Plant Circular RNA Database

Detail information of AT1G18870_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G18870_circ_g.1
					
						ID in PlantcircBase
						ath_circ_003358
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 6515722-6516950  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT1G18870						
					
						Parent gene annotation
						
							Isochorismate synthase 2, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						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
						AT1G18870.3:3
AT1G18870.2:3
AT1G18870.1:3

General Information
CircRNA Name	AT1G18870_circ_g.1
ID in PlantcircBase	ath_circ_003358
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 6515722-6516950 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	KNIFE, PcircRNA_finder
Parent gene	AT1G18870
Parent gene annotation	Isochorismate synthase 2, chloroplastic
Parent gene strand	+
Alternative splicing	NA
Support reads	1
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	AT1G18870.3:3 AT1G18870.2:3 AT1G18870.1:3

			
						 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  
						
							TCCTCTGATTCGTGCCTATGGAGGTCTTCGATTTGATCCTACAGGGAAGATCGCTGTGGAATGG
GAACATTTTGGCTCGTTTTACTTTACAGTGCCCCAGaggttcctacgctgtacactgtctatga
acggatgtgaggctgaccacaaagcaccacttggcacggtagaaacaaggactctatcaacggt
gccatctc

									
								

					

						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: 543
Transcript exons: 6515722-6515910,6516504-6516739,6516833-6516950
AGGTTCCTACGCTGTACACTGTCTATGAACGGATGTGAGGCTGACCACAAAGCACCACTTGGCA
CGGTAGAAACAAGGACTCTATCAACGGTGCCATCTCCGGCAGCCGCGACGGAGAGGCTGATAAC
CGCCGTCTCTGACCTCAAATCTCAACCGCCTCCATTCTCCTCCGGCATTGTCCGATTACAGGTA
CCAATTGAGCAGAAAATTGGAGCAATCGATTGGCTTCATGCACAGAACGAAATTCTTCCTCGCA
GTTTCTTTTCCCGTCGTAGCGATTCTGGCCGTCCAGATCTTCTTCAAGACTTCTCAAGTGACAA
TGGATCATCTGATCATAATCCAGTTAGTGTCGCTGGAATCGGGTCTGCTGTCTTTTTCCGCGAT
CTCGACCCGTTTTCTCATGATGACTGGAGATCAATCCGAAGGTTCTTGTCTTCAAAGTCTCCTC
TGATTCGTGCCTATGGAGGTCTTCGATTTGATCCTACAGGGAAGATCGCTGTGGAATGGGAACA
TTTTGGCTCGTTTTACTTTACAGTGCCCCAG
						
					

						Genomic sequence
						
							AGGTTCCTACGCTGTACACTGTCTATGAACGGATGTGAGGCTGACCACAAAGCACCACTTGGCA
CGGTAGAAACAAGGACTCTATCAACGGTGCCATCTCCGGCAGCCGCGACGGAGAGGCTGATAAC
CGCCGTCTCTGACCTCAAATCTCAACCGCCTCCATTCTCCTCCGGCATTGTCCGATTACAGGTA
CGTAAATTCGTAATAATTTCTTCATTAGTTTGTGGCTTTGTGCCATTCCAAAAATTCGTAAGGC
AAACAATGATTAAAAAACAAATGAGCTTAAGCCACGTGGAGCTCTTACATTGGTATGTGTGATA
TTGTTCCATTTCTTGCTGTCGGACTGTCGGTTGCATAAACATAGATTGACTCAACTTTATTGTT
AGATTTAAAATCTATCTACCCAAATAGTATGGGGGTCAGGTTTGAACTATTTTGCATCATTGGT
TCAATATTTTTGTATTTCTGCAAATAAATAAATTATTGTTAGATTTTTAGAAAAATATCAAGCA
AGTAGTCTCTTTTTATGAATGTTATCAATACTATTATAATGGATTTATCTGTTTATGAAAATAA
TTAAGGTAAATAGTTATTTCATGATGTAAGAAAGTAAGATTTTAATTTCATGGGTTTATCTGGA
AGAAAAATATTTGACTTTTAAGATAAAAGAAAATAAATAGTGGTAAAAAATCAAAAATCGAAAC
ATTAGCGACTTATATTCTCTCCCGCGCAAAAATAAAAATAAAGCCCTATTTTCATAGACGTTAA
TCTTGTGATTGAAGGTACCAATTGAGCAGAAAATTGGAGCAATCGATTGGCTTCATGCACAGAA
CGAAATTCTTCCTCGCAGTTTCTTTTCCCGTCGTAGCGATTCTGGCCGTCCAGATCTTCTTCAA
GACTTCTCAAGTGACAATGGATCATCTGATCATAATCCAGTTAGTGTCGCTGGAATCGGGTCTG
CTGTCTTTTTCCGCGATCTCGACCCGTTTTCTCATGATGACTGGAGATCAATCCGAAGGTACCA
GCACCGAAAGTTTTTTATCTTCATGAAGTTTGATTCTTTCTGCTGTTTATCTCTTCGCTTCTTA
TGTTCATTTCCCCTGTTTTGAAGGTTCTTGTCTTCAAAGTCTCCTCTGATTCGTGCCTATGGAG
GTCTTCGATTTGATCCTACAGGGAAGATCGCTGTGGAATGGGAACATTTTGGCTCGTTTTACTT
TACAGTGCCCCAG
						
