Plant Circular RNA Database

Detail information of AT4G12420_circ_g.8

			
						 General Information
					
						CircRNA Name
						AT4G12420_circ_g.8
					
						ID in PlantcircBase
						ath_circ_030547
					
						Alias
						Ath_circ_FC2608
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7350570-7352177  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, 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.9 AT4G12420_circ_g.10 AT4G12420_circ_g.11 						
					
						Support reads
						2
					
						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  
						
							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
						AT4G12420.2:5
AT4G12420.1:5

General Information
CircRNA Name	AT4G12420_circ_g.8
ID in PlantcircBase	ath_circ_030547
Alias	Ath_circ_FC2608
Organism	Arabidpsis thaliana
Position	chr4: 7350570-7352177 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, 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.9 AT4G12420_circ_g.10 AT4G12420_circ_g.11
Support reads	2
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	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	AT4G12420.2:5 AT4G12420.1:5

			
						 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  
						
							GAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTTCATTGGTTGTAACATTGAT
TGTAGGACCAGGAAACTTTCCATTTATAGCAATGACccgacgacaaagaaggcgtagccactca
tgtgatagctttgcatcttagtgtcattgttctgaagaacgacttccatgaatccacgataagt
accattga

									
								

					

						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: 1253
Transcript exons: 7350570-7350935,7351017-7351383,7351466-7351604,7351690-
7351960,7352068-7352177
CCGACGACAAAGAAGGCGTAGCCACTCATGTGATAGCTTTGCATCTTAGTGTCATTGTTCTGAA
GAACGACTTCCATGAATCCACGATAAGTACCATTGATAATCGAAGTCGCCACTTTAGCTGGTCC
AGTTAAAGGTCTCTTAGGGAAATCAAGCTTATACACATCTTTAACTTTAAGCTTATCAGCTAGT
CTAATAGGTGTTGAAGGATTCTTGAACGATATGCCATTAAGCGTTGTTCTTCTCTTCCCACTAA
TCGTCACAGGCGGCATGTTCCTTAGAACGTAGACATCGGTTACATTGATCGAACCGTATTTAAA
TGATCCTTGCGGGTTAGGACGTGCACCACTTGCTGATACATTCCATCTGATGGATCTTGCTTGA
TTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTAACTGACCTTTAGCTTTTC
CTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCTCCATATGGTTTCGTTAAC
AACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGATCCATTGTAACCAAGAAA
GAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTTGAACTGTGTATGATCCTT
CTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAAACTCGTCGAGATTCCCAC
ATTCGACACTCGAAGTCTATAAGTTTTTCCAGGATGGACTGTGATTGTTTCGAAATCGATCCCA
TCAGCAACAAGCGTGTCATTGTATCGGTAAGGTCCTTTTCCATTAATGAGAACTCCATCAGGCA
TTCCAAGATCTTTACCATCATCCAAAGCCTTCCTCAAAGCCGTGTGGTTCCTTATGTACCAATC
ACCAATGGTAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACTGGAATAATAGCTCTAGGA
TTGACAACAAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTAGAGATGGAAAGTAGAAGA
AACTACCAATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCACTTTGGTGGGATTGGACA
ATTGGTTCCTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGGATTCCATTCCAATGAAGA
AGAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTTCATTGGTTGTAACATTGA
TTGTAGGACCAGGAAACTTTCCATTTATAGCAATGAC
						
					

