGGTTTGTCTTCCTCCAGTGAGAAATTTAGAACCTATCAAAGAGGCAGG AATTTTGGAGGGTCGCAATGGTATAAAGGAGACTTGCCTTCAGCATGCAGCCAGGTATCTCGCG AATCAAGAGTGGGTAAAAACTGACTCCCTGAAGACAGTTGAAAACACAGCTATACCAATTATCA TGCTTGTTGTGGAAGTCCCTTGTGATCTGATATGCAGTATACAGTCACCAAAAGATGGTCCAGA CTGTATCACCGTTGACCAGGATAGCAATGGTAACACTGAAATGGTTGGATTTGAAGACTCTGCA GCAGCAAACTCTTTGCCAACAAACACTGGAAACTTGGCAATTGCAAAATCTGTCCGTCTTGACA TCAGTTTCAAAACTCCATCCCATACGGGTCTTCAAACCACGCAGCTG
Genomic sequence	CCTGATGTGGCCTTCCCTCTGCAACCACCCGAGTTATTGAACTGTCCAATGCAAGGGGAATCTC TCTCACTGATCCACGGTATTCTTAATGACGAGATAGATTCTTTCTGCAAGCAGGTAATCACAAT ACCTCTTTTTTTTCTCCATATGCTTTAGTAACTGCCTTTAGTTTGCAGAGAACTATATGAGCAT CTTTGAAGTGTGTATTTACTTTTCTTGGGATGGCGTTTCTTCTAATCCTTTGAATTATATACTG CTCGCGAAGGTTGCTGCAGAGAATATGGCCCGCAAACCTTATATCAATTGGGCAATCAAGCGGG TTACCCGATCTCTCCAAGTTCTGTGGCCCAGGTCTAGGACGAACATATTTGGTTCATCTGCAAC TGGTTTGTCTCTCCCTTCTAGTGATGTGGATCTTGTGGTTTGTCTTCCTCCAGTGAGAAATTTA GTAAGCAAACCCAAAATCATTCCTCGTGTGCATTACTTGTTGAACTGGAAGATCTGATATATAA TACCCGCCTCAGGAACCTATCAAAGAGGCAGGAATTTTGGAGGGTCGCAATGGTATAAAGGAGA CTTGCCTTCAGGTATGGTTAGTGGCGCAAGTCATGTTGCAACTGTTGAATGTCTTTGGGCTTGG CAGATCTTGTTCTTAAAATCTATATTTCGTTACTCTTGAAATGGGTAGTAGTATACAATCAAGA TTCTGTTCTTAAGTTTTACATTTACTTTATTTTGATGATGAATACGTGCTTGTATATTTTTGTA TTAGGCGCTAGTCTAATTATTCCATATATGGTTCTATTTTTCTTAATATGTGGTTGCTCAGGTC ATGTTATATATGAGGTAACGAGAATTGCTTTAGTATTGTGTAAGCATTGTAATTTACTAATTTG AATAATGCTTGAGCCGACATTCAACTCTACTTCTTTTTCTTTCTTAGAACTGTTTTTATCCTGT TAAGTAAATAAGAGTCCTATATCTGACAGTTCACGTGCTGCATTTTATAACTGAATCCACTTTG CTACATGTTTTTGCTATTCAGCATGCAGCCAGGTATCTCGCGAATCAAGAGTGGGTAAAAACTG ACTCCCTGAAGACAGTTGAAAACACAGCTGTAATGCGTCACTTATTGATGTTTTTCTTTATCCA CGATTGCTAGTACTTATCATGCTTTTGTTGATATGATCCCTTTATGCTTGTGTAGATACCAATT ATCATGCTTGTTGTGGAAGTCCCTTGTGATCTGATATGCAGTATACAGTCACCAAAAGATGGTC CAGACTGTATCACCGTTGACCAGGATAGCAATGGTAACACTGAAATGGTTGGATTTGAAGACTC TGCAGCAGCAAACTCTTTGCCAACAAACACTGGAAACTTGGCAATTGCAAAATCTGTCCGTCTT GACATCAGTTTCAAAACTCCATCCCATACGGGTCTTCAAACCACGCAGCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.26530558

