Plant Circular RNA Database

Detail information of 4_circ_ag.11

			
						 General Information
					
						CircRNA Name
						4_circ_ag.11
					
						ID in PlantcircBase
						ath_circ_029968
					
						Alias
						At_ciR531, Ath_circ_FC2235, Ath_circ_FC4957
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 5389946-5405831  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI, find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							4_circ_ag.2 AT4G08470_circ_g.1 4_circ_ag.2 AT4G08470_circ_g.3 4_circ_ag.4 AT4G08470_circ_g.5 4_circ_ag.6 4_circ_ag.7 AT4G08470_circ_g.8 AT4G08470_circ_g.9 4_circ_ag.10 						
					
						Support reads
						7/28
					
						Tissues
						leaf/root, aerial, inflorescences, seed, 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
						NA

General Information
CircRNA Name	4_circ_ag.11
ID in PlantcircBase	ath_circ_029968
Alias	At_ciR531, Ath_circ_FC2235, Ath_circ_FC4957
Organism	Arabidpsis thaliana
Position	chr4: 5389946-5405831 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	CIRI, find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	4_circ_ag.2 AT4G08470_circ_g.1 4_circ_ag.2 AT4G08470_circ_g.3 4_circ_ag.4 AT4G08470_circ_g.5 4_circ_ag.6 4_circ_ag.7 AT4G08470_circ_g.8 AT4G08470_circ_g.9 4_circ_ag.10
Support reads	7/28
Tissues	leaf/root, aerial, inflorescences, seed, 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	NA

			
						 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  
						
							CTTCCATTTCCATACCCCCTCAAGTTGTTGTATGCATTCTTGTGCCTGACTTCCCTGATCAAGA
AGTGAAACTTCCTTGACAGCAAAGAAGTCCCCATCTtctgaaatggcttcatacacagagccaa
acgatccttgtcgcagaagttgacccttttgccaagaagtattgatagatcccccagagacaca
aatcggtg

									
								

					

						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: 347
Transcript exons: 5389946-5390110,5405326-5405465,5405550-5405591
TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG
AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC
ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCGTGGAGATATTTCAAACCGTCAAGAAT
CTGTCTAGTGTACAAGGAGACTACAGAGTCCCGAAGCTGGTATCTTTGGTAGAGTTTTAGAAGG
GACCCTTGGGTTACAAGCTCAAGAAAAATGTACAAGTTTGACCCATCCTCCTTGGCTGTGCCAC
GATATCTCACAATATTCTGATGCTGAA
Transcript length: 383
Transcript exons: 5389946-5390123,5405305-5405465,5405550-5405593
TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG
AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC
ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCGTATCCTCCAACTCCTGTGAATAAAAC
CTTTATCGTGGAGATATTTCAAACCGTCAAGAATCTGTCTAGTGTACAAGGAGACTACAGAGTC
CCGAAGCTGGTATCTTTGGTAGAGTTTTAGAAGGGACCCTTGGGTTACAAGCTCAAGAAAAATG
TACAAGTTTGACCCATCCTCCTTGGCTGTGCCACGATATCTCACAATATTCTGATGCTGAAGC
Transcript length: 507
Transcript exons: 5389946-5390110,5404602-5404719,5405307-5405465,5405550-
5405614
TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG
AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC
ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCACGGGTTCGAGATCAGAGTAGGGGATC
TGACCAGTACACATTTCCAGCACAGTGCACCCGAGGCTCCATATATCAGCTGGACTTCCATAGC
CATCACTATCCTTTCGGTTAATAACCTTGTGAATAAAACCTTTATCGTGGAGATATTTCAAACC
GTCAAGAATCTGTCTAGTGTACAAGGAGACTACAGAGTCCCGAAGCTGGTATCTTTGGTAGAGT
TTTAGAAGGGACCCTTGGGTTACAAGCTCAAGAAAAATGTACAAGTTTGACCCATCCTCCTTGG
CTGTGCCACGATATCTCACAATATTCTGATGCTGAAGCTGACTAAGTAGTTTAATCTCC
Transcript length: 524
Transcript exons: 5389946-5390132,5404606-5404719,5405308-5405465,5405550-
5405614
TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG
AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC
ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCGTATCCTCCAACTGGATAAACAGTTCG
AGATCAGAGTAGGGGATCTGACCAGTACACATTTCCAGCACAGTGCACCCGAGGCTCCATATAT
CAGCTGGACTTCCATAGCCATCACTATCCTTTCGGTTAATAACCTGTGAATAAAACCTTTATCG
TGGAGATATTTCAAACCGTCAAGAATCTGTCTAGTGTACAAGGAGACTACAGAGTCCCGAAGCT
GGTATCTTTGGTAGAGTTTTAGAAGGGACCCTTGGGTTACAAGCTCAAGAAAAATGTACAAGTT
TGACCCATCCTCCTTGGCTGTGCCACGATATCTCACAATATTCTGATGCTGAAGCTGACTAAGT
AGTTTAATCTCC
						
