Plant Circular RNA Database

Detail information of AT3G29390_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G29390_circ_g.3
					
						ID in PlantcircBase
						ath_circ_024335
					
						Alias
						3:11289661-11292828
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 11289661-11292828  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G29390						
					
						Parent gene annotation
						
							Protein RIK
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G29390_circ_g.1 AT3G29390_circ_g.2 AT3G29390_circ_g.4 AT3G29390_circ_g.5 AT3G29390_circ_g.6 AT3G29390_circ_g.7 						
					
						Support reads
						2
					
						Tissues
						root
					
						Exon boundary  
						
							No-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
						AT3G29390.1:10
AT3G29390.2:10

General Information
CircRNA Name	AT3G29390_circ_g.3
ID in PlantcircBase	ath_circ_024335
Alias	3:11289661-11292828
Organism	Arabidpsis thaliana
Position	chr3: 11289661-11292828 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G29390
Parent gene annotation	Protein RIK
Parent gene strand	+
Alternative splicing	AT3G29390_circ_g.1 AT3G29390_circ_g.2 AT3G29390_circ_g.4 AT3G29390_circ_g.5 AT3G29390_circ_g.6 AT3G29390_circ_g.7
Support reads	2
Tissues	root
Exon boundary	No-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	AT3G29390.1:10 AT3G29390.2:10

			
						 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  
						
							AAGTGATAATGCAAGTAATGAAATGGAAAGGCGTCCACCCCGGAAGCGAAAGTTTCAGGAACTT
CCAGCTGATTGTAAGGTTCCAGAAAAAGACAAACAGagcacgtctgtaagatgacagaggacaa
cgatgaggctagggttcctctcagcgactcgtctacaacgaacgatgcttctcgaacgagacaa
aggtatca

