Plant Circular RNA Database

Detail information of AT5G20160_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G20160_circ_g.1
					
						ID in PlantcircBase
						ath_circ_039422
					
						Alias
						5:6804201-6804979
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 6804201-6804979  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G20160						
					
						Parent gene annotation
						
							Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G20160_circ_g.2 AT5G20160_circ_g.3 AT5G20160_circ_g.4 						
					
						Support reads
						1/1
					
						Tissues
						seedling;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  
						
							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
						AT5G20160.1:3
AT5G20160.3:1
AT5G20160.2:2

General Information
CircRNA Name	AT5G20160_circ_g.1
ID in PlantcircBase	ath_circ_039422
Alias	5:6804201-6804979
Organism	Arabidpsis thaliana
Position	chr5: 6804201-6804979 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G20160
Parent gene annotation	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein
Parent gene strand	-
Alternative splicing	AT5G20160_circ_g.2 AT5G20160_circ_g.3 AT5G20160_circ_g.4
Support reads	1/1
Tissues	seedling;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	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	AT5G20160.1:3 AT5G20160.3:1 AT5G20160.2:2

			
						 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  
						
							GCTGCTTGTAGTTAGTAGCTTGTTGAACGAGGTCAAGAATTGTTATCGATAACTGAGAATCTGC
AAGCGGATACGCTTTAGGGTTGACGACTTCTCCGGTcttgagatgttgaatctgtgatttcaat
tgactagcttcgttagatgtgactgaacaagcgataacaggtctagtcacaccacaggctcttc
ccaaggct

						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: 357
Transcript exons: 6804201-6804332,6804659-6804762,6804859-6804979
CTTGAGATGTTGAATCTGTGATTTCAATTGACTAGCTTCGTTAGATGTGACTGAACAAGCGATA
ACAGGTCTAGTCACACCACAGGCTCTTCCCAAGGCTTGCTTTGAAGGCACAAAGACATAAGGAA
CATTCTTATCCTCAGCAAGTAGGGGAAGATGAAGAAGAATCTCTAGAGGCTCAGCATCTGCAGC
CATGACAACAAACTCGGAGATTCCACGATTAAGAGTCTTCGTAGCTTCATTAGCACCCTTCTTG
AGCTGCTTGTAGTTAGTAGCTTGTTGAACGAGGTCAAGAATTGTTATCGATAACTGAGAATCTG
CAAGCGGATACGCTTTAGGGTTGACGACTTCTCCGGT
						
						Genomic sequence
						
							CTTGAGATGTTGAATCTGTGATTTCAATTGACTAGCTTCGTTAGATGTGACTGAACAAGCGATA
ACAGGTCTAGTCACACCACAGGCTCTTCCCAAGGCTTGCTTTGAAGGCACAAAGACATAAGGAA
CATTCTACAAAACATTCACAAAGAAAGTAAGAATATAGAAAACTAGTATATAAGAACAACAAAG
CATTACAGAATCAAAAACATACAAGCTAAACAAAATCATAAAAGACAATCATAAAGCTGTCATT
TTAAACTCCAACAAGTATGAAATCAGAGTTTAGTTAACAAAATGATATACAAAACTTGGCTGAA
CATTGGCACAAACTAATCAAACTATATCCTCAGCAAGTAAACTTAATTCTCTTCTATGAACTAA
GGAAACAAATATCTCATTTGCTAAATAAACTGGTGTATAATAAAAGAGAAACCCAGAGAAAGAA
GAAGTCAAACCTTATCCTCAGCAAGTAGGGGAAGATGAAGAAGAATCTCTAGAGGCTCAGCATC
TGCAGCCATGACAACAAACTCGGAGATTCCACGATTAAGAGTCTTCGTAGCTGAAATGAACAAA
TTTAAATAAATCAGGAACAACTTCACAAACATTAAACTCAATAAATAAGAGAGACAAACACACA
TGAGTAACAAGCGGATACCTTCATTAGCACCCTTCTTGAGCTGCTTGTAGTTAGTAGCTTGTTG
AACGAGGTCAAGAATTGTTATCGATAACTGAGAATCTGCAAGCGGATACGCTTTAGGGTTGACG
ACTTCTCCGGT

Sequences
Splice junction sequence	GCTGCTTGTAGTTAGTAGCTTGTTGAACGAGGTCAAGAATTGTTATCGATAACTGAGAATCTGC AAGCGGATACGCTTTAGGGTTGACGACTTCTCCGGTcttgagatgttgaatctgtgatttcaat tgactagcttcgttagatgtgactgaacaagcgataacaggtctagtcacaccacaggctcttc ccaaggct
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: 357 Transcript exons: 6804201-6804332,6804659-6804762,6804859-6804979 CTTGAGATGTTGAATCTGTGATTTCAATTGACTAGCTTCGTTAGATGTGACTGAACAAGCGATA ACAGGTCTAGTCACACCACAGGCTCTTCCCAAGGCTTGCTTTGAAGGCACAAAGACATAAGGAA CATTCTTATCCTCAGCAAGTAGGGGAAGATGAAGAAGAATCTCTAGAGGCTCAGCATCTGCAGC CATGACAACAAACTCGGAGATTCCACGATTAAGAGTCTTCGTAGCTTCATTAGCACCCTTCTTG AGCTGCTTGTAGTTAGTAGCTTGTTGAACGAGGTCAAGAATTGTTATCGATAACTGAGAATCTG CAAGCGGATACGCTTTAGGGTTGACGACTTCTCCGGT
Genomic sequence	CTTGAGATGTTGAATCTGTGATTTCAATTGACTAGCTTCGTTAGATGTGACTGAACAAGCGATA ACAGGTCTAGTCACACCACAGGCTCTTCCCAAGGCTTGCTTTGAAGGCACAAAGACATAAGGAA CATTCTACAAAACATTCACAAAGAAAGTAAGAATATAGAAAACTAGTATATAAGAACAACAAAG CATTACAGAATCAAAAACATACAAGCTAAACAAAATCATAAAAGACAATCATAAAGCTGTCATT TTAAACTCCAACAAGTATGAAATCAGAGTTTAGTTAACAAAATGATATACAAAACTTGGCTGAA CATTGGCACAAACTAATCAAACTATATCCTCAGCAAGTAAACTTAATTCTCTTCTATGAACTAA GGAAACAAATATCTCATTTGCTAAATAAACTGGTGTATAATAAAAGAGAAACCCAGAGAAAGAA GAAGTCAAACCTTATCCTCAGCAAGTAGGGGAAGATGAAGAAGAATCTCTAGAGGCTCAGCATC TGCAGCCATGACAACAAACTCGGAGATTCCACGATTAAGAGTCTTCGTAGCTGAAATGAACAAA TTTAAATAAATCAGGAACAACTTCACAAACATTAAACTCAATAAATAAGAGAGACAAACACACA TGAGTAACAAGCGGATACCTTCATTAGCACCCTTCTTGAGCTGCTTGTAGTTAGTAGCTTGTTG AACGAGGTCAAGAATTGTTATCGATAACTGAGAATCTGCAAGCGGATACGCTTTAGGGTTGACG ACTTCTCCGGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.280140499

Conservation Information
Conserved circRNAs	NA
PMCS	0.280140499

			
						 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 AT5G20160_circ_g.1

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