Plant Circular RNA Database

Detail information of AT4G35730_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT4G35730_circ_g.4
					
						ID in PlantcircBase
						ath_circ_034856
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 16931494-16932497  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							AT4G35730						
					
						Parent gene annotation
						
							Regulator of Vps4 activity in the MVB pathway protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G35730_circ_g.1 AT4G35730_circ_g.2 AT4G35730_circ_g.3 AT4G35730_circ_g.5 AT4G35730_circ_g.6 AT4G35730_circ_g.7 						
					
						Support reads
						7
					
						Tissues
						inflorescences, 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
						AT4G35730.1:5

General Information
CircRNA Name	AT4G35730_circ_g.4
ID in PlantcircBase	ath_circ_034856
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 16931494-16932497 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	AT4G35730
Parent gene annotation	Regulator of Vps4 activity in the MVB pathway protein
Parent gene strand	+
Alternative splicing	AT4G35730_circ_g.1 AT4G35730_circ_g.2 AT4G35730_circ_g.3 AT4G35730_circ_g.5 AT4G35730_circ_g.6 AT4G35730_circ_g.7
Support reads	7
Tissues	inflorescences, 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	AT4G35730.1:5

			
						 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  
						
							TCTTGCAGGACGGGCCACGTAAGTTTGTTAGCGCTTCAAGCTTACCAGTTAATCGTGCAGCTAT
CAACGAGCCTATTGATCCTACCAAAGCAGTGCCAAGcaaaacggcggcgaagatggctgtggct
cgtataaagcttataaggaacaagagattagttgtggtgaagcaaatgaggcgtgacatcgctg
ttcttctt

									
								

					

						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: 642
Transcript exons: 16931494-16931626,16931713-16931816,16931908-16932079,16
932185-16932325,16932406-16932497
CAAAACGGCGGCGAAGATGGCTGTGGCTCGTATAAAGCTTATAAGGAACAAGAGATTAGTTGTG
GTGAAGCAAATGAGGCGTGACATCGCTGTTCTTCTTCAATCCGGTCAAGATGCCACTGCTCGAA
TCAGAGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTT
CTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGCAAAAGCAATGTCCTGTGGATCTT
AAGGAAGGTATTGCTAGTTTGATTTTTGCTGCGCCTAGATGCTCTGAAATTCCTGAGCTTGGAG
ATCTTAGAGACATCTTTGCGAAGAAATATGGGAAAGATTTTGTATCTGCTGCTACTGATTTGCG
TCCTAGCTGCGGTGTTAACCGGATGTTGATTGATAAGCTTTCGGTTAGAAATCCCGGTGGAGAA
TACAAACTGAAAATCATGAAGGAAATTGCAAAGGAATTCCAGGTTGATTGGGATACTACAGAGA
CAGAGCAAGAACTTCTCAAACCTCAAGAAGAAAGCATAGACGGGCCACGTAAGTTTGTTAGCGC
TTCAAGCTTACCAGTTAATCGTGCAGCTATCAACGAGCCTATTGATCCTACCAAAGCAGTGCCA
AG
						
					

						Genomic sequence
						
							CAAAACGGCGGCGAAGATGGCTGTGGCTCGTATAAAGCTTATAAGGAACAAGAGATTAGTTGTG
GTGAAGCAAATGAGGCGTGACATCGCTGTTCTTCTTCAATCCGGTCAAGATGCCACTGCTCGAA
TCAGAGTATTTCACTTTCCTGGTTCACTTTGTTAGAGTTTTCCCTGGATCGTTCAATTCAATGA
AGATTTTGCTTTTTTTGACAAATTTAGGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAG
CAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGCA
AAAGTATGTTCATATCTACTATCAGTTTTCATTTGTCTCTTTGCTTTGCTTCAGTTTGGCTTCT
TATATGTGTATGTGTTTGGCTTTCTTTTAGGCAATGTCCTGTGGATCTTAAGGAAGGTATTGCT
AGTTTGATTTTTGCTGCGCCTAGATGCTCTGAAATTCCTGAGCTTGGAGATCTTAGAGACATCT
TTGCGAAGAAATATGGGAAAGATTTTGTATCTGCTGCTACTGATTTGCGTCCTAGCTGCGGTGT
TAACCGGATGGTAACTAAATCATTCATGTTTCTGATTAGTCTAACTTGAACTGTGATTCGTTTT
TAGATGCAAGATGAAATCGAACTTGTTTTCTTCTTTCTTGTGCGTTTGTAGTTGATTGATAAGC
TTTCGGTTAGAAATCCCGGTGGAGAATACAAACTGAAAATCATGAAGGAAATTGCAAAGGAATT
CCAGGTTGATTGGGATACTACAGAGACAGAGCAAGAACTTCTCAAACCTCAAGAAGAAAGCATA
GTATGTCTCTTAATCTCCCCTCTCAACTTCCTCTTTCATTATTCAAAATCAGAATCTTAGAAGC
TGTGTTCTTCTTGCAGGACGGGCCACGTAAGTTTGTTAGCGCTTCAAGCTTACCAGTTAATCGT
GCAGCTATCAACGAGCCTATTGATCCTACCAAAGCAGTGCCAAG
						