					

			
		

Sequences
Splice junction sequence	TCCTCTGATTCGTGCCTATGGAGGTCTTCGATTTGATCCTACAGGGAAGATCGCTGTGGAATGG GAACATTTTGGCTCGTTTTACTTTACAGTGCCCCAGaggttcctacgctgtacactgtctatga acggatgtgaggctgaccacaaagcaccacttggcacggtagaaacaaggactctatcaacggt gccatctc
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: 543 Transcript exons: 6515722-6515910,6516504-6516739,6516833-6516950 AGGTTCCTACGCTGTACACTGTCTATGAACGGATGTGAGGCTGACCACAAAGCACCACTTGGCA CGGTAGAAACAAGGACTCTATCAACGGTGCCATCTCCGGCAGCCGCGACGGAGAGGCTGATAAC CGCCGTCTCTGACCTCAAATCTCAACCGCCTCCATTCTCCTCCGGCATTGTCCGATTACAGGTA CCAATTGAGCAGAAAATTGGAGCAATCGATTGGCTTCATGCACAGAACGAAATTCTTCCTCGCA GTTTCTTTTCCCGTCGTAGCGATTCTGGCCGTCCAGATCTTCTTCAAGACTTCTCAAGTGACAA TGGATCATCTGATCATAATCCAGTTAGTGTCGCTGGAATCGGGTCTGCTGTCTTTTTCCGCGAT CTCGACCCGTTTTCTCATGATGACTGGAGATCAATCCGAAGGTTCTTGTCTTCAAAGTCTCCTC TGATTCGTGCCTATGGAGGTCTTCGATTTGATCCTACAGGGAAGATCGCTGTGGAATGGGAACA TTTTGGCTCGTTTTACTTTACAGTGCCCCAG
Genomic sequence	AGGTTCCTACGCTGTACACTGTCTATGAACGGATGTGAGGCTGACCACAAAGCACCACTTGGCA CGGTAGAAACAAGGACTCTATCAACGGTGCCATCTCCGGCAGCCGCGACGGAGAGGCTGATAAC CGCCGTCTCTGACCTCAAATCTCAACCGCCTCCATTCTCCTCCGGCATTGTCCGATTACAGGTA CGTAAATTCGTAATAATTTCTTCATTAGTTTGTGGCTTTGTGCCATTCCAAAAATTCGTAAGGC AAACAATGATTAAAAAACAAATGAGCTTAAGCCACGTGGAGCTCTTACATTGGTATGTGTGATA TTGTTCCATTTCTTGCTGTCGGACTGTCGGTTGCATAAACATAGATTGACTCAACTTTATTGTT AGATTTAAAATCTATCTACCCAAATAGTATGGGGGTCAGGTTTGAACTATTTTGCATCATTGGT TCAATATTTTTGTATTTCTGCAAATAAATAAATTATTGTTAGATTTTTAGAAAAATATCAAGCA AGTAGTCTCTTTTTATGAATGTTATCAATACTATTATAATGGATTTATCTGTTTATGAAAATAA TTAAGGTAAATAGTTATTTCATGATGTAAGAAAGTAAGATTTTAATTTCATGGGTTTATCTGGA AGAAAAATATTTGACTTTTAAGATAAAAGAAAATAAATAGTGGTAAAAAATCAAAAATCGAAAC ATTAGCGACTTATATTCTCTCCCGCGCAAAAATAAAAATAAAGCCCTATTTTCATAGACGTTAA TCTTGTGATTGAAGGTACCAATTGAGCAGAAAATTGGAGCAATCGATTGGCTTCATGCACAGAA CGAAATTCTTCCTCGCAGTTTCTTTTCCCGTCGTAGCGATTCTGGCCGTCCAGATCTTCTTCAA GACTTCTCAAGTGACAATGGATCATCTGATCATAATCCAGTTAGTGTCGCTGGAATCGGGTCTG CTGTCTTTTTCCGCGATCTCGACCCGTTTTCTCATGATGACTGGAGATCAATCCGAAGGTACCA GCACCGAAAGTTTTTTATCTTCATGAAGTTTGATTCTTTCTGCTGTTTATCTCTTCGCTTCTTA TGTTCATTTCCCCTGTTTTGAAGGTTCTTGTCTTCAAAGTCTCCTCTGATTCGTGCCTATGGAG GTCTTCGATTTGATCCTACAGGGAAGATCGCTGTGGAATGGGAACATTTTGGCTCGTTTTACTT TACAGTGCCCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.227246909