					

						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	CTTCCATTTCCATACCCCCTCAAGTTGTTGTATGCATTCTTGTGCCTGACTTCCCTGATCAAGA AGTGAAACTTCCTTGACAGCAAAGAAGTCCCCATCTtctgaaatggcttcatacacagagccaa acgatccttgtcgcagaagttgacccttttgccaagaagtattgatagatcccccagagacaca aatcggtg
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: 347 Transcript exons: 5389946-5390110,5405326-5405465,5405550-5405591 TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCGTGGAGATATTTCAAACCGTCAAGAAT CTGTCTAGTGTACAAGGAGACTACAGAGTCCCGAAGCTGGTATCTTTGGTAGAGTTTTAGAAGG GACCCTTGGGTTACAAGCTCAAGAAAAATGTACAAGTTTGACCCATCCTCCTTGGCTGTGCCAC GATATCTCACAATATTCTGATGCTGAA Transcript length: 383 Transcript exons: 5389946-5390123,5405305-5405465,5405550-5405593 TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCGTATCCTCCAACTCCTGTGAATAAAAC CTTTATCGTGGAGATATTTCAAACCGTCAAGAATCTGTCTAGTGTACAAGGAGACTACAGAGTC CCGAAGCTGGTATCTTTGGTAGAGTTTTAGAAGGGACCCTTGGGTTACAAGCTCAAGAAAAATG TACAAGTTTGACCCATCCTCCTTGGCTGTGCCACGATATCTCACAATATTCTGATGCTGAAGC Transcript length: 507 Transcript exons: 5389946-5390110,5404602-5404719,5405307-5405465,5405550- 5405614 TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCACGGGTTCGAGATCAGAGTAGGGGATC TGACCAGTACACATTTCCAGCACAGTGCACCCGAGGCTCCATATATCAGCTGGACTTCCATAGC CATCACTATCCTTTCGGTTAATAACCTTGTGAATAAAACCTTTATCGTGGAGATATTTCAAACC GTCAAGAATCTGTCTAGTGTACAAGGAGACTACAGAGTCCCGAAGCTGGTATCTTTGGTAGAGT TTTAGAAGGGACCCTTGGGTTACAAGCTCAAGAAAAATGTACAAGTTTGACCCATCCTCCTTGG CTGTGCCACGATATCTCACAATATTCTGATGCTGAAGCTGACTAAGTAGTTTAATCTCC Transcript length: 524 Transcript exons: 5389946-5390132,5404606-5404719,5405308-5405465,5405550- 5405614 TCTGAAATGGCTTCATACACAGAGCCAAACGATCCTTGTCGCAGAAGTTGACCCTTTTGCCAAG AAGTATTGATAGATCCCCCAGAGACACAAATCGGTGAGGTATTGGATACTGTACTTGAGGAGTC ACCCTCGTTTGTAGTGAATGAGCATGCCTCATCAGTCGTATCCTCCAACTGGATAAACAGTTCG AGATCAGAGTAGGGGATCTGACCAGTACACATTTCCAGCACAGTGCACCCGAGGCTCCATATAT CAGCTGGACTTCCATAGCCATCACTATCCTTTCGGTTAATAACCTGTGAATAAAACCTTTATCG TGGAGATATTTCAAACCGTCAAGAATCTGTCTAGTGTACAAGGAGACTACAGAGTCCCGAAGCT GGTATCTTTGGTAGAGTTTTAGAAGGGACCCTTGGGTTACAAGCTCAAGAAAAATGTACAAGTT TGACCCATCCTCCTTGGCTGTGCCACGATATCTCACAATATTCTGATGCTGAAGCTGACTAAGT AGTTTAATCTCC
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
						0.780977634

Conservation Information
Conserved circRNAs	NA
PMCS	0.780977634

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR830-3p 						
					
						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	ath-miR830-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of 4_circ_ag.11

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