					

			
		

Sequences
Splice junction sequence	TCTTGCAGGACGGGCCACGTAAGTTTGTTAGCGCTTCAAGCTTACCAGTTAATCGTGCAGCTAT CAACGAGCCTATTGATCCTACCAAAGCAGTGCCAAGcaaaacggcggcgaagatggctgtggct cgtataaagcttataaggaacaagagattagttgtggtgaagcaaatgaggcgtgacatcgctg ttcttctt
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: 642 Transcript exons: 16931494-16931626,16931713-16931816,16931908-16932079,16 932185-16932325,16932406-16932497 CAAAACGGCGGCGAAGATGGCTGTGGCTCGTATAAAGCTTATAAGGAACAAGAGATTAGTTGTG GTGAAGCAAATGAGGCGTGACATCGCTGTTCTTCTTCAATCCGGTCAAGATGCCACTGCTCGAA TCAGAGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTT CTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGCAAAAGCAATGTCCTGTGGATCTT AAGGAAGGTATTGCTAGTTTGATTTTTGCTGCGCCTAGATGCTCTGAAATTCCTGAGCTTGGAG ATCTTAGAGACATCTTTGCGAAGAAATATGGGAAAGATTTTGTATCTGCTGCTACTGATTTGCG TCCTAGCTGCGGTGTTAACCGGATGTTGATTGATAAGCTTTCGGTTAGAAATCCCGGTGGAGAA TACAAACTGAAAATCATGAAGGAAATTGCAAAGGAATTCCAGGTTGATTGGGATACTACAGAGA CAGAGCAAGAACTTCTCAAACCTCAAGAAGAAAGCATAGACGGGCCACGTAAGTTTGTTAGCGC TTCAAGCTTACCAGTTAATCGTGCAGCTATCAACGAGCCTATTGATCCTACCAAAGCAGTGCCA AG
Genomic sequence	CAAAACGGCGGCGAAGATGGCTGTGGCTCGTATAAAGCTTATAAGGAACAAGAGATTAGTTGTG GTGAAGCAAATGAGGCGTGACATCGCTGTTCTTCTTCAATCCGGTCAAGATGCCACTGCTCGAA TCAGAGTATTTCACTTTCCTGGTTCACTTTGTTAGAGTTTTCCCTGGATCGTTCAATTCAATGA AGATTTTGCTTTTTTTGACAAATTTAGGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAG CAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGCA AAAGTATGTTCATATCTACTATCAGTTTTCATTTGTCTCTTTGCTTTGCTTCAGTTTGGCTTCT TATATGTGTATGTGTTTGGCTTTCTTTTAGGCAATGTCCTGTGGATCTTAAGGAAGGTATTGCT AGTTTGATTTTTGCTGCGCCTAGATGCTCTGAAATTCCTGAGCTTGGAGATCTTAGAGACATCT TTGCGAAGAAATATGGGAAAGATTTTGTATCTGCTGCTACTGATTTGCGTCCTAGCTGCGGTGT TAACCGGATGGTAACTAAATCATTCATGTTTCTGATTAGTCTAACTTGAACTGTGATTCGTTTT TAGATGCAAGATGAAATCGAACTTGTTTTCTTCTTTCTTGTGCGTTTGTAGTTGATTGATAAGC TTTCGGTTAGAAATCCCGGTGGAGAATACAAACTGAAAATCATGAAGGAAATTGCAAAGGAATT CCAGGTTGATTGGGATACTACAGAGACAGAGCAAGAACTTCTCAAACCTCAAGAAGAAAGCATA GTATGTCTCTTAATCTCCCCTCTCAACTTCCTCTTTCATTATTCAAAATCAGAATCTTAGAAGC TGTGTTCTTCTTGCAGGACGGGCCACGTAAGTTTGTTAGCGCTTCAAGCTTACCAGTTAATCGT GCAGCTATCAACGAGCCTATTGATCCTACCAAAGCAGTGCCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.406317871

Conservation Information
Conserved circRNAs	NA
PMCS	0.406317871

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16931510-16932494(+)
						
						Potential amino acid sequence
						
							MAVARIKLIRNKRLVVVKQMRRDIAVLLQSGQDATARIRVEHVIREQNIQAANEIIELFCELIV
SRLTIITKQKQCPVDLKEGIASLIFAAPRCSEIPELGDLRDIFAKKYGKDFVSAATDLRPSCGV
NRMLIDKLSVRNPGGEYKLKIMKEIAKEFQVDWDTTETEQELLKPQEESIDGPRKFVSASSLPV
NRAAINEPIDPTKAVPSKTAAKMAVARIKLIRNKRLVVVKQMRRDIAVLLQSGQDATARIRVEH
VIREQNIQAANEIIELFCELIVSRLTIITKQKQCPVDLKEGIASLIFAAPRCSEIPELGDLRDI
FAKKYGKDFVSAATDLRPSCGVNRMLIDKLSVRNPGGEYKLKIMKEIAKEFQVDWDTTETEQEL
LKPQEESIDGPRKFVSASSLPVNRAAINEPIDPTKAVPSKTAAKMAVARIKLIRNKRLVVVKQM
RRDIAVLLQSGQDATARIRVEHVIREQNIQAANEIIELFCELIVSRLTIITKQKQCPVDLKEGI
ASLIFAAPRCSEIPELGDLRDIFAKKYGKDFVSAATDLRPSCGVNRMLIDKLSVRNPGGEYKLK
IMKEIAKEFQVDWDTTETEQELLKPQEESIDGPRKFVSASSLPVNRAAINEPIDPTKAVPSKTA
AKMAVARIKLIRNKRLVVVKQMRRDIAVLLQSGQDATARIRVEHVIREQNIQAANEIIELFCEL
IVSRLTIITKQKQCPVDLKEGIASLIFAAPRCSEIPELGDLRDIFAKKYGKDFVSAATDLRPSC
GVNRMLIDKLSVRNPGGEYKLKIMKEIAKEFQVDWDTTETEQELLKPQEESIDGPRKFVSASSL
PVNRAAINEPIDPTKAVP(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16931510-16932494(+)
Potential amino acid sequence	MAVARIKLIRNKRLVVVKQMRRDIAVLLQSGQDATARIRVEHVIREQNIQAANEIIELFCELIV SRLTIITKQKQCPVDLKEGIASLIFAAPRCSEIPELGDLRDIFAKKYGKDFVSAATDLRPSCGV NRMLIDKLSVRNPGGEYKLKIMKEIAKEFQVDWDTTETEQELLKPQEESIDGPRKFVSASSLPV NRAAINEPIDPTKAVPSKTAAKMAVARIKLIRNKRLVVVKQMRRDIAVLLQSGQDATARIRVEH VIREQNIQAANEIIELFCELIVSRLTIITKQKQCPVDLKEGIASLIFAAPRCSEIPELGDLRDI FAKKYGKDFVSAATDLRPSCGVNRMLIDKLSVRNPGGEYKLKIMKEIAKEFQVDWDTTETEQEL LKPQEESIDGPRKFVSASSLPVNRAAINEPIDPTKAVPSKTAAKMAVARIKLIRNKRLVVVKQM RRDIAVLLQSGQDATARIRVEHVIREQNIQAANEIIELFCELIVSRLTIITKQKQCPVDLKEGI ASLIFAAPRCSEIPELGDLRDIFAKKYGKDFVSAATDLRPSCGVNRMLIDKLSVRNPGGEYKLK IMKEIAKEFQVDWDTTETEQELLKPQEESIDGPRKFVSASSLPVNRAAINEPIDPTKAVPSKTA AKMAVARIKLIRNKRLVVVKQMRRDIAVLLQSGQDATARIRVEHVIREQNIQAANEIIELFCEL IVSRLTIITKQKQCPVDLKEGIASLIFAAPRCSEIPELGDLRDIFAKKYGKDFVSAATDLRPSC GVNRMLIDKLSVRNPGGEYKLKIMKEIAKEFQVDWDTTETEQELLKPQEESIDGPRKFVSASSL PVNRAAINEPIDPTKAVP(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT4G35730_circ_g.4

Address

Any questions?

Supported by