Plant Circular RNA Database

Detail information of AT5G18620_circ_g.9

			
						 General Information
					
						CircRNA Name
						AT5G18620_circ_g.9
					
						ID in PlantcircBase
						ath_circ_039049
					
						Alias
						At_ciR5359
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 6200145-6201561  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, find_circ
					
						Parent gene
						
							AT5G18620						
					
						Parent gene annotation
						
							Chromatin remodeling factor17
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G18620_circ_g.8 AT5G18620_circ_g.10 						
					
						Support reads
						2/3
					
						Tissues
						leaf/seed
					
						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  
						
							CT-AC							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
						AT5G18620.1:6
AT5G18620.2:6

General Information
CircRNA Name	AT5G18620_circ_g.9
ID in PlantcircBase	ath_circ_039049
Alias	At_ciR5359
Organism	Arabidpsis thaliana
Position	chr5: 6200145-6201561 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, find_circ
Parent gene	AT5G18620
Parent gene annotation	Chromatin remodeling factor17
Parent gene strand	-
Alternative splicing	AT5G18620_circ_g.8 AT5G18620_circ_g.10
Support reads	2/3
Tissues	leaf/seed
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	CT-AC 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	AT5G18620.1:6 AT5G18620.2:6

			
						 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  
						
							CTAAGATTTGCTGAATTTTCTGCTTCTTCATCTTCTGCATTTCTTTGAGTCTAGCCTTCTCACG
TTTGCTGATCTCAGCTTTCTCCTCGTCTTCTTCGTCctgaaggggggttcccgtgataagaagc
cgatagttggtgctgaaaagtctcatggttttcgaaaggagtgaattctcatttttaattcgat
gtgcttca

									
								

					

						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: 852
Transcript exons: 6200145-6200366,6200450-6200629,6200722-6200819,6201041-
6201153,6201246-6201352,6201430-6201561
CTGAAGGGGGGTTCCCGTGATAAGAAGCCGATAGTTGGTGCTGAAAAGTCTCATGGTTTTCGAA
AGGAGTGAATTCTCATTTTTAATTCGATGTGCTTCATCAATGATTATATATCGCCAGCTAAAAC
GGCGCAATGTTGTCTTCTCTTTGATAGCCATCTCAAAGCTTGTTACACAAATGTCGAATTTCCC
TGCAACTAGCAGTTCTTCACGAATATGTCTTCTTTCCTCGGGATTACCGAGAAATTTCACAGCA
CGCAGGACAGGACAAAATCGGCGAATTTCATTCATCCAGTTACCAAGGGTTGATTTTGGAGCAA
CTACCATATGAGGGCCATTAATTCCCCTGTACTCATGCAGGTAAGCCAACAAAGAAATGGTTTG
AAGCGTCTTCCCCAGACCCATTTCATCTGCAAGAATCCCATTTATGCCGTTCTCATACAGCCGA
ATGAGCCAGTTTAAACCAGCTAATTGGTAATCTCTTAACTTCCCCTGAATACAAGCGGGCTGAG
TGAGCAACCGTGTGCCTCCAGATCCAACTATACCACCCTCTTCTTCTTTTAAACACTCTTCATC
TTCCTCTTCCTCGGTTAGTTTGGAAGAATGGCGACCCCTTCCTTTTCCCTTCTTCTGGGACGGA
GACGGGTCACTTTTAGCAAAATGTGCAAATAACTCAGTTTGCTGCAGAAGATACTTTATCCTCC
CCTTTCCTTTATTGTTCATATCAGCATCTATGGAAGCATTTTGGGAGTCTAAGATTTGCTGAAT
TTTCTGCTTCTTCATCTTCTGCATTTCTTTGAGTCTAGCCTTCTCACGTTTGCTGATCTCAGCT
TTCTCCTCGTCTTCTTCGTC
						
					

						Genomic sequence
						
							CTGAAGGGGGGTTCCCGTGATAAGAAGCCGATAGTTGGTGCTGAAAAGTCTCATGGTTTTCGAA
AGGAGTGAATTCTCATTTTTAATTCGATGTGCTTCATCAATGATTATATATCGCCAGCTAAAAC
GGCGCAATGTTGTCTTCTCTTTGATAGCCATCTCAAAGCTTGTTACACAAATGTCGAATTTCCC
TGCAACTAGCAGTTCTTCACGAATATGTCTCTGCATTATTTAAAATATATCTCAGAATCCTGCC
AGGTGCATATAAATGCAACCATTCAAATGTAAGAGCTATTATGACTTACTCTTTCCTCGGGATT
ACCGAGAAATTTCACAGCACGCAGGACAGGACAAAATCGGCGAATTTCATTCATCCAGTTACCA
AGGGTTGATTTTGGAGCAACTACCATATGAGGGCCATTAATTCCCCTGTACTCATGCAGGTAAG
CCAACAAAGAAATGGTTTGAAGCGTCTTCCCCAGACCCTAGACCATGAACAAAAACAATAAAGA
TTAGCATCAGATAACATTAGAGAGCTGAAAAATCTTATTATATGCTAAGATAATTAGTGGTTTA
CCATTTCATCTGCAAGAATCCCATTTATGCCGTTCTCATACAGCCGAATGAGCCAGTTTAAACC
AGCTAATTGGTAATCTCTTAACTTCCCCTGAATACCTGCAATATGAAGAGTATGAAGATCAGAT
CTCTAAATTCTACAGAATTTATGCAGTCCTACCTAGAAATTGTGAGCTCGCAACTGAAGAATAT
ATCAAACAACTCTACCAATCAAAGAAGTGGGCATAAGGTGTCAAATCCTATAATAACTTCGACT
CGCAATAGGACTTGAGCAAACATACGCTATATCAAGATATTAGGAGCAAAACAAAGGTACTTAC
AAGCGGGCTGAGTGAGCAACCGTGTGCCTCCAGATCCAACTATACCACCCTCTTCTTCTTTTAA
ACACTCTTCATCTTCCTCTTCCTCGGTTAGTTTGGAAGAATGGCGACCCCTGACGATAAAGTGA
AACCCAATAAATTATATTTCTGGAAACTTAATATGAATAACCACAATTTATTTTGAGATAAGTT
GCACTCAACACACCTTCCTTTTCCCTTCTTCTGGGACGGAGACGGGTCACTTTTAGCAAAATGT
GCAAATAACTCAGTTTGCTGCAGAAGATACTTTATCCTCCCCTTTCCTTTATTGTTCTAATAAA
TGGAATGATTGAGTTATTTCAATACCTCTGGATACTAAAGACAAGCAGCTCAGTTATTTACTAA
CTTACCATATCAGCATCTATGGAAGCATTTTGGGAGTCTAAGATTTGCTGAATTTTCTGCTTCT
TCATCTTCTGCATTTCTTTGAGTCTAGCCTTCTCACGTTTGCTGATCTCAGCTTTCTCCTCGTC
TTCTTCGTC
						
					

			
		

