Plant Circular RNA Database

Detail information of AT4G34900_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G34900_circ_g.3
					
						ID in PlantcircBase
						ath_circ_034725
					
						Alias
						4:16628016-16629114
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 16628016-16629114  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G34900						
					
						Parent gene annotation
						
							Xanthine dehydrogenase 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							4_circ_ag.3 4_circ_ag.4 4_circ_ag.5 AT4G34890_circ_g.1 4_circ_ag.2 AT4G34890_circ_g.3 4_circ_ag.4 4_circ_ag.5 AT4G34900_circ_g.1 AT4G34900_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						seedling
					
						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
						AT4G34900.3:3
AT4G34900.1:3
AT4G34900.2:3

General Information
CircRNA Name	AT4G34900_circ_g.3
ID in PlantcircBase	ath_circ_034725
Alias	4:16628016-16629114
Organism	Arabidpsis thaliana
Position	chr4: 16628016-16629114 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G34900
Parent gene annotation	Xanthine dehydrogenase 2
Parent gene strand	-
Alternative splicing	4_circ_ag.3 4_circ_ag.4 4_circ_ag.5 AT4G34890_circ_g.1 4_circ_ag.2 AT4G34890_circ_g.3 4_circ_ag.4 4_circ_ag.5 AT4G34900_circ_g.1 AT4G34900_circ_g.2
Support reads	2
Tissues	seedling
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	AT4G34900.3:3 AT4G34900.1:3 AT4G34900.2:3

			
						 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  
						
							AAAGGATGCGGGCATGTGGAACTTTACTTAGCACTAAAGCAGCATGCAAGGTACAAGGCGGCAA
TGGGGTATCATCAGTATATTCTGCTTCCCCTGTGACcttgtactttccaacgaaactatggcga
tgaccagtaatcatcatgtccacatctctgtccagtatgagtttcacgggtcgattcaataggt
aggaagga

									
								

					

						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: 798
Transcript exons: 16628016-16628255,16628390-16628704,16628872-16629114
CTTGTACTTTCCAACGAAACTATGGCGATGACCAGTAATCATCATGTCCACATCTCTGTCCAGT
ATGAGTTTCACGGGTCGATTCAATAGGTAGGAAGGAACAGAAGCTGCTGCAGCAATGAAAGCTG
ATCTTGTTTCCTTACCACCAAAGCCACCACCAAGTCGTTTGGTTTTGCATACCACTTTAGACAT
TGGAAGACCAAGAACATGAGACACATATTTCTGGTGCTGTTGAGGAGCTTGTGTGGATGAAATC
ATATGAACTTCGTTGCCTCCATCTATAGTCCAAACCAAACTACCATTAGGCTCCAAGTAAAAGT
GTTCCTGACCACCCATTTGAACCTCTCCCTCTATTATTCTGTCACACTGACCAGATTGAAAGCA
CAGCTCGACATCCCCTTTTCTAAGCCTTCTCTCTGTGTTCGGATGGAAACTTTTAGCATTAATC
GCCTCCTTGATTGATAATATTGCTGGCAGTTCCTGATACCTAACGTCAACTTTTCTTGCTGCAG
TTTTTGCATTTTCATGTGTATCCGCGACAAGCACACCAATGACTTGTCCCACACACGTGACCAC
GTCTGTAGCAAATAATTCTTCGTCGGCAACAATTGGTCCAATCATATTATTCCCGGGAACATCT
TTGGCAAGAAACAGACCAACAAAACCAGATGAAGATTTGGCTGCCGAATCATCAACTGAAAGGA
TGCGGGCATGTGGAACTTTACTTAGCACTAAAGCAGCATGCAAGGTACAAGGCGGCAATGGGGT
ATCATCAGTATATTCTGCTTCCCCTGTGAC
						
					

						Genomic sequence
						
							CTTGTACTTTCCAACGAAACTATGGCGATGACCAGTAATCATCATGTCCACATCTCTGTCCAGT
ATGAGTTTCACGGGTCGATTCAATAGGTAGGAAGGAACAGAAGCTGCTGCAGCAATGAAAGCTG
ATCTTGTTTCCTTACCACCAAAGCCACCACCAAGTCGTTTGGTTTTGCATACCACTTTAGACAT
TGGAAGACCAAGAACATGAGACACATATTTCTGGTGCTGTTGAGGAGCCTGTATATAAATCATA
ACTACCAATATTGGCATACGCAGAGACAACATTATCATTTAATATCTTAAACTGGCTGATGCCT
AATGGTTTTTTGTACGTTATTCTAAATGATGTAAATACTAAATAATATGCTCACTTGTGTGGAT
GAAATCATATGAACTTCGTTGCCTCCATCTATAGTCCAAACCAAACTACCATTAGGCTCCAAGT
AAAAGTGTTCCTGACCACCCATTTGAACCTCTCCCTCTATTATTCTGTCACACTGACCAGATTG
AAAGCACAGCTCGACATCCCCTTTTCTAAGCCTTCTCTCTGTGTTCGGATGGAAACTTTTAGCA
TTAATCGCCTCCTTGATTGATAATATTGCTGGCAGTTCCTGATACCTAACGTCAACTTTTCTTG
CTGCAGTTTTTGCATTTTCATGTGTATCCGCGACAAGCACACCAATGACCTGAAATACAAGATT
AGCTTAGAAATAAGGGAACGAAAGCAGTACATGAAAACTTTTTAAACTTATTTGACGTAACAAA
ATCAATACATGCTCCTTTACTTTTCTGGTATCACTTCTTCTAAGATACAGATAAACTAAAAGTT
CCCCATTGAGGTTTATTTTCTTACTTGTCCCACACACGTGACCACGTCTGTAGCAAATAATTCT
TCGTCGGCAACAATTGGTCCAATCATATTATTCCCGGGAACATCTTTGGCAAGAAACAGACCAA
CAAAACCAGATGAAGATTTGGCTGCCGAATCATCAACTGAAAGGATGCGGGCATGTGGAACTTT
ACTTAGCACTAAAGCAGCATGCAAGGTACAAGGCGGCAATGGGGTATCATCAGTATATTCTGCT
TCCCCTGTGAC
						
