Plant Circular RNA Database

Detail information of AT5G56580_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G56580_circ_g.2
					
						ID in PlantcircBase
						ath_circ_044401
					
						Alias
						5:22904851-22906674
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 22904851-22906674  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G56580						
					
						Parent gene annotation
						
							Mitogen-activated protein kinase kinase 6
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G56580_circ_g.1 						
					
						Support reads
						2/1
					
						Tissues
						seedling;root
					
						Exon boundary  
						
							No-No							"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
						AT5G56580.1:8

General Information
CircRNA Name	AT5G56580_circ_g.2
ID in PlantcircBase	ath_circ_044401
Alias	5:22904851-22906674
Organism	Arabidpsis thaliana
Position	chr5: 22904851-22906674 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G56580
Parent gene annotation	Mitogen-activated protein kinase kinase 6
Parent gene strand	-
Alternative splicing	AT5G56580_circ_g.1
Support reads	2/1
Tissues	seedling;root
Exon boundary	No-No "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	AT5G56580.1:8

			
						 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  
						
							GAACGGAGAGCTTAAGCTGCTTCAAGTTCGATTTGATCTTCACCATTTTTTTTCTTTGGTTTCT
TCCTTGGGATTATCGCTCTCTTTCTAGGGTTTCTATttatctaaggtagttaacaggtggttcc
agagtgccaacaagtatcccgagatcgatatccttgtcctcaaacttttttatgaatggatgac
tctgagaa

									
								

					

						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: 201
Transcript exons: 22904851-22904935,22906559-22906674
TTATCTAAGGTAGTTAACAGGTGGTTCCAGAGTGCCAACAAGTATCCCGAGATCGATATCCTTG
TCCTCAAACTTTTTTATGAATGGGGATTCTTGAGCTGGAACGGAGAGCTTAAGCTGCTTCAAGT
TCGATTTGATCTTCACCATTTTTTTTCTTTGGTTTCTTCCTTGGGATTATCGCTCTCTTTCTAG
GGTTTCTAT
						
					

						Genomic sequence
						
							TTATCTAAGGTAGTTAACAGGTGGTTCCAGAGTGCCAACAAGTATCCCGAGATCGATATCCTTG
TCCTCAAACTTTTTTATGAATGGATGACTCTGAGAACATGAACAAACAAATCTTAGAATGTTTC
ATCAGAGATACTAATAACCAAGACTGAAAGAGGGTGGTGAGTAGGAATTACTTACCAAGAGGTC
CAAAGATGATGCTCTTGCTGGAGGATCTTTTTGTATGCTGTTATGAATGTAAAGAAGAATCATT
TAACCATTAGTTTTAATTCTTTGTGTGCCAATGCCAAGTATATGAAGATGAAAATAATGAGTTG
CCACTTACCAGGCTGATACAAAGGAGCAGAATTCAGGTGAGAATTGATCAGAAGGAGCAGTTGG
TGGTGGATTCTCTACTATTGCTGCCAAGAGTTCATAAAAGCTTGGCGGGTTTTGCTGATCTTCA
GATTCTAAATAAGGAAATCTTCCTATTGCACATTCTAACACTGACATCCCCAAACTCCAAATGT
CACTGCTGTAGTCATATGTGCTTCCACTAATCCTCTCAGGCTGTGAAGTGAAAAAAGAGACAAG
TCATGATTATGTATGTATACAATACAGAAACATCAAGAAATTTGTAATGTAGATGATTTTTGGA
ATGCTTTCGTACCGACATATAGTTGTAGGTTCCAACAAATGTGTCCCTCTGTCCCATGGAGCTA
GCAAGACTTGCACTTACACCAAAATCTGAGATTTTCACTTCCCCTTTATGGTTTACAAGAAGGT
TTGATGGCTTAATGTCTCTGTGTATGACATGTCTTTCGTTGTGTAGGTACACAAGACCTAGCAA
AACCTGTTCACAAGGAATAATATAAGTAAGAGTGACCGATAAATCATAAGAATGCTTTGAATAA
GCTGGTGGTGTATTTGACCTGTTTACAGACAACAGCAAGGTAAGGTTCAAGAATAGTCTTGACT
TGTCTAATCACATCCGCAAGAGATCCACGGTCCATGTATTCAAGCACAAGCGAAAAGGCTCCAT
TGTGATAGAAAGAATGGTAGCAAACTACTACATGTGGACATTGTGATGATGCTTGGTTTATTTT
AAGCTCCTGAACAATTTGCTTACGGATTTCTTCTTGTATATTCATCTGTATGACCTGTGATTCA
TAACATAAGCAAACTCAAACCCCAAGTCTACTCAAAGGCCTTAGTCACTAGCATAAAATCAAAA
GAAAGAAAAACAAGTAGTTTACCTTCATAGCAAAGAATTTGCCAACCCATTTATGACGAACTAA
TTGAACAACACCACCACTGCCTTTTCCGATGACTTTGACAGTCTCTAAGTCTTCAGCAGTAATT
TCGAAATCAAGCTCCTTGCTATCAGATTGCTATAAATGGAAGATAAAACACATACACAAGAAAT
CTCCTTTAATTCTCTGGAACATTGAGGTCTCTCATAAAACAAGATTTAGGGTTGAAAAATTTAC
CCTTGATTGCTTCTCATCTGACGTCAACCTTAGCCCCTTTTGATTCAGAAGAAAATCTCCATCG
TGAAATGTTCCACTCGCAGTCCTGTTTTCAAATTCAATGAAATTTCACAGAATCAATTCAAACC
CAGAAACAATGGATCAAATCTAATCGATTCTTGTTTACAATCTCGCCAAACAAAACAGATCCAA
GTAAAGAAAGGAGAAATCGCGAAACTTACAGGAAGGAAGAGATTGGGGATTCTTGAGCTGGAAC
GGAGAGCTTAAGCTGCTTCAAGTTCGATTTGATCTTCACCATTTTTTTTCTTTGGTTTCTTCCT
TGGGATTATCGCTCTCTTTCTAGGGTTTCTAT
						