Sequences
Splice junction sequence	CTAAGATTTGCTGAATTTTCTGCTTCTTCATCTTCTGCATTTCTTTGAGTCTAGCCTTCTCACG TTTGCTGATCTCAGCTTTCTCCTCGTCTTCTTCGTCctgaaggggggttcccgtgataagaagc cgatagttggtgctgaaaagtctcatggttttcgaaaggagtgaattctcatttttaattcgat gtgcttca
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: 852 Transcript exons: 6200145-6200366,6200450-6200629,6200722-6200819,6201041- 6201153,6201246-6201352,6201430-6201561 CTGAAGGGGGGTTCCCGTGATAAGAAGCCGATAGTTGGTGCTGAAAAGTCTCATGGTTTTCGAA AGGAGTGAATTCTCATTTTTAATTCGATGTGCTTCATCAATGATTATATATCGCCAGCTAAAAC GGCGCAATGTTGTCTTCTCTTTGATAGCCATCTCAAAGCTTGTTACACAAATGTCGAATTTCCC TGCAACTAGCAGTTCTTCACGAATATGTCTTCTTTCCTCGGGATTACCGAGAAATTTCACAGCA CGCAGGACAGGACAAAATCGGCGAATTTCATTCATCCAGTTACCAAGGGTTGATTTTGGAGCAA CTACCATATGAGGGCCATTAATTCCCCTGTACTCATGCAGGTAAGCCAACAAAGAAATGGTTTG AAGCGTCTTCCCCAGACCCATTTCATCTGCAAGAATCCCATTTATGCCGTTCTCATACAGCCGA ATGAGCCAGTTTAAACCAGCTAATTGGTAATCTCTTAACTTCCCCTGAATACAAGCGGGCTGAG TGAGCAACCGTGTGCCTCCAGATCCAACTATACCACCCTCTTCTTCTTTTAAACACTCTTCATC TTCCTCTTCCTCGGTTAGTTTGGAAGAATGGCGACCCCTTCCTTTTCCCTTCTTCTGGGACGGA GACGGGTCACTTTTAGCAAAATGTGCAAATAACTCAGTTTGCTGCAGAAGATACTTTATCCTCC CCTTTCCTTTATTGTTCATATCAGCATCTATGGAAGCATTTTGGGAGTCTAAGATTTGCTGAAT TTTCTGCTTCTTCATCTTCTGCATTTCTTTGAGTCTAGCCTTCTCACGTTTGCTGATCTCAGCT TTCTCCTCGTCTTCTTCGTC
Genomic sequence	CTGAAGGGGGGTTCCCGTGATAAGAAGCCGATAGTTGGTGCTGAAAAGTCTCATGGTTTTCGAA AGGAGTGAATTCTCATTTTTAATTCGATGTGCTTCATCAATGATTATATATCGCCAGCTAAAAC GGCGCAATGTTGTCTTCTCTTTGATAGCCATCTCAAAGCTTGTTACACAAATGTCGAATTTCCC TGCAACTAGCAGTTCTTCACGAATATGTCTCTGCATTATTTAAAATATATCTCAGAATCCTGCC AGGTGCATATAAATGCAACCATTCAAATGTAAGAGCTATTATGACTTACTCTTTCCTCGGGATT ACCGAGAAATTTCACAGCACGCAGGACAGGACAAAATCGGCGAATTTCATTCATCCAGTTACCA AGGGTTGATTTTGGAGCAACTACCATATGAGGGCCATTAATTCCCCTGTACTCATGCAGGTAAG CCAACAAAGAAATGGTTTGAAGCGTCTTCCCCAGACCCTAGACCATGAACAAAAACAATAAAGA TTAGCATCAGATAACATTAGAGAGCTGAAAAATCTTATTATATGCTAAGATAATTAGTGGTTTA CCATTTCATCTGCAAGAATCCCATTTATGCCGTTCTCATACAGCCGAATGAGCCAGTTTAAACC AGCTAATTGGTAATCTCTTAACTTCCCCTGAATACCTGCAATATGAAGAGTATGAAGATCAGAT CTCTAAATTCTACAGAATTTATGCAGTCCTACCTAGAAATTGTGAGCTCGCAACTGAAGAATAT ATCAAACAACTCTACCAATCAAAGAAGTGGGCATAAGGTGTCAAATCCTATAATAACTTCGACT CGCAATAGGACTTGAGCAAACATACGCTATATCAAGATATTAGGAGCAAAACAAAGGTACTTAC AAGCGGGCTGAGTGAGCAACCGTGTGCCTCCAGATCCAACTATACCACCCTCTTCTTCTTTTAA ACACTCTTCATCTTCCTCTTCCTCGGTTAGTTTGGAAGAATGGCGACCCCTGACGATAAAGTGA AACCCAATAAATTATATTTCTGGAAACTTAATATGAATAACCACAATTTATTTTGAGATAAGTT GCACTCAACACACCTTCCTTTTCCCTTCTTCTGGGACGGAGACGGGTCACTTTTAGCAAAATGT GCAAATAACTCAGTTTGCTGCAGAAGATACTTTATCCTCCCCTTTCCTTTATTGTTCTAATAAA TGGAATGATTGAGTTATTTCAATACCTCTGGATACTAAAGACAAGCAGCTCAGTTATTTACTAA CTTACCATATCAGCATCTATGGAAGCATTTTGGGAGTCTAAGATTTGCTGAATTTTCTGCTTCT TCATCTTCTGCATTTCTTTGAGTCTAGCCTTCTCACGTTTGCTGATCTCAGCTTTCTCCTCGTC TTCTTCGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.309487929

Conservation Information
Conserved circRNAs	NA
PMCS	0.309487929

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6201502-6200147(-)
						
						Potential amino acid sequence
						
							MQKMKKQKIQQILDSQNASIDADMNNKGKGRIKYLLQQTELFAHFAKSDPSPSQKKGKGRGRHS
SKLTEEEEDEECLKEEEGGIVGSGGTRLLTQPACIQGKLRDYQLAGLNWLIRLYENGINGILAD
EMGLGKTLQTISLLAYLHEYRGINGPHMVVAPKSTLGNWMNEIRRFCPVLRAVKFLGNPEERRH
IREELLVAGKFDICVTSFEMAIKEKTTLRRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRL
LITGTPLQDEEDEEKAEISKREKARLKEMQKMKKQKIQQILDSQNASIDADMNNKGKGRIKYLL
QQTELFAHFAKSDPSPSQKKGKGRGRHSSKLTEEEEDEECLKEEEGGIVGSGGTRLLTQPACIQ
GKLRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLAYLHEYRGINGPHMVVAPKSTL
GNWMNEIRRFCPVLRAVKFLGNPEERRHIREELLVAGKFDICVTSFEMAIKEKTTLRRFSWRYI
IIDEAHRIKNENSLLSKTMRLFSTNYRLLITGTPLQDEEDEEKAEISKREKARLKEMQKMKKQK
IQQILDSQNASIDADMNNKGKGRIKYLLQQTELFAHFAKSDPSPSQKKGKGRGRHSSKLTEEEE
DEECLKEEEGGIVGSGGTRLLTQPACIQGKLRDYQLAGLNWLIRLYENGINGILADEMGLGKTL
QTISLLAYLHEYRGINGPHMVVAPKSTLGNWMNEIRRFCPVLRAVKFLGNPEERRHIREELLVA
GKFDICVTSFEMAIKEKTTLRRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRLLITGTPLQ
DEEDEEKAEISKREKARLKEMQKMKKQKIQQILDSQNASIDADMNNKGKGRIKYLLQQTELFAH
FAKSDPSPSQKKGKGRGRHSSKLTEEEEDEECLKEEEGGIVGSGGTRLLTQPACIQGKLRDYQL
AGLNWLIRLYENGINGILADEMGLGKTLQTISLLAYLHEYRGINGPHMVVAPKSTLGNWMNEIR
RFCPVLRAVKFLGNPEERRHIREELLVAGKFDICVTSFEMAIKEKTTLRRFSWRYIIIDEAHRI
KNENSLLSKTMRLFSTNYRLLITGTPLQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6201502-6200147(-)
Potential amino acid sequence	MQKMKKQKIQQILDSQNASIDADMNNKGKGRIKYLLQQTELFAHFAKSDPSPSQKKGKGRGRHS SKLTEEEEDEECLKEEEGGIVGSGGTRLLTQPACIQGKLRDYQLAGLNWLIRLYENGINGILAD EMGLGKTLQTISLLAYLHEYRGINGPHMVVAPKSTLGNWMNEIRRFCPVLRAVKFLGNPEERRH IREELLVAGKFDICVTSFEMAIKEKTTLRRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRL LITGTPLQDEEDEEKAEISKREKARLKEMQKMKKQKIQQILDSQNASIDADMNNKGKGRIKYLL QQTELFAHFAKSDPSPSQKKGKGRGRHSSKLTEEEEDEECLKEEEGGIVGSGGTRLLTQPACIQ GKLRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLAYLHEYRGINGPHMVVAPKSTL GNWMNEIRRFCPVLRAVKFLGNPEERRHIREELLVAGKFDICVTSFEMAIKEKTTLRRFSWRYI IIDEAHRIKNENSLLSKTMRLFSTNYRLLITGTPLQDEEDEEKAEISKREKARLKEMQKMKKQK IQQILDSQNASIDADMNNKGKGRIKYLLQQTELFAHFAKSDPSPSQKKGKGRGRHSSKLTEEEE DEECLKEEEGGIVGSGGTRLLTQPACIQGKLRDYQLAGLNWLIRLYENGINGILADEMGLGKTL QTISLLAYLHEYRGINGPHMVVAPKSTLGNWMNEIRRFCPVLRAVKFLGNPEERRHIREELLVA GKFDICVTSFEMAIKEKTTLRRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRLLITGTPLQ DEEDEEKAEISKREKARLKEMQKMKKQKIQQILDSQNASIDADMNNKGKGRIKYLLQQTELFAH FAKSDPSPSQKKGKGRGRHSSKLTEEEEDEECLKEEEGGIVGSGGTRLLTQPACIQGKLRDYQL AGLNWLIRLYENGINGILADEMGLGKTLQTISLLAYLHEYRGINGPHMVVAPKSTLGNWMNEIR RFCPVLRAVKFLGNPEERRHIREELLVAGKFDICVTSFEMAIKEKTTLRRFSWRYIIIDEAHRI KNENSLLSKTMRLFSTNYRLLITGTPLQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of AT5G18620_circ_g.9

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