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							AGCACGTCTGTAAGATGACAGAGGACAACGATGAGGCTAGGGTTCCTCTCAGCGACTCGTCTAC
AACGAACGATGCTTCTCGAACGAGACAAAGGTATCAACTTTCATTGTTTAACCAAGCCAATTAT
CAGCTTCAATCTGATACATTTTTTCGTGAAATTGACATTGAGTTTTAACCATTCGATTCGTGCC
CTTCTTTGGATTGTTACTTCAACTACTTCGATTTTGGTTTTGGAATCTCTTTTGTGAATAAAGC
TTTTGGCTTTTTTGATTTTTGTCTCTGAATCCTCATGTTTAGGCTATGGTATGGTAATCTCTAG
TCTCTTAATCAATTTTGAACTGATAGAGAATCTTATGAATTGTGAATAAAGATTGTGGCTTGTT
TGCTTTTGGCTCTGAAACCTCATGTTAAGGCTCTATGCTCATCTTTCTAGTCTCTTAATCAATT
TTGCTTCTTTAGTTTTTAACTGAGAAAATTCTATGAATTATGAATAAAGATTGTGGCTTTGTTT
GGTTTTGGCTCTGTCCCTTATGTTTAGGCTATGTTCATCTCTAATTCCTAACCTGTTTGCATCT
GTAGTTGTTAACTGATAGAGAATTTTATAATTTGGGTGGCAGGAGAAAGAGAAAGTGGGATAAG
CCAGCGGAGCAACTTGTTGCGGCTGGAGTTGCGTTTCCTCAGTTACTTCCTTTAGGCAACACTA
TGAATGTTCCTTCTATGTCACCATTGCTCCAAACGCTTTCGGTGCCTCTAGCAGTTCCAAAAGT
TAATCAAGTAAATGACTCTTACGCTCTTGCGGTGTTTGTTATACTTATTTTCGGGTCTAACCTT
TTTCTCACTTAGCTATTGCATTATGTACTATGGTATAGATGATATGTCATGTTTTCATCTAGTT
TGGTGTCTTGATGTATGTTCTTAGTGAATTGTAATACCTTCTTAAAATTGTTGCATCACTTGAA
TCATGTTGTCCCATGATTAGTAGTTTTACCATGTATTGGTCCAGTTCCCTCTGGTCATGTATGA
GACTCCACAAGCACCCGAAATATACTGTGTTTGTGACTTTAACATTATTGCCTTTATACTGAAC
GAGCTGTTTTTCGTGGATACGTCTTTTGTCTCCTTTTATCCTGTAATTCAAACATGGTGATTCG
TTGTAATTTTTCTTGCATGTGGTATCTAGCCTAAAATCCAGGATGAGGTGATCATAGCGCGAGA
AATTGTTATCAACGATGCTGAGGCTTCTCTTAGGCACAGGCTTACCAAACGCTCAACTCAAGAA
GATGTATGTGTAACTTTGCTATGCGTATTAGTTACACTTTTCCTATCTCTAGTTTAACTTCTAT
TCGTCGTGCAGATTCAGAGGTCTACCGGTGCTGTGGTGATTACTAGGTTTGTACAACATCCAAC
TCATGGAGAAGAAAGTCTTACAATAATCTTTCTAGATTCAATTGTTTAACTTCTTTTGTAGGGG
CAAGTATCGTCCTCCAAATGCACCTCCTGATGGTGAAAAGCCATTATATCTTCACATATCTGCC
GCTGCCCAGGTTTGTTATCCTTTTTGGCCTAAAGGATAGACTCTATAATATGGCAGAAAGTAAA
ACGTTTGTGGCTTAAAGAAATTCCCATATTCATATTTGAGAAGCTTTATTTGACCGCCTAGCTT
TGAGATGTTGGCCTGGTTTTTACGTATGTTATTGCAGTTGCAGTTAAAAGAGACTACAGAACGT
ATCTTAGCAGTTGATCGTGCAGCAGCTATGATTGAGGAGATGATGAAACAGAAATCAATTTCAC
AGATCGGATCAGTTGGTTTACAGACGGTCAAGGTATATACTGCGTGACACTTCTTTTTTGTAGT
TATGAAATTGGAACAGTAAGAAATTAAACCATATTTCCAGATGCTGAGCACATGCGTATATTTG
GGTTTCGAAGCTGACCCATCATCTAATGTTGCTGCTCGTATTCGTGGGCCTAATGTGAGTCTTC
CTTCAATATCTCCCCCCTTGCTTCTTTCTAATTTACACCAAAAGAATTGAATCTACAGTCTAAT
ATCAATCAAGAGAAGGGTTAGCCATTTGGTGTTAGGTTTTCATCTTTGATTAATAGTTGCACTT
TTTTTTATTTGTCTCAATCCATGAATTCGAGAGATTCTAATGTTGAAGCTCTCTCTGACATCTC
CGTGCAATCGGGAGAGAACTTTTTTTGTGTTGGTGGTGGTTGGCTTTCGTACATGCAGGATCAG
TATATAAATCACATTATGAATGAAACAGGAGCAACTGTTGTATTAAGAGGGCGTGGTTCAGGAA
GCCTTGAGAATCAACATGGAGATGGTAATATTTCCTTCGTTTGTGTTTTTATTTGCCTACTTAT
GAAGGTGTTATTTACCTCAAGGTGGATGTATCTGAATGATATTGTTAATGTAAATCCCTTTAAC
GCATTATGGTAGAAGCACAGCTACCGCTGCATCTATTATTATCCGGCAGCAACCCAAAGAGCAT
CGACGATGCAAAACGTTTAGCTGAGAATCTTATGGATACAATCAGTGTAGAATTTGGGGCTTCA
AGGTTAATTTTTCCTTCTATGTCTTCTATATTATATTCAGAAGCATGTTCCTACATCTTTGTCA
TTTCATTTGCTGATCTGTAATTGTATTTGGTTTTGCTACAAAATGTTTCAGGGTTTCCTCAAGC
AAGGTGTATGGTGCAGTACCACCACCACAGCAACTGATTTCTGGAGCTCCGGGTTCTGACCAGG
AGAACCAAAATTTGATTTCAACGTATGGTTTGATGACATCGATACCCATCACAGCACCACCATA
CGCTGTTAGTTCGTTTCCAGTTACTCCAGCAACAAGTCTTTATCCTCAGTTTCCAGTAATGCAA
TCTCTAGGAATATCAAATGGTGGCCCCTCGCAGCCCGTGGCTGGAGGAACTAGCTATAGTGGGT
ATGCTGGAATATACCCTCAAGCCACACCATTGCAACAAGTTGCTCAAGTCCTTAAGCAATCAAT
TTCTCCTGTTATCTCTACTGTGCCCCCTACTATGTTGACAGCTACGTCCTTATCGATCCCAAGT
GATAATGCAAGTAATGAAATGGAAAGGCGTCCACCCCGGAAGCGAAAGTTTCAGGAACTTCCAG
CTGATTGTAAGGTTCCAGAAAAAGACAAACAG
						