Conservation Information
Conserved circRNAs	NA
PMCS	0.26530558

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25342-26749(+)
						
						Potential amino acid sequence
						
							MQGESLSLIHGILNDEIDSFCKQVAAENMARKPYINWAIKRVTRSLQVLWPRSRTNIFGSSATG
LSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVKTDSLKTVENT
AIPIIMLVVEVPCDLICSIQSPKDGPDCITVDQDSNGNTEMVGFEDSAAANSLPTNTGNLAIAK
SVRLDISFKTPSHTGLQTTQLPDVAFPLQPPELLNCPMQGESLSLIHGILNDEIDSFCKQVAAE
NMARKPYINWAIKRVTRSLQVLWPRSRTNIFGSSATGLSLPSSDVDLVVCLPPVRNLEPIKEAG
ILEGRNGIKETCLQHAARYLANQEWVKTDSLKTVENTAIPIIMLVVEVPCDLICSIQSPKDGPD
CITVDQDSNGNTEMVGFEDSAAANSLPTNTGNLAIAKSVRLDISFKTPSHTGLQTTQLPDVAFP
LQPPELLNCPMQGESLSLIHGILNDEIDSFCKQVAAENMARKPYINWAIKRVTRSLQVLWPRSR
TNIFGSSATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVK
TDSLKTVENTAIPIIMLVVEVPCDLICSIQSPKDGPDCITVDQDSNGNTEMVGFEDSAAANSLP
TNTGNLAIAKSVRLDISFKTPSHTGLQTTQLPDVAFPLQPPELLNCPMQGESLSLIHGILNDEI
DSFCKQVAAENMARKPYINWAIKRVTRSLQVLWPRSRTNIFGSSATGLSLPSSDVDLVVCLPPV
RNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVKTDSLKTVENTAIPIIMLVVEVPCDLIC
SIQSPKDGPDCITVDQDSNGNTEMVGFEDSAAANSLPTNTGNLAIAKSVRLDISFKTPSHTGLQ
TTQL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25342-26749(+)
Potential amino acid sequence	MQGESLSLIHGILNDEIDSFCKQVAAENMARKPYINWAIKRVTRSLQVLWPRSRTNIFGSSATG LSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVKTDSLKTVENT AIPIIMLVVEVPCDLICSIQSPKDGPDCITVDQDSNGNTEMVGFEDSAAANSLPTNTGNLAIAK SVRLDISFKTPSHTGLQTTQLPDVAFPLQPPELLNCPMQGESLSLIHGILNDEIDSFCKQVAAE NMARKPYINWAIKRVTRSLQVLWPRSRTNIFGSSATGLSLPSSDVDLVVCLPPVRNLEPIKEAG ILEGRNGIKETCLQHAARYLANQEWVKTDSLKTVENTAIPIIMLVVEVPCDLICSIQSPKDGPD CITVDQDSNGNTEMVGFEDSAAANSLPTNTGNLAIAKSVRLDISFKTPSHTGLQTTQLPDVAFP LQPPELLNCPMQGESLSLIHGILNDEIDSFCKQVAAENMARKPYINWAIKRVTRSLQVLWPRSR TNIFGSSATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVK TDSLKTVENTAIPIIMLVVEVPCDLICSIQSPKDGPDCITVDQDSNGNTEMVGFEDSAAANSLP TNTGNLAIAKSVRLDISFKTPSHTGLQTTQLPDVAFPLQPPELLNCPMQGESLSLIHGILNDEI DSFCKQVAAENMARKPYINWAIKRVTRSLQVLWPRSRTNIFGSSATGLSLPSSDVDLVVCLPPV RNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVKTDSLKTVENTAIPIIMLVVEVPCDLIC SIQSPKDGPDCITVDQDSNGNTEMVGFEDSAAANSLPTNTGNLAIAKSVRLDISFKTPSHTGLQ TTQL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Liu et al., 2017

circRNA

Detail information of AT4G00060_circ_g.3

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