Plant Circular RNA Database

Detail information of AT4G09730_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G09730_circ_g.2
					
						ID in PlantcircBase
						ath_circ_030096
					
						Alias
						4:6137117-6138688
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 6137117-6138688  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G09730						
					
						Parent gene annotation
						
							RH39
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G09730_circ_g.1 AT4G09730_circ_g.3 AT4G09730_circ_g.4 AT4G09730_circ_g.5 AT4G09730_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						flower
					
						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
						AT4G09730.1:6

General Information
CircRNA Name	AT4G09730_circ_g.2
ID in PlantcircBase	ath_circ_030096
Alias	4:6137117-6138688
Organism	Arabidpsis thaliana
Position	chr4: 6137117-6138688 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G09730
Parent gene annotation	RH39
Parent gene strand	+
Alternative splicing	AT4G09730_circ_g.1 AT4G09730_circ_g.3 AT4G09730_circ_g.4 AT4G09730_circ_g.5 AT4G09730_circ_g.6
Support reads	2
Tissues	flower
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	AT4G09730.1:6

			
						 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  
						
							AGAAGGAGACTGTCCCACGCTAGTGTGCACGGATTTGGCTGCAAGGGGTCTGGACCTCGACGTT
GATCATGTAGTCATGTTTGATTTCCCAAAGAACTCGctgatgagagaagatgaagcaaaccttg
gtaaaaaaacaaagcctagacgtcccaggactgttgttctttgtcctacaagagaactatctga
gcaggttt

									
								

					

						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: 840
Transcript exons: 6137117-6137212,6137466-6137654,6137751-6137891,6138026-
6138166,6138318-6138460,6138559-6138688
CTGATGAGAGAAGATGAAGCAAACCTTGGTAAAAAAACAAAGCCTAGACGTCCCAGGACTGTTG
TTCTTTGTCCTACAAGAGAACTATCTGAGCAGGTTTACCGTGTGGCGAAGTCCATAAGTCATCA
CGCGAGGTTTAGATCTATATTGGTTAGTGGTGGTTCTCGGATAAGACCCCAGGAGGATTCTTTG
AACAATGCAATAGATATGGTTGTTGGAACCCCTGGTAGGATTCTTCAGCATATCGAAGAAGGAA
ACATGGTGTATGGAGATATCGCATATTTGGTATTGGATGAGGCAGATACTATGTTTGATCGTGG
CTTTGGTCCCGAAATTCGTAAATTCCTTGCCCCACTGAATCAACGTGCGTTGAAAACAAATGAC
CAAGGATTTCAAACCGTCTTAGTGACTGCTACTATGACAATGGCTGTTCAGAAGTTAGTCGATG
AGGAGTTTCAAGGGATAGAGCATTTGCGTACATCAACACTGCATAAAAAGATAGCAAACGCTCG
CCATGACTTCATCAAGCTTTCAGGTGGTGAAGATAAGCTAGAAGCACTTCTACAGGTTCTTGAA
CCTAGCCTAGCCAAAGGGAGCAAGGTGATGGTCTTCTGTAACACTTTGAACTCCAGTCGCGCTG
TTGATCACTATCTTTCTGAAAACCAGATCTCCACTGTAAATTATCACGGTGAAGTTCCAGCAGA
ACAAAGGGTTGAGAATTTGAAAAAGTTCAAGGACGAAGAAGGAGACTGTCCCACGCTAGTGTGC
ACGGATTTGGCTGCAAGGGGTCTGGACCTCGACGTTGATCATGTAGTCATGTTTGATTTCCCAA
AGAACTCG
						
					