					

			
		

Sequences
Splice junction sequence	AAGTGATAATGCAAGTAATGAAATGGAAAGGCGTCCACCCCGGAAGCGAAAGTTTCAGGAACTT CCAGCTGATTGTAAGGTTCCAGAAAAAGACAAACAGagcacgtctgtaagatgacagaggacaa cgatgaggctagggttcctctcagcgactcgtctacaacgaacgatgcttctcgaacgagacaa aggtatca
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AGCACGTCTGTAAGATGACAGAGGACAACGATGAGGCTAGGGTTCCTCTCAGCGACTCGTCTAC AACGAACGATGCTTCTCGAACGAGACAAAGGTATCAACTTTCATTGTTTAACCAAGCCAATTAT CAGCTTCAATCTGATACATTTTTTCGTGAAATTGACATTGAGTTTTAACCATTCGATTCGTGCC CTTCTTTGGATTGTTACTTCAACTACTTCGATTTTGGTTTTGGAATCTCTTTTGTGAATAAAGC TTTTGGCTTTTTTGATTTTTGTCTCTGAATCCTCATGTTTAGGCTATGGTATGGTAATCTCTAG TCTCTTAATCAATTTTGAACTGATAGAGAATCTTATGAATTGTGAATAAAGATTGTGGCTTGTT TGCTTTTGGCTCTGAAACCTCATGTTAAGGCTCTATGCTCATCTTTCTAGTCTCTTAATCAATT TTGCTTCTTTAGTTTTTAACTGAGAAAATTCTATGAATTATGAATAAAGATTGTGGCTTTGTTT GGTTTTGGCTCTGTCCCTTATGTTTAGGCTATGTTCATCTCTAATTCCTAACCTGTTTGCATCT GTAGTTGTTAACTGATAGAGAATTTTATAATTTGGGTGGCAGGAGAAAGAGAAAGTGGGATAAG CCAGCGGAGCAACTTGTTGCGGCTGGAGTTGCGTTTCCTCAGTTACTTCCTTTAGGCAACACTA TGAATGTTCCTTCTATGTCACCATTGCTCCAAACGCTTTCGGTGCCTCTAGCAGTTCCAAAAGT TAATCAAGTAAATGACTCTTACGCTCTTGCGGTGTTTGTTATACTTATTTTCGGGTCTAACCTT TTTCTCACTTAGCTATTGCATTATGTACTATGGTATAGATGATATGTCATGTTTTCATCTAGTT TGGTGTCTTGATGTATGTTCTTAGTGAATTGTAATACCTTCTTAAAATTGTTGCATCACTTGAA TCATGTTGTCCCATGATTAGTAGTTTTACCATGTATTGGTCCAGTTCCCTCTGGTCATGTATGA GACTCCACAAGCACCCGAAATATACTGTGTTTGTGACTTTAACATTATTGCCTTTATACTGAAC GAGCTGTTTTTCGTGGATACGTCTTTTGTCTCCTTTTATCCTGTAATTCAAACATGGTGATTCG TTGTAATTTTTCTTGCATGTGGTATCTAGCCTAAAATCCAGGATGAGGTGATCATAGCGCGAGA AATTGTTATCAACGATGCTGAGGCTTCTCTTAGGCACAGGCTTACCAAACGCTCAACTCAAGAA GATGTATGTGTAACTTTGCTATGCGTATTAGTTACACTTTTCCTATCTCTAGTTTAACTTCTAT TCGTCGTGCAGATTCAGAGGTCTACCGGTGCTGTGGTGATTACTAGGTTTGTACAACATCCAAC TCATGGAGAAGAAAGTCTTACAATAATCTTTCTAGATTCAATTGTTTAACTTCTTTTGTAGGGG CAAGTATCGTCCTCCAAATGCACCTCCTGATGGTGAAAAGCCATTATATCTTCACATATCTGCC GCTGCCCAGGTTTGTTATCCTTTTTGGCCTAAAGGATAGACTCTATAATATGGCAGAAAGTAAA ACGTTTGTGGCTTAAAGAAATTCCCATATTCATATTTGAGAAGCTTTATTTGACCGCCTAGCTT TGAGATGTTGGCCTGGTTTTTACGTATGTTATTGCAGTTGCAGTTAAAAGAGACTACAGAACGT ATCTTAGCAGTTGATCGTGCAGCAGCTATGATTGAGGAGATGATGAAACAGAAATCAATTTCAC AGATCGGATCAGTTGGTTTACAGACGGTCAAGGTATATACTGCGTGACACTTCTTTTTTGTAGT TATGAAATTGGAACAGTAAGAAATTAAACCATATTTCCAGATGCTGAGCACATGCGTATATTTG GGTTTCGAAGCTGACCCATCATCTAATGTTGCTGCTCGTATTCGTGGGCCTAATGTGAGTCTTC CTTCAATATCTCCCCCCTTGCTTCTTTCTAATTTACACCAAAAGAATTGAATCTACAGTCTAAT ATCAATCAAGAGAAGGGTTAGCCATTTGGTGTTAGGTTTTCATCTTTGATTAATAGTTGCACTT TTTTTTATTTGTCTCAATCCATGAATTCGAGAGATTCTAATGTTGAAGCTCTCTCTGACATCTC CGTGCAATCGGGAGAGAACTTTTTTTGTGTTGGTGGTGGTTGGCTTTCGTACATGCAGGATCAG TATATAAATCACATTATGAATGAAACAGGAGCAACTGTTGTATTAAGAGGGCGTGGTTCAGGAA GCCTTGAGAATCAACATGGAGATGGTAATATTTCCTTCGTTTGTGTTTTTATTTGCCTACTTAT GAAGGTGTTATTTACCTCAAGGTGGATGTATCTGAATGATATTGTTAATGTAAATCCCTTTAAC GCATTATGGTAGAAGCACAGCTACCGCTGCATCTATTATTATCCGGCAGCAACCCAAAGAGCAT CGACGATGCAAAACGTTTAGCTGAGAATCTTATGGATACAATCAGTGTAGAATTTGGGGCTTCA AGGTTAATTTTTCCTTCTATGTCTTCTATATTATATTCAGAAGCATGTTCCTACATCTTTGTCA TTTCATTTGCTGATCTGTAATTGTATTTGGTTTTGCTACAAAATGTTTCAGGGTTTCCTCAAGC AAGGTGTATGGTGCAGTACCACCACCACAGCAACTGATTTCTGGAGCTCCGGGTTCTGACCAGG AGAACCAAAATTTGATTTCAACGTATGGTTTGATGACATCGATACCCATCACAGCACCACCATA CGCTGTTAGTTCGTTTCCAGTTACTCCAGCAACAAGTCTTTATCCTCAGTTTCCAGTAATGCAA TCTCTAGGAATATCAAATGGTGGCCCCTCGCAGCCCGTGGCTGGAGGAACTAGCTATAGTGGGT ATGCTGGAATATACCCTCAAGCCACACCATTGCAACAAGTTGCTCAAGTCCTTAAGCAATCAAT TTCTCCTGTTATCTCTACTGTGCCCCCTACTATGTTGACAGCTACGTCCTTATCGATCCCAAGT GATAATGCAAGTAATGAAATGGAAAGGCGTCCACCCCGGAAGCGAAAGTTTCAGGAACTTCCAG CTGATTGTAAGGTTCCAGAAAAAGACAAACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.175932779

Conservation Information
Conserved circRNAs	NA
PMCS	0.175932779

			
						 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 AT3G29390_circ_g.3

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