					

			
		

Sequences
Splice junction sequence	GAACGGAGAGCTTAAGCTGCTTCAAGTTCGATTTGATCTTCACCATTTTTTTTCTTTGGTTTCT TCCTTGGGATTATCGCTCTCTTTCTAGGGTTTCTATttatctaaggtagttaacaggtggttcc agagtgccaacaagtatcccgagatcgatatccttgtcctcaaacttttttatgaatggatgac tctgagaa
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: 201 Transcript exons: 22904851-22904935,22906559-22906674 TTATCTAAGGTAGTTAACAGGTGGTTCCAGAGTGCCAACAAGTATCCCGAGATCGATATCCTTG TCCTCAAACTTTTTTATGAATGGGGATTCTTGAGCTGGAACGGAGAGCTTAAGCTGCTTCAAGT TCGATTTGATCTTCACCATTTTTTTTCTTTGGTTTCTTCCTTGGGATTATCGCTCTCTTTCTAG GGTTTCTAT
Genomic sequence	TTATCTAAGGTAGTTAACAGGTGGTTCCAGAGTGCCAACAAGTATCCCGAGATCGATATCCTTG TCCTCAAACTTTTTTATGAATGGATGACTCTGAGAACATGAACAAACAAATCTTAGAATGTTTC ATCAGAGATACTAATAACCAAGACTGAAAGAGGGTGGTGAGTAGGAATTACTTACCAAGAGGTC CAAAGATGATGCTCTTGCTGGAGGATCTTTTTGTATGCTGTTATGAATGTAAAGAAGAATCATT TAACCATTAGTTTTAATTCTTTGTGTGCCAATGCCAAGTATATGAAGATGAAAATAATGAGTTG CCACTTACCAGGCTGATACAAAGGAGCAGAATTCAGGTGAGAATTGATCAGAAGGAGCAGTTGG TGGTGGATTCTCTACTATTGCTGCCAAGAGTTCATAAAAGCTTGGCGGGTTTTGCTGATCTTCA GATTCTAAATAAGGAAATCTTCCTATTGCACATTCTAACACTGACATCCCCAAACTCCAAATGT CACTGCTGTAGTCATATGTGCTTCCACTAATCCTCTCAGGCTGTGAAGTGAAAAAAGAGACAAG TCATGATTATGTATGTATACAATACAGAAACATCAAGAAATTTGTAATGTAGATGATTTTTGGA ATGCTTTCGTACCGACATATAGTTGTAGGTTCCAACAAATGTGTCCCTCTGTCCCATGGAGCTA GCAAGACTTGCACTTACACCAAAATCTGAGATTTTCACTTCCCCTTTATGGTTTACAAGAAGGT TTGATGGCTTAATGTCTCTGTGTATGACATGTCTTTCGTTGTGTAGGTACACAAGACCTAGCAA AACCTGTTCACAAGGAATAATATAAGTAAGAGTGACCGATAAATCATAAGAATGCTTTGAATAA GCTGGTGGTGTATTTGACCTGTTTACAGACAACAGCAAGGTAAGGTTCAAGAATAGTCTTGACT TGTCTAATCACATCCGCAAGAGATCCACGGTCCATGTATTCAAGCACAAGCGAAAAGGCTCCAT TGTGATAGAAAGAATGGTAGCAAACTACTACATGTGGACATTGTGATGATGCTTGGTTTATTTT AAGCTCCTGAACAATTTGCTTACGGATTTCTTCTTGTATATTCATCTGTATGACCTGTGATTCA TAACATAAGCAAACTCAAACCCCAAGTCTACTCAAAGGCCTTAGTCACTAGCATAAAATCAAAA GAAAGAAAAACAAGTAGTTTACCTTCATAGCAAAGAATTTGCCAACCCATTTATGACGAACTAA TTGAACAACACCACCACTGCCTTTTCCGATGACTTTGACAGTCTCTAAGTCTTCAGCAGTAATT TCGAAATCAAGCTCCTTGCTATCAGATTGCTATAAATGGAAGATAAAACACATACACAAGAAAT CTCCTTTAATTCTCTGGAACATTGAGGTCTCTCATAAAACAAGATTTAGGGTTGAAAAATTTAC CCTTGATTGCTTCTCATCTGACGTCAACCTTAGCCCCTTTTGATTCAGAAGAAAATCTCCATCG TGAAATGTTCCACTCGCAGTCCTGTTTTCAAATTCAATGAAATTTCACAGAATCAATTCAAACC CAGAAACAATGGATCAAATCTAATCGATTCTTGTTTACAATCTCGCCAAACAAAACAGATCCAA GTAAAGAAAGGAGAAATCGCGAAACTTACAGGAAGGAAGAGATTGGGGATTCTTGAGCTGGAAC GGAGAGCTTAAGCTGCTTCAAGTTCGATTTGATCTTCACCATTTTTTTTCTTTGGTTTCTTCCT TGGGATTATCGCTCTCTTTCTAGGGTTTCTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.362830553

Conservation Information
Conserved circRNAs	NA
PMCS	0.362830553

			
						 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 AT5G56580_circ_g.2

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