						Genomic sequence
						
							CCGACGACAAAGAAGGCGTAGCCACTCATGTGATAGCTTTGCATCTTAGTGTCATTGTTCTGAA
GAACGACTTCCATGAATCCACGATAAGTACCATTGATAATCGAAGTCGCCACTTTAGCTGGTCC
AGTTAAAGGTCTCTTAGGGAAATCAAGCTTATACACATCTTTAACTTTAAGCTTATCAGCTAGT
CTAATAGGTGTTGAAGGATTCTTGAACGATATGCCATTAAGCGTTGTTCTTCTCTTCCCACTAA
TCGTCACAGGCGGCATGTTCCTTAGAACGTAGACATCGGTTACATTGATCGAACCGTATTTAAA
TGATCCTTGCGGGTTAGGACGTGCACCACTTGCTGATACATTCCATCTGCAATAACAAAGTATG
ATTCAAAGGTCAAAACTTGATGAAACTACAAGGAAAAAGAATTCGCTTTTTCGGATAACCAACC
TGATGGATCTTGCTTGATTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTAA
CTGACCTTTAGCTTTTCCTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCTC
CATATGGTTTCGTTAACAACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGAT
CCATTGTAACCAAGAAAGAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTTG
AACTGTGTATGATCCTTCTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAAA
CTCGTCGAGATTCCCACATTCGACACTCGAAGTCTATAAGTTTTTCCTGTTACCATCAGAAGAG
AATATAGTCCATTAAAAACCTGTAAACAAACCAAAACAAAGACTCTTGGATTATAAAGACTCAC
CAGGATGGACTGTGATTGTTTCGAAATCGATCCCATCAGCAACAAGCGTGTCATTGTATCGGTA
AGGTCCTTTTCCATTAATGAGAACTCCATCAGGCATTCCAAGATCTTTACCATCATCCAAAGCC
TTCCTCAAAGCCTACATTTTCACAAAATGTTAGAAAGAAACCTCTCAAAATGTCAATTGCTTGA
AGAGAAAGCGAAGATGGCTAAAAACTACTAACCGTGTGGTTCCTTATGTACCAATCACCAATGG
TAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACTGGAATAATAGCTCTAGGATTGACAAC
AAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTAGAGATGGAAAGTAGAAGAAACTACCA
ATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCACTTTGGTGGGATTGGACAATTGGTTC
CTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGGATTCCATTCCTATAATATCAAAACAT
ATTCATTAGAGCTTTCTTCTTTCTTATTTCTTCTTCTTCACAACAATGTGAAGTCTCATAAATA
CACAAACTTTTTGTGTTTCTTCTTACCAATGAAGAAGAAGTCCCTCGTCTAACTTGTTTCTGAC
ATTAACAACCAGATTTTCATTGGTTGTAACATTGATTGTAGGACCAGGAAACTTTCCATTTATA
GCAATGAC
						
					

			
		

