Plant Circular RNA Database

Detail information of AT4G05020_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT4G05020_circ_g.3
					
						ID in PlantcircBase
						ath_circ_029748
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 2573231-2575338  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT4G05020						
					
						Parent gene annotation
						
							NAD(P)H dehydrogenase B2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G05020_circ_g.1 AT4G05020_circ_g.2 AT4G05020_circ_g.4 						
					
						Support reads
						9
					
						Tissues
						inflorescences
					
						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  
						
							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
						AT4G05020.1:7
AT4G05020.2:7

General Information
CircRNA Name	AT4G05020_circ_g.3
ID in PlantcircBase	ath_circ_029748
Alias	NA
Organism	Arabidpsis thaliana
Position	chr4: 2573231-2575338 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT4G05020
Parent gene annotation	NAD(P)H dehydrogenase B2
Parent gene strand	+
Alternative splicing	AT4G05020_circ_g.1 AT4G05020_circ_g.2 AT4G05020_circ_g.4
Support reads	9
Tissues	inflorescences
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	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	AT4G05020.1:7 AT4G05020.2:7

			
						 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  
						
							ACCTAGCTAAATGCTTTGACCGTATGGAAGAGTGTGAGAAGAGTCCAGAAGGTCCCATTAGGAT
GAGAGGAGAAGGTCGTCACCGTTTCCGCCCCTTCAGtggtggtggacttatagcgtattctgag
gcaaacgcatcttatggagcaaatggtggtgctgttgttgaaactggaaccaagaagaagaagg
tggtgctg

									
								

					

						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
						
							TGGTGGTGGACTTATAGCGTATTCTGAGGCAAACGCATCTTATGGAGCAAATGGTGGTGCTGTT
GTTGAAACTGGAACCAAGAAGAAGAAGGTGGTGCTGCTCGGAACTGGATGGGCTGGAACTAGTT
TCTTGAAGAATTTGAACAATTCTCAATATGAGGTTCAGATTATATCGCCTCGGAACTACTTTGC
TTTCACTCCTTTACTACCTAGTGTTACTTGTGGAACTGTTGAAGCTCGTAGTGTTGTTGAGCCT
ATTCGAAACATTGGAAGAAAGGTAATTCTGCTGTAAATATGGCTAACTCTAAATGGAAATTTTG
GTTGAAAAAATAGCTAATGCACATTCGTTTTCCTGCCTTGACAAATAGAAGAATGTTGATACTT
CTTACTTGGAGGCAGAATGTTTCAAAATTGATCCAGCTAGCAAGAAGGTTTACTGCCGATCCAA
ACAAGGCCTTAGTTCAAATGGAAAGAAAGAATTTTCTGTTGACTATGACTACCTTGTAATTGCT
ACTGGAGCTCAGTCTAACACCTTTAACATACCCGGAGTGGAGGAGAACTGTCATTTTCTGAAAG
TATGTTCTCTTGGCTCTTAATTCCTTTTCCTGCTCTACTTGGTATGCATTGATAGTTTAAAGCT
GAAAAGCATGTGAAAGTAGAGTGATCATTTGTAGGATGTTAACTTTCTGTGGCTTTAATTGGTT
TCATTATGTGCTTATAGGAGGTTGAAGATGCTCAGAGAATCCGTAAAACTGTAATTGATTCCTT
TGAGAAGGCAAGTCTACCAGAACTAAGCGATGAAGAGAGAAAGAGAATCCTGCATTTTGTGGTT
GTTGGTGGTGGGCCAACAGGTGTTGAGTTTGCCGCTGAGCTACATGATTTTGTTACTGAGGATC
TAGTCAGTCTCTATCCTAGAGCCAAGGGTTCAGTGCGAATCACGCTTCTGGAGGCCGCAGACCA
CATCCTGACCATGTGAAATTTCTTTACTCTAAAATTTTTGATCAATCGTCTCCCTATAATTTTT
GGTCAGACGATTAGAAGTTTCAGGTTTCCATAAAAACCTCGTTACTAATTCATGGAAAGCTTTT
CTTTCACAGGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATT
GATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGATATATCTGCTAAAACCAAAG
GAGGAGAGGTTTCCTCGATTCCTTATGGAATGATTGTCTGGTCAACTGGTATTGGAACTCGTCC
TGTGATAAAAGATTTTATGAAACAAATTGGTCAGGTAAAGTAATGCGCTTTAGATTTAAACTCA
CACTTTACAATTTTCAACATCTCCTAGCAAACAAATTTCAACAACTCGCTCTAAGAAATTGTCT
TTGTAATTTCAGGGTAATAGACGAGCTCTGGCAACTGATGAATGGCTTCGCGTAGAAGGAACTG
ATAATATATATGCCCTTGGTGATTGCGCAACCATTAACