Plant Circular RNA Database

Detail information of AT5G05560_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G05560_circ_g.3
					
						ID in PlantcircBase
						ath_circ_036574
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 1643188-1648192  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT5G05560						
					
						Parent gene annotation
						
							E3 ubiquitin ligase, putative
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G05560_circ_g.2 AT5G05560_circ_g.4 AT5G05560_circ_g.5 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						AT5G05560.2:13
AT5G05560.1:13
AT5G05560.3:13

General Information
CircRNA Name	AT5G05560_circ_g.3
ID in PlantcircBase	ath_circ_036574
Alias	NA
Organism	Arabidpsis thaliana
Position	chr5: 1643188-1648192 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	AT5G05560
Parent gene annotation	E3 ubiquitin ligase, putative
Parent gene strand	+
Alternative splicing	AT5G05560_circ_g.2 AT5G05560_circ_g.4 AT5G05560_circ_g.5
Support reads	1
Tissues	root
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	AT5G05560.2:13 AT5G05560.1:13 AT5G05560.3:13

			
						 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  
						
							AGAGCCAAATGCTGTTCATGCTGGACTTCTGTTTGGCCTGGGATTACAGGGATATTTGCATGTG
TTAAACCTTAGTGACATATACCAATATTTCACTCAGccaacctacgttgaagagagggggaagt
tgaccataatgaaggactacgatgagaggacaatttggacaagtgaccgtctacctcttatgac
gtcgtata

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AGAGCCAAATGCTGTTCATGCTGGACTTCTGTTTGGCCTGGGATTACAGGGATATTTGCATGTG TTAAACCTTAGTGACATATACCAATATTTCACTCAGccaacctacgttgaagagagggggaagt tgaccataatgaaggactacgatgagaggacaatttggacaagtgaccgtctacctcttatgac gtcgtata
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.116756778

Conservation Information
Conserved circRNAs	NA
PMCS	0.116756778

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							1643224-1648189(+)
						
					

						Potential amino acid sequence
						
							MKDYDERTIWTSDRLPLMTSYNKGKMQHSVWAAEFIESNLEASASCSSGIVPDAVLSKRVSFRR
IWQAKGAKKAASKVFLATDNSVPVICFLILEQKKLLSVGLQTVEINNEILFDVKPDISWSVSAI
AAAPVVVTRSQVKIGLLPHLDIIVLSPENDLFLYSGKQCLCRYVLPSWLGESIGSGDGESAKTD
SGFRNLKITGLSDAVLGSINLSVNHSQIFRCALTGKPSSSLANDCIAAIAEGLRSDLYSLFLSL
LWGDGHSDLQGSSIHFEWEALCNIFLEICQKPTVVHRKQPKTASESSWEFLLISKFHKTYSRFH
NGITSINRLDLEGIVPFDSKICSEETLGSSCELMVQSLDCLHAVYESLKMDNLRKQDLHHLAVL
LCNIAKFLDEKCYLDYYIRDFPRLSTTIGACTTLSSSRKPPNLFRWLENCLRRGCLSTNFDDLP
DLIRRDGCSIVSWARKVVSFYSVLFGDKPEGRTLSSGVPCNIAPGSYSCNEELTILAMAGERFG
LHQLDLLPSGVSLPLRHALDSCRESPPADWPAIAYVLLGREDMALSVFRNFSSSKEFEMQSNTS
LISMSIPYMLHLHPVIVPSSESIGLENTKIEDTNSVDGSVIDGMEHIFNSYTQLRYGRDLRLNE
VRRLLCSARPVVVQTAANPTISDQEQQQDHLWRIAQRTAVLPLGRGAFTLSTIHTLLTEAFTVP
KLVLAGRLPSQQNAIVNLDPNIRNIQELKTWPEFHNAVAAGLRLAPLQGKVSRTWIRYNKPGEP
NAVHAGLLFGLGLQGYLHVLNLSDIYQYFTQPTYVEERGKLTIMKDYDERTIWTSDRLPLMTSY
NKGKMQHSVWAAEFIESNLEASASCSSGIVPDAVLSKRVSFRRIWQAKGAKKAASKVFLATDNS
VPVICFLILEQKKLLSVGLQTVEINNEILFDVKPDISWSVSAIAAAPVVVTRSQVKIGLLPHLD
IIVLSPENDLFLYSGKQCLCRYVLPSWLGESIGSGDGESAKTDSGFRNLKITGLSDAVLGSINL
SVNHSQIFRCALTGKPSSSLANDCIAAIAEGLRSDLYSLFLSLLWGDGHSDLQGSSIHFEWEAL
CNIFLEICQKPTVVHRKQPKTASESSWEFLLISKFHKTYSRFHNGITSINRLDLEGIVPFDSKI
CSEETLGSSCELMVQSLDCLHAVYESLKMDNLRKQDLHHLAVLLCNIAKFLDEKCYLDYYIRDF
PRLSTTIGACTTLSSSRKPPNLFRWLENCLRRGCLSTNFDDLPDLIRRDGCSIVSWARKVVSFY
SVLFGDKPEGRTLSSGVPCNIAPGSYSCNEELTILAMAGERFGLHQLDLLPSGVSLPLRHALDS
CRESPPADWPAIAYVLLGREDMALSVFRNFSSSKEFEMQSNTSLISMSIPYMLHLHPVIVPSSE
SIGLENTKIEDTNSVDGSVIDGMEHIFNSYTQLRYGRDLRLNEVRRLLCSARPVVVQTAANPTI
SDQEQQQDHLWRIAQRTAVLPLGRGAFTLSTIHTLLTEAFTVPKLVLAGRLPSQQNAIVNLDPN
IRNIQELKTWPEFHNAVAAGLRLAPLQGKVSRTWIRYNKPGEPNAVHAGLLFGLGLQGYLHVLN
LSDIYQYFTQPTYVEERGKLTIMKDYDERTIWTSDRLPLMTSYNKGKMQHSVWAAEFIESNLEA
SASCSSGIVPDAVLSKRVSFRRIWQAKGAKKAASKVFLATDNSVPVICFLILEQKKLLSVGLQT
VEINNEILFDVKPDISWSVSAIAAAPVVVTRSQVKIGLLPHLDIIVLSPENDLFLYSGKQCLCR
YVLPSWLGESIGSGDGESAKTDSGFRNLKITGLSDAVLGSINLSVNHSQIFRCALTGKPSSSLA
NDCIAAIAEGLRSDLYSLFLSLLWGDGHSDLQGSSIHFEWEALCNIFLEICQKPTVVHRKQPKT
ASESSWEFLLISKFHKTYSRFHNGITSINRLDLEGIVPFDSKICSEETLGSSCELMVQSLDCLH
AVYESLKMDNLRKQDLHHLAVLLCNIAKFLDEKCYLDYYIRDFPRLSTTIGACTTLSSSRKPPN
LFRWLENCLRRGCLSTNFDDLPDLIRRDGCSIVSWARKVVSFYSVLFGDKPEGRTLSSGVPCNI
APGSYSCNEELTILAMAGERFGLHQLDLLPSGVSLPLRHALDSCRESPPADWPAIAYVLLGRED
MALSVFRNFSSSKEFEMQSNTSLISMSIPYMLHLHPVIVPSSESIGLENTKIEDTNSVDGSVID
GMEHIFNSYTQLRYGRDLRLNEVRRLLCSARPVVVQTAANPTISDQEQQQDHLWRIAQRTAVLP
LGRGAFTLSTIHTLLTEAFTVPKLVLAGRLPSQQNAIVNLDPNIRNIQELKTWPEFHNAVAAGL
RLAPLQGKVSRTWIRYNKPGEPNAVHAGLLFGLGLQGYLHVLNLSDIYQYFTQPTYVEERGKLT
IMKDYDERTIWTSDRLPLMTSYNKGKMQHSVWAAEFIESNLEASASCSSGIVPDAVLSKRVSFR
RIWQAKGAKKAASKVFLATDNSVPVICFLILEQKKLLSVGLQTVEINNEILFDVKPDISWSVSA
IAAAPVVVTRSQVKIGLLPHLDIIVLSPENDLFLYSGKQCLCRYVLPSWLGESIGSGDGESAKT
DSGFRNLKITGLSDAVLGSINLSVNHSQIFRCALTGKPSSSLANDCIAAIAEGLRSDLYSLFLS
LLWGDGHSDLQGSSIHFEWEALCNIFLEICQKPTVVHRKQPKTASESSWEFLLISKFHKTYSRF
HNGITSINRLDLEGIVPFDSKICSEETLGSSCELMVQSLDCLHAVYESLKMDNLRKQDLHHLAV
LLCNIAKFLDEKCYLDYYIRDFPRLSTTIGACTTLSSSRKPPNLFRWLENCLRRGCLSTNFDDL
PDLIRRDGCSIVSWARKVVSFYSVLFGDKPEGRTLSSGVPCNIAPGSYSCNEELTILAMAGERF
GLHQLDLLPSGVSLPLRHALDSCRESPPADWPAIAYVLLGREDMALSVFRNFSSSKEFEMQSNT
SLISMSIPYMLHLHPVIVPSSESIGLENTKIEDTNSVDGSVIDGMEHIFNSYTQLRYGRDLRLN
EVRRLLCSARPVVVQTAANPTISDQEQQQDHLWRIAQRTAVLPLGRGAFTLSTIHTLLTEAFTV
PKLVLAGRLPSQQNAIVNLDPNIRNIQELKTWPEFHNAVAAGLRLAPLQGKVSRTWIRYNKPGE
PNAVHAGLLFGLGLQGYLHVLNLSDIYQYFTQ(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	1643224-1648189(+)
Potential amino acid sequence	MKDYDERTIWTSDRLPLMTSYNKGKMQHSVWAAEFIESNLEASASCSSGIVPDAVLSKRVSFRR IWQAKGAKKAASKVFLATDNSVPVICFLILEQKKLLSVGLQTVEINNEILFDVKPDISWSVSAI AAAPVVVTRSQVKIGLLPHLDIIVLSPENDLFLYSGKQCLCRYVLPSWLGESIGSGDGESAKTD SGFRNLKITGLSDAVLGSINLSVNHSQIFRCALTGKPSSSLANDCIAAIAEGLRSDLYSLFLSL LWGDGHSDLQGSSIHFEWEALCNIFLEICQKPTVVHRKQPKTASESSWEFLLISKFHKTYSRFH NGITSINRLDLEGIVPFDSKICSEETLGSSCELMVQSLDCLHAVYESLKMDNLRKQDLHHLAVL LCNIAKFLDEKCYLDYYIRDFPRLSTTIGACTTLSSSRKPPNLFRWLENCLRRGCLSTNFDDLP DLIRRDGCSIVSWARKVVSFYSVLFGDKPEGRTLSSGVPCNIAPGSYSCNEELTILAMAGERFG LHQLDLLPSGVSLPLRHALDSCRESPPADWPAIAYVLLGREDMALSVFRNFSSSKEFEMQSNTS LISMSIPYMLHLHPVIVPSSESIGLENTKIEDTNSVDGSVIDGMEHIFNSYTQLRYGRDLRLNE VRRLLCSARPVVVQTAANPTISDQEQQQDHLWRIAQRTAVLPLGRGAFTLSTIHTLLTEAFTVP KLVLAGRLPSQQNAIVNLDPNIRNIQELKTWPEFHNAVAAGLRLAPLQGKVSRTWIRYNKPGEP NAVHAGLLFGLGLQGYLHVLNLSDIYQYFTQPTYVEERGKLTIMKDYDERTIWTSDRLPLMTSY NKGKMQHSVWAAEFIESNLEASASCSSGIVPDAVLSKRVSFRRIWQAKGAKKAASKVFLATDNS VPVICFLILEQKKLLSVGLQTVEINNEILFDVKPDISWSVSAIAAAPVVVTRSQVKIGLLPHLD IIVLSPENDLFLYSGKQCLCRYVLPSWLGESIGSGDGESAKTDSGFRNLKITGLSDAVLGSINL SVNHSQIFRCALTGKPSSSLANDCIAAIAEGLRSDLYSLFLSLLWGDGHSDLQGSSIHFEWEAL