Sequences
Splice junction sequence	GAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTTCATTGGTTGTAACATTGAT TGTAGGACCAGGAAACTTTCCATTTATAGCAATGACccgacgacaaagaaggcgtagccactca tgtgatagctttgcatcttagtgtcattgttctgaagaacgacttccatgaatccacgataagt accattga
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: 1253 Transcript exons: 7350570-7350935,7351017-7351383,7351466-7351604,7351690- 7351960,7352068-7352177 CCGACGACAAAGAAGGCGTAGCCACTCATGTGATAGCTTTGCATCTTAGTGTCATTGTTCTGAA GAACGACTTCCATGAATCCACGATAAGTACCATTGATAATCGAAGTCGCCACTTTAGCTGGTCC AGTTAAAGGTCTCTTAGGGAAATCAAGCTTATACACATCTTTAACTTTAAGCTTATCAGCTAGT CTAATAGGTGTTGAAGGATTCTTGAACGATATGCCATTAAGCGTTGTTCTTCTCTTCCCACTAA TCGTCACAGGCGGCATGTTCCTTAGAACGTAGACATCGGTTACATTGATCGAACCGTATTTAAA TGATCCTTGCGGGTTAGGACGTGCACCACTTGCTGATACATTCCATCTGATGGATCTTGCTTGA TTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTAACTGACCTTTAGCTTTTC CTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCTCCATATGGTTTCGTTAAC AACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGATCCATTGTAACCAAGAAA GAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTTGAACTGTGTATGATCCTT CTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAAACTCGTCGAGATTCCCAC ATTCGACACTCGAAGTCTATAAGTTTTTCCAGGATGGACTGTGATTGTTTCGAAATCGATCCCA TCAGCAACAAGCGTGTCATTGTATCGGTAAGGTCCTTTTCCATTAATGAGAACTCCATCAGGCA TTCCAAGATCTTTACCATCATCCAAAGCCTTCCTCAAAGCCGTGTGGTTCCTTATGTACCAATC ACCAATGGTAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACTGGAATAATAGCTCTAGGA TTGACAACAAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTAGAGATGGAAAGTAGAAGA AACTACCAATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCACTTTGGTGGGATTGGACA ATTGGTTCCTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGGATTCCATTCCAATGAAGA AGAAGTCCCTCGTCTAACTTGTTTCTGACATTAACAACCAGATTTTCATTGGTTGTAACATTGA TTGTAGGACCAGGAAACTTTCCATTTATAGCAATGAC
Genomic sequence	CCGACGACAAAGAAGGCGTAGCCACTCATGTGATAGCTTTGCATCTTAGTGTCATTGTTCTGAA GAACGACTTCCATGAATCCACGATAAGTACCATTGATAATCGAAGTCGCCACTTTAGCTGGTCC AGTTAAAGGTCTCTTAGGGAAATCAAGCTTATACACATCTTTAACTTTAAGCTTATCAGCTAGT CTAATAGGTGTTGAAGGATTCTTGAACGATATGCCATTAAGCGTTGTTCTTCTCTTCCCACTAA TCGTCACAGGCGGCATGTTCCTTAGAACGTAGACATCGGTTACATTGATCGAACCGTATTTAAA TGATCCTTGCGGGTTAGGACGTGCACCACTTGCTGATACATTCCATCTGCAATAACAAAGTATG ATTCAAAGGTCAAAACTTGATGAAACTACAAGGAAAAAGAATTCGCTTTTTCGGATAACCAACC TGATGGATCTTGCTTGATTCATGGAGAAAGTTTTGTCGAATTCGTCTTGTGGTCCAGGGGGTAA CTGACCTTTAGCTTTTCCTTTAGAGTTGGTATACTTCAAGATTCCAACTCCAGTGACTCTTCTC CATATGGTTTCGTTAACAACCCGAGCACTCGCGACAATGTAGTAATCAGAGCTCGCGTTTTGAT CCATTGTAACCAAGAAAGAATAAGACTGTCCAACATGAATATCCAAGCTTGTATAGTTTTGTTG AACTGTGTATGATCCTTCTGATTCCGCAAGAACTAAGTTGTGACCTTGAATCCTAAAGTTCAAA CTCGTCGAGATTCCCACATTCGACACTCGAAGTCTATAAGTTTTTCCTGTTACCATCAGAAGAG AATATAGTCCATTAAAAACCTGTAAACAAACCAAAACAAAGACTCTTGGATTATAAAGACTCAC CAGGATGGACTGTGATTGTTTCGAAATCGATCCCATCAGCAACAAGCGTGTCATTGTATCGGTA AGGTCCTTTTCCATTAATGAGAACTCCATCAGGCATTCCAAGATCTTTACCATCATCCAAAGCC TTCCTCAAAGCCTACATTTTCACAAAATGTTAGAAAGAAACCTCTCAAAATGTCAATTGCTTGA AGAGAAAGCGAAGATGGCTAAAAACTACTAACCGTGTGGTTCCTTATGTACCAATCACCAATGG TAACGGTAATATCACCGTCTGGAGTAGAGAAAGGGACTGGAATAATAGCTCTAGGATTGACAAC AAAGGAGCCAAAACCACCAGAAGCTCTCTGGAAATGTAGAGATGGAAAGTAGAAGAAACTACCA ATTTGGTCTTTAACTTGAAACTCATAAGTCCAATTCCACTTTGGTGGGATTGGACAATTGGTTC CTAAAACTCCATCTTGCCATGACACACGTCTCTGTTGGATTCCATTCCTATAATATCAAAACAT ATTCATTAGAGCTTTCTTCTTTCTTATTTCTTCTTCTTCACAACAATGTGAAGTCTCATAAATA CACAAACTTTTTGTGTTTCTTCTTACCAATGAAGAAGAAGTCCCTCGTCTAACTTGTTTCTGAC ATTAACAACCAGATTTTCATTGGTTGTAACATTGATTGTAGGACCAGGAAACTTTCCATTTATA GCAATGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.32095675

Conservation Information
Conserved circRNAs	NA
PMCS	0.32095675

			
						 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.8

Address

Any questions?

Supported by