					

			
		

Sequences
Splice junction sequence	AAAGGATGCGGGCATGTGGAACTTTACTTAGCACTAAAGCAGCATGCAAGGTACAAGGCGGCAA TGGGGTATCATCAGTATATTCTGCTTCCCCTGTGACcttgtactttccaacgaaactatggcga tgaccagtaatcatcatgtccacatctctgtccagtatgagtttcacgggtcgattcaataggt aggaagga
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: 798 Transcript exons: 16628016-16628255,16628390-16628704,16628872-16629114 CTTGTACTTTCCAACGAAACTATGGCGATGACCAGTAATCATCATGTCCACATCTCTGTCCAGT ATGAGTTTCACGGGTCGATTCAATAGGTAGGAAGGAACAGAAGCTGCTGCAGCAATGAAAGCTG ATCTTGTTTCCTTACCACCAAAGCCACCACCAAGTCGTTTGGTTTTGCATACCACTTTAGACAT TGGAAGACCAAGAACATGAGACACATATTTCTGGTGCTGTTGAGGAGCTTGTGTGGATGAAATC ATATGAACTTCGTTGCCTCCATCTATAGTCCAAACCAAACTACCATTAGGCTCCAAGTAAAAGT GTTCCTGACCACCCATTTGAACCTCTCCCTCTATTATTCTGTCACACTGACCAGATTGAAAGCA CAGCTCGACATCCCCTTTTCTAAGCCTTCTCTCTGTGTTCGGATGGAAACTTTTAGCATTAATC GCCTCCTTGATTGATAATATTGCTGGCAGTTCCTGATACCTAACGTCAACTTTTCTTGCTGCAG TTTTTGCATTTTCATGTGTATCCGCGACAAGCACACCAATGACTTGTCCCACACACGTGACCAC GTCTGTAGCAAATAATTCTTCGTCGGCAACAATTGGTCCAATCATATTATTCCCGGGAACATCT TTGGCAAGAAACAGACCAACAAAACCAGATGAAGATTTGGCTGCCGAATCATCAACTGAAAGGA TGCGGGCATGTGGAACTTTACTTAGCACTAAAGCAGCATGCAAGGTACAAGGCGGCAATGGGGT ATCATCAGTATATTCTGCTTCCCCTGTGAC
Genomic sequence	CTTGTACTTTCCAACGAAACTATGGCGATGACCAGTAATCATCATGTCCACATCTCTGTCCAGT ATGAGTTTCACGGGTCGATTCAATAGGTAGGAAGGAACAGAAGCTGCTGCAGCAATGAAAGCTG ATCTTGTTTCCTTACCACCAAAGCCACCACCAAGTCGTTTGGTTTTGCATACCACTTTAGACAT TGGAAGACCAAGAACATGAGACACATATTTCTGGTGCTGTTGAGGAGCCTGTATATAAATCATA ACTACCAATATTGGCATACGCAGAGACAACATTATCATTTAATATCTTAAACTGGCTGATGCCT AATGGTTTTTTGTACGTTATTCTAAATGATGTAAATACTAAATAATATGCTCACTTGTGTGGAT GAAATCATATGAACTTCGTTGCCTCCATCTATAGTCCAAACCAAACTACCATTAGGCTCCAAGT AAAAGTGTTCCTGACCACCCATTTGAACCTCTCCCTCTATTATTCTGTCACACTGACCAGATTG AAAGCACAGCTCGACATCCCCTTTTCTAAGCCTTCTCTCTGTGTTCGGATGGAAACTTTTAGCA TTAATCGCCTCCTTGATTGATAATATTGCTGGCAGTTCCTGATACCTAACGTCAACTTTTCTTG CTGCAGTTTTTGCATTTTCATGTGTATCCGCGACAAGCACACCAATGACCTGAAATACAAGATT AGCTTAGAAATAAGGGAACGAAAGCAGTACATGAAAACTTTTTAAACTTATTTGACGTAACAAA ATCAATACATGCTCCTTTACTTTTCTGGTATCACTTCTTCTAAGATACAGATAAACTAAAAGTT CCCCATTGAGGTTTATTTTCTTACTTGTCCCACACACGTGACCACGTCTGTAGCAAATAATTCT TCGTCGGCAACAATTGGTCCAATCATATTATTCCCGGGAACATCTTTGGCAAGAAACAGACCAA CAAAACCAGATGAAGATTTGGCTGCCGAATCATCAACTGAAAGGATGCGGGCATGTGGAACTTT ACTTAGCACTAAAGCAGCATGCAAGGTACAAGGCGGCAATGGGGTATCATCAGTATATTCTGCT TCCCCTGTGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.280041598

Conservation Information
Conserved circRNAs	NA
PMCS	0.280041598

			
						 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 AT4G34900_circ_g.3

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