						Genomic sequence
						
							CTGATGAGAGAAGATGAAGCAAACCTTGGTAAAAAAACAAAGCCTAGACGTCCCAGGACTGTTG
TTCTTTGTCCTACAAGAGAACTATCTGAGCAGGTTTGTCTTCACCAAGATTAGTTTCGTTGTTT
AGTTCGACTATAGTAACAATATGACTCTGCTGTTTCGGGGAAAAGGAAAAGTTGGAATCTTTAC
TTTAGCATAAAGTTTTGGTTACTTTCTTATAGGATGATGATAAAATTGGAGAATGTTTTAATAT
GTGATTATAGAATTTTTTACCAGTTTGTTATATCATAAATGTTTGTAGACAGAGAAATGGCGAA
AGAAAAACTAATTAAGGAATCTGCATTAGGTTTACCGTGTGGCGAAGTCCATAAGTCATCACGC
GAGGTTTAGATCTATATTGGTTAGTGGTGGTTCTCGGATAAGACCCCAGGAGGATTCTTTGAAC
AATGCAATAGATATGGTTGTTGGAACCCCTGGTAGGATTCTTCAGCATATCGAAGAAGGAAACA
TGGTGTATGGAGATATCGCATATTTGGTACGCACTACTTTGGGATCTTGACTTTATGTTCCATG
ATTCTTATGGTTTTAGGATCAACATTAAATTAAGGGCAATGCGAATCTCTTTACTCAGGTATTG
GATGAGGCAGATACTATGTTTGATCGTGGCTTTGGTCCCGAAATTCGTAAATTCCTTGCCCCAC
TGAATCAACGTGCGTTGAAAACAAATGACCAAGGATTTCAAACCGTCTTAGTGACTGCTACTAT
GACAATGGTATGCACATGTTCATTGGGCTCAATATTACACACTTGCACCATTCTTTGCTATTAT
CATGATTTATAAATTTGTTGCTCCATGCATCTTGAACTTCAGATATTAAGGTAGTGAATGAAAT
TGTGAGTTTTCAGGCTGTTCAGAAGTTAGTCGATGAGGAGTTTCAAGGGATAGAGCATTTGCGT
ACATCAACACTGCATAAAAAGATAGCAAACGCTCGCCATGACTTCATCAAGCTTTCAGGTGGTG
AAGATAAGCTAGAAGCACTTCTACAGGTAAACTACATCATTCAGTCTCTGATTTTTGAAGGCAA
TCAGAAATGTTAGGGTTCCTGTTTGGGTGCAAACATGTCCGAGTTACATGCACATTCTTTCTGG
TATGCTCCTGCTGTACTTATACATTATTTTTGCTTGGATGAGAATGCAGGTTCTTGAACCTAGC
CTAGCCAAAGGGAGCAAGGTGATGGTCTTCTGTAACACTTTGAACTCCAGTCGCGCTGTTGATC
ACTATCTTTCTGAAAACCAGATCTCCACTGTAAATTATCACGGTGAAGTTCCAGCAGAACAAAG
GTGGGATTAAAACAGCTTAGCCTTAAACGTGATCCATTTCTTGAGGAATGCAGTGCTTAGTATT
AACGTGTAAAATTGGTTTGCACTCATCTATCCAGGGTTGAGAATTTGAAAAAGTTCAAGGACGA
AGAAGGAGACTGTCCCACGCTAGTGTGCACGGATTTGGCTGCAAGGGGTCTGGACCTCGACGTT
GATCATGTAGTCATGTTTGATTTCCCAAAGAACTCG
						
					

			
		