CNIFLEICQKPTVVHRKQPKTASESSWEFLLISKFHKTYSRFHNGITSINRLDLEGIVPFDSKI CSEETLGSSCELMVQSLDCLHAVYESLKMDNLRKQDLHHLAVLLCNIAKFLDEKCYLDYYIRDF PRLSTTIGACTTLSSSRKPPNLFRWLENCLRRGCLSTNFDDLPDLIRRDGCSIVSWARKVVSFY SVLFGDKPEGRTLSSGVPCNIAPGSYSCNEELTILAMAGERFGLHQLDLLPSGVSLPLRHALDS CRESPPADWPAIAYVLLGREDMALSVFRNFSSSKEFEMQSNTSLISMSIPYMLHLHPVIVPSSE SIGLENTKIEDTNSVDGSVIDGMEHIFNSYTQLRYGRDLRLNEVRRLLCSARPVVVQTAANPTI SDQEQQQDHLWRIAQRTAVLPLGRGAFTLSTIHTLLTEAFTVPKLVLAGRLPSQQNAIVNLDPN IRNIQELKTWPEFHNAVAAGLRLAPLQGKVSRTWIRYNKPGEPNAVHAGLLFGLGLQGYLHVLN LSDIYQYFTQPTYVEERGKLTIMKDYDERTIWTSDRLPLMTSYNKGKMQHSVWAAEFIESNLEA SASCSSGIVPDAVLSKRVSFRRIWQAKGAKKAASKVFLATDNSVPVICFLILEQKKLLSVGLQT VEINNEILFDVKPDISWSVSAIAAAPVVVTRSQVKIGLLPHLDIIVLSPENDLFLYSGKQCLCR YVLPSWLGESIGSGDGESAKTDSGFRNLKITGLSDAVLGSINLSVNHSQIFRCALTGKPSSSLA NDCIAAIAEGLRSDLYSLFLSLLWGDGHSDLQGSSIHFEWEALCNIFLEICQKPTVVHRKQPKT ASESSWEFLLISKFHKTYSRFHNGITSINRLDLEGIVPFDSKICSEETLGSSCELMVQSLDCLH AVYESLKMDNLRKQDLHHLAVLLCNIAKFLDEKCYLDYYIRDFPRLSTTIGACTTLSSSRKPPN LFRWLENCLRRGCLSTNFDDLPDLIRRDGCSIVSWARKVVSFYSVLFGDKPEGRTLSSGVPCNI APGSYSCNEELTILAMAGERFGLHQLDLLPSGVSLPLRHALDSCRESPPADWPAIAYVLLGRED MALSVFRNFSSSKEFEMQSNTSLISMSIPYMLHLHPVIVPSSESIGLENTKIEDTNSVDGSVID GMEHIFNSYTQLRYGRDLRLNEVRRLLCSARPVVVQTAANPTISDQEQQQDHLWRIAQRTAVLP LGRGAFTLSTIHTLLTEAFTVPKLVLAGRLPSQQNAIVNLDPNIRNIQELKTWPEFHNAVAAGL RLAPLQGKVSRTWIRYNKPGEPNAVHAGLLFGLGLQGYLHVLNLSDIYQYFTQPTYVEERGKLT IMKDYDERTIWTSDRLPLMTSYNKGKMQHSVWAAEFIESNLEASASCSSGIVPDAVLSKRVSFR RIWQAKGAKKAASKVFLATDNSVPVICFLILEQKKLLSVGLQTVEINNEILFDVKPDISWSVSA IAAAPVVVTRSQVKIGLLPHLDIIVLSPENDLFLYSGKQCLCRYVLPSWLGESIGSGDGESAKT DSGFRNLKITGLSDAVLGSINLSVNHSQIFRCALTGKPSSSLANDCIAAIAEGLRSDLYSLFLS LLWGDGHSDLQGSSIHFEWEALCNIFLEICQKPTVVHRKQPKTASESSWEFLLISKFHKTYSRF HNGITSINRLDLEGIVPFDSKICSEETLGSSCELMVQSLDCLHAVYESLKMDNLRKQDLHHLAV LLCNIAKFLDEKCYLDYYIRDFPRLSTTIGACTTLSSSRKPPNLFRWLENCLRRGCLSTNFDDL PDLIRRDGCSIVSWARKVVSFYSVLFGDKPEGRTLSSGVPCNIAPGSYSCNEELTILAMAGERF GLHQLDLLPSGVSLPLRHALDSCRESPPADWPAIAYVLLGREDMALSVFRNFSSSKEFEMQSNT SLISMSIPYMLHLHPVIVPSSESIGLENTKIEDTNSVDGSVIDGMEHIFNSYTQLRYGRDLRLN EVRRLLCSARPVVVQTAANPTISDQEQQQDHLWRIAQRTAVLPLGRGAFTLSTIHTLLTEAFTV PKLVLAGRLPSQQNAIVNLDPNIRNIQELKTWPEFHNAVAAGLRLAPLQGKVSRTWIRYNKPGE PNAVHAGLLFGLGLQGYLHVLNLSDIYQYFTQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT5G05560_circ_g.3

Address

Any questions?

Supported by