Conservation Information
Conserved circRNAs	NA
PMCS	0.227246909

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6515746-6516947(+)
						
						Potential amino acid sequence
						
							MNGCEADHKAPLGTVETRTLSTVPSPAAATERLITAVSDLKSQPPPFSSGIVRLQVPIEQKIGA
IDWLHAQNEILPRSFFSRRSDSGRPDLLQDFSSDNGSSDHNPVSVAGIGSAVFFRDLDPFSHDD
WRSIRRFLSSKSPLIRAYGGLRFDPTGKIAVEWEHFGSFYFTVPQRFLRCTLSMNGCEADHKAP
LGTVETRTLSTVPSPAAATERLITAVSDLKSQPPPFSSGIVRLQVPIEQKIGAIDWLHAQNEIL
PRSFFSRRSDSGRPDLLQDFSSDNGSSDHNPVSVAGIGSAVFFRDLDPFSHDDWRSIRRFLSSK
SPLIRAYGGLRFDPTGKIAVEWEHFGSFYFTVPQRFLRCTLSMNGCEADHKAPLGTVETRTLST
VPSPAAATERLITAVSDLKSQPPPFSSGIVRLQVPIEQKIGAIDWLHAQNEILPRSFFSRRSDS
GRPDLLQDFSSDNGSSDHNPVSVAGIGSAVFFRDLDPFSHDDWRSIRRFLSSKSPLIRAYGGLR
FDPTGKIAVEWEHFGSFYFTVPQRFLRCTLSMNGCEADHKAPLGTVETRTLSTVPSPAAATERL
ITAVSDLKSQPPPFSSGIVRLQVPIEQKIGAIDWLHAQNEILPRSFFSRRSDSGRPDLLQDFSS
DNGSSDHNPVSVAGIGSAVFFRDLDPFSHDDWRSIRRFLSSKSPLIRAYGGLRFDPTGKIAVEW
EHFGSFYFTVPQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6515746-6516947(+)
Potential amino acid sequence	MNGCEADHKAPLGTVETRTLSTVPSPAAATERLITAVSDLKSQPPPFSSGIVRLQVPIEQKIGA IDWLHAQNEILPRSFFSRRSDSGRPDLLQDFSSDNGSSDHNPVSVAGIGSAVFFRDLDPFSHDD WRSIRRFLSSKSPLIRAYGGLRFDPTGKIAVEWEHFGSFYFTVPQRFLRCTLSMNGCEADHKAP LGTVETRTLSTVPSPAAATERLITAVSDLKSQPPPFSSGIVRLQVPIEQKIGAIDWLHAQNEIL PRSFFSRRSDSGRPDLLQDFSSDNGSSDHNPVSVAGIGSAVFFRDLDPFSHDDWRSIRRFLSSK SPLIRAYGGLRFDPTGKIAVEWEHFGSFYFTVPQRFLRCTLSMNGCEADHKAPLGTVETRTLST VPSPAAATERLITAVSDLKSQPPPFSSGIVRLQVPIEQKIGAIDWLHAQNEILPRSFFSRRSDS GRPDLLQDFSSDNGSSDHNPVSVAGIGSAVFFRDLDPFSHDDWRSIRRFLSSKSPLIRAYGGLR FDPTGKIAVEWEHFGSFYFTVPQRFLRCTLSMNGCEADHKAPLGTVETRTLSTVPSPAAATERL ITAVSDLKSQPPPFSSGIVRLQVPIEQKIGAIDWLHAQNEILPRSFFSRRSDSGRPDLLQDFSS DNGSSDHNPVSVAGIGSAVFFRDLDPFSHDDWRSIRRFLSSKSPLIRAYGGLRFDPTGKIAVEW EHFGSFYFTVPQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT1G18870_circ_g.1

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