Plant Circular RNA Database

Detail information of AT4G12420_circ_g.10

			
						 General Information
					
						CircRNA Name
						AT4G12420_circ_g.10
					
						ID in PlantcircBase
						ath_circ_030549
					
						Alias
						Ath_circ_FC2609, Ath_circ_FC2610
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7351017-7352177  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, circRNA_finder
					
						Parent gene
						
							AT4G12420						
					
						Parent gene annotation
						
							Monocopper oxidase-like protein SKU5
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G12420_circ_g.1 AT4G12420_circ_g.2 AT4G12420_circ_g.3 AT4G12420_circ_g.4 AT4G12420_circ_g.5 AT4G12420_circ_g.6 AT4G12420_circ_g.7 AT4G12420_circ_g.8 AT4G12420_circ_g.9 AT4G12420_circ_g.11 						
					
						Support reads
						8
					
						Tissues
						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  
						
							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
						AT4G12420.2:4
AT4G12420.1:4

General Information
CircRNA Name	AT4G12420_circ_g.10
ID in PlantcircBase	ath_circ_030549
Alias	Ath_circ_FC2609, Ath_circ_FC2610
Organism	Arabidpsis thaliana
Position	chr4: 7351017-7352177 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, circRNA_finder
Parent gene	AT4G12420
Parent gene annotation	Monocopper oxidase-like protein SKU5
Parent gene strand	-
Alternative splicing	AT4G12420_circ_g.1 AT4G12420_circ_g.2 AT4G12420_circ_g.3 AT4G12420_circ_g.4 AT4G12420_circ_g.5 AT4G12420_circ_g.6 AT4G12420_circ_g.7 AT4G12420_circ_g.8 AT4G12420_circ_g.9 AT4G12420_circ_g.11
Support reads	8
Tissues	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	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	AT4G12420.2:4 AT4G12420.1:4

			
						 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  
						
							GAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTTCATTGGTTGTAACATTGAT
TGTAGGACCAGGAAACTTTCCATTTATAGCAATGACctgatggatcttgcttgattcatggaga
aagttttgtcgaattcgtcttgtggtccagggggtaactgacctttagcttttcctttagagtt
ggtatact

									
								

					

						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: 887
Transcript exons: 7351017-7351383,7351466-7351604,7351690-7351960,7352068-
7352177
CTGATGGATCTTGCTTGATTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTA
ACTGACCTTTAGCTTTTCCTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCT
CCATATGGTTTCGTTAACAACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGA
TCCATTGTAACCAAGAAAGAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTT
GAACTGTGTATGATCCTTCTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAA
ACTCGTCGAGATTCCCACATTCGACACTCGAAGTCTATAAGTTTTTCCAGGATGGACTGTGATT
GTTTCGAAATCGATCCCATCAGCAACAAGCGTGTCATTGTATCGGTAAGGTCCTTTTCCATTAA
TGAGAACTCCATCAGGCATTCCAAGATCTTTACCATCATCCAAAGCCTTCCTCAAAGCCGTGTG
GTTCCTTATGTACCAATCACCAATGGTAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACT
GGAATAATAGCTCTAGGATTGACAACAAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTA
GAGATGGAAAGTAGAAGAAACTACCAATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCA
CTTTGGTGGGATTGGACAATTGGTTCCTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGG
ATTCCATTCCAATGAAGAAGAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTT
CATTGGTTGTAACATTGATTGTAGGACCAGGAAACTTTCCATTTATAGCAATGAC
						
					

						Genomic sequence
						
							CTGATGGATCTTGCTTGATTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTA
ACTGACCTTTAGCTTTTCCTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCT
CCATATGGTTTCGTTAACAACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGA
TCCATTGTAACCAAGAAAGAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTT
GAACTGTGTATGATCCTTCTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAA
ACTCGTCGAGATTCCCACATTCGACACTCGAAGTCTATAAGTTTTTCCTGTTACCATCAGAAGA
GAATATAGTCCATTAAAAACCTGTAAACAAACCAAAACAAAGACTCTTGGATTATAAAGACTCA
CCAGGATGGACTGTGATTGTTTCGAAATCGATCCCATCAGCAACAAGCGTGTCATTGTATCGGT
AAGGTCCTTTTCCATTAATGAGAACTCCATCAGGCATTCCAAGATCTTTACCATCATCCAAAGC
CTTCCTCAAAGCCTACATTTTCACAAAATGTTAGAAAGAAACCTCTCAAAATGTCAATTGCTTG
AAGAGAAAGCGAAGATGGCTAAAAACTACTAACCGTGTGGTTCCTTATGTACCAATCACCAATG
GTAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACTGGAATAATAGCTCTAGGATTGACAA
CAAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTAGAGATGGAAAGTAGAAGAAACTACC
AATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCACTTTGGTGGGATTGGACAATTGGTT
CCTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGGATTCCATTCCTATAATATCAAAACA
TATTCATTAGAGCTTTCTTCTTTCTTATTTCTTCTTCTTCACAACAATGTGAAGTCTCATAAAT
ACACAAACTTTTTGTGTTTCTTCTTACCAATGAAGAAGAAGTCCCTCGTCTAACTTGTTTCTGA
CATTAACAACCAGATTTTCATTGGTTGTAACATTGATTGTAGGACCAGGAAACTTTCCATTTAT
AGCAATGAC
						
					

			
		

Sequences
Splice junction sequence	GAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTTCATTGGTTGTAACATTGAT TGTAGGACCAGGAAACTTTCCATTTATAGCAATGACctgatggatcttgcttgattcatggaga aagttttgtcgaattcgtcttgtggtccagggggtaactgacctttagcttttcctttagagtt ggtatact
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: 887 Transcript exons: 7351017-7351383,7351466-7351604,7351690-7351960,7352068- 7352177 CTGATGGATCTTGCTTGATTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTA ACTGACCTTTAGCTTTTCCTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCT CCATATGGTTTCGTTAACAACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGA TCCATTGTAACCAAGAAAGAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTT GAACTGTGTATGATCCTTCTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAA ACTCGTCGAGATTCCCACATTCGACACTCGAAGTCTATAAGTTTTTCCAGGATGGACTGTGATT GTTTCGAAATCGATCCCATCAGCAACAAGCGTGTCATTGTATCGGTAAGGTCCTTTTCCATTAA TGAGAACTCCATCAGGCATTCCAAGATCTTTACCATCATCCAAAGCCTTCCTCAAAGCCGTGTG GTTCCTTATGTACCAATCACCAATGGTAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACT GGAATAATAGCTCTAGGATTGACAACAAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTA GAGATGGAAAGTAGAAGAAACTACCAATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCA CTTTGGTGGGATTGGACAATTGGTTCCTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGG ATTCCATTCCAATGAAGAAGAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTT CATTGGTTGTAACATTGATTGTAGGACCAGGAAACTTTCCATTTATAGCAATGAC
Genomic sequence	CTGATGGATCTTGCTTGATTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTA ACTGACCTTTAGCTTTTCCTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCT CCATATGGTTTCGTTAACAACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGA TCCATTGTAACCAAGAAAGAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTT GAACTGTGTATGATCCTTCTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAA ACTCGTCGAGATTCCCACATTCGACACTCGAAGTCTATAAGTTTTTCCTGTTACCATCAGAAGA GAATATAGTCCATTAAAAACCTGTAAACAAACCAAAACAAAGACTCTTGGATTATAAAGACTCA CCAGGATGGACTGTGATTGTTTCGAAATCGATCCCATCAGCAACAAGCGTGTCATTGTATCGGT AAGGTCCTTTTCCATTAATGAGAACTCCATCAGGCATTCCAAGATCTTTACCATCATCCAAAGC CTTCCTCAAAGCCTACATTTTCACAAAATGTTAGAAAGAAACCTCTCAAAATGTCAATTGCTTG AAGAGAAAGCGAAGATGGCTAAAAACTACTAACCGTGTGGTTCCTTATGTACCAATCACCAATG GTAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACTGGAATAATAGCTCTAGGATTGACAA CAAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTAGAGATGGAAAGTAGAAGAAACTACC AATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCACTTTGGTGGGATTGGACAATTGGTT CCTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGGATTCCATTCCTATAATATCAAAACA TATTCATTAGAGCTTTCTTCTTTCTTATTTCTTCTTCTTCACAACAATGTGAAGTCTCATAAAT ACACAAACTTTTTGTGTTTCTTCTTACCAATGAAGAAGAAGTCCCTCGTCTAACTTGTTTCTGA CATTAACAACCAGATTTTCATTGGTTGTAACATTGATTGTAGGACCAGGAAACTTTCCATTTAT AGCAATGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.283121525

Conservation Information
Conserved circRNAs	NA
PMCS	0.283121525

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT4G12420_circ_g.10

Address

Any questions?

Supported by