Sequences
Splice junction sequence	AGAAGGAGACTGTCCCACGCTAGTGTGCACGGATTTGGCTGCAAGGGGTCTGGACCTCGACGTT GATCATGTAGTCATGTTTGATTTCCCAAAGAACTCGctgatgagagaagatgaagcaaaccttg gtaaaaaaacaaagcctagacgtcccaggactgttgttctttgtcctacaagagaactatctga gcaggttt
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: 840 Transcript exons: 6137117-6137212,6137466-6137654,6137751-6137891,6138026- 6138166,6138318-6138460,6138559-6138688 CTGATGAGAGAAGATGAAGCAAACCTTGGTAAAAAAACAAAGCCTAGACGTCCCAGGACTGTTG TTCTTTGTCCTACAAGAGAACTATCTGAGCAGGTTTACCGTGTGGCGAAGTCCATAAGTCATCA CGCGAGGTTTAGATCTATATTGGTTAGTGGTGGTTCTCGGATAAGACCCCAGGAGGATTCTTTG AACAATGCAATAGATATGGTTGTTGGAACCCCTGGTAGGATTCTTCAGCATATCGAAGAAGGAA ACATGGTGTATGGAGATATCGCATATTTGGTATTGGATGAGGCAGATACTATGTTTGATCGTGG CTTTGGTCCCGAAATTCGTAAATTCCTTGCCCCACTGAATCAACGTGCGTTGAAAACAAATGAC CAAGGATTTCAAACCGTCTTAGTGACTGCTACTATGACAATGGCTGTTCAGAAGTTAGTCGATG AGGAGTTTCAAGGGATAGAGCATTTGCGTACATCAACACTGCATAAAAAGATAGCAAACGCTCG CCATGACTTCATCAAGCTTTCAGGTGGTGAAGATAAGCTAGAAGCACTTCTACAGGTTCTTGAA CCTAGCCTAGCCAAAGGGAGCAAGGTGATGGTCTTCTGTAACACTTTGAACTCCAGTCGCGCTG TTGATCACTATCTTTCTGAAAACCAGATCTCCACTGTAAATTATCACGGTGAAGTTCCAGCAGA ACAAAGGGTTGAGAATTTGAAAAAGTTCAAGGACGAAGAAGGAGACTGTCCCACGCTAGTGTGC ACGGATTTGGCTGCAAGGGGTCTGGACCTCGACGTTGATCATGTAGTCATGTTTGATTTCCCAA AGAACTCG
Genomic sequence	CTGATGAGAGAAGATGAAGCAAACCTTGGTAAAAAAACAAAGCCTAGACGTCCCAGGACTGTTG TTCTTTGTCCTACAAGAGAACTATCTGAGCAGGTTTGTCTTCACCAAGATTAGTTTCGTTGTTT AGTTCGACTATAGTAACAATATGACTCTGCTGTTTCGGGGAAAAGGAAAAGTTGGAATCTTTAC TTTAGCATAAAGTTTTGGTTACTTTCTTATAGGATGATGATAAAATTGGAGAATGTTTTAATAT GTGATTATAGAATTTTTTACCAGTTTGTTATATCATAAATGTTTGTAGACAGAGAAATGGCGAA AGAAAAACTAATTAAGGAATCTGCATTAGGTTTACCGTGTGGCGAAGTCCATAAGTCATCACGC GAGGTTTAGATCTATATTGGTTAGTGGTGGTTCTCGGATAAGACCCCAGGAGGATTCTTTGAAC AATGCAATAGATATGGTTGTTGGAACCCCTGGTAGGATTCTTCAGCATATCGAAGAAGGAAACA TGGTGTATGGAGATATCGCATATTTGGTACGCACTACTTTGGGATCTTGACTTTATGTTCCATG ATTCTTATGGTTTTAGGATCAACATTAAATTAAGGGCAATGCGAATCTCTTTACTCAGGTATTG GATGAGGCAGATACTATGTTTGATCGTGGCTTTGGTCCCGAAATTCGTAAATTCCTTGCCCCAC TGAATCAACGTGCGTTGAAAACAAATGACCAAGGATTTCAAACCGTCTTAGTGACTGCTACTAT GACAATGGTATGCACATGTTCATTGGGCTCAATATTACACACTTGCACCATTCTTTGCTATTAT CATGATTTATAAATTTGTTGCTCCATGCATCTTGAACTTCAGATATTAAGGTAGTGAATGAAAT TGTGAGTTTTCAGGCTGTTCAGAAGTTAGTCGATGAGGAGTTTCAAGGGATAGAGCATTTGCGT ACATCAACACTGCATAAAAAGATAGCAAACGCTCGCCATGACTTCATCAAGCTTTCAGGTGGTG AAGATAAGCTAGAAGCACTTCTACAGGTAAACTACATCATTCAGTCTCTGATTTTTGAAGGCAA TCAGAAATGTTAGGGTTCCTGTTTGGGTGCAAACATGTCCGAGTTACATGCACATTCTTTCTGG TATGCTCCTGCTGTACTTATACATTATTTTTGCTTGGATGAGAATGCAGGTTCTTGAACCTAGC CTAGCCAAAGGGAGCAAGGTGATGGTCTTCTGTAACACTTTGAACTCCAGTCGCGCTGTTGATC ACTATCTTTCTGAAAACCAGATCTCCACTGTAAATTATCACGGTGAAGTTCCAGCAGAACAAAG GTGGGATTAAAACAGCTTAGCCTTAAACGTGATCCATTTCTTGAGGAATGCAGTGCTTAGTATT AACGTGTAAAATTGGTTTGCACTCATCTATCCAGGGTTGAGAATTTGAAAAAGTTCAAGGACGA AGAAGGAGACTGTCCCACGCTAGTGTGCACGGATTTGGCTGCAAGGGGTCTGGACCTCGACGTT GATCATGTAGTCATGTTTGATTTCCCAAAGAACTCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.204294346

Conservation Information
Conserved circRNAs	NA
PMCS	0.204294346

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT4G09730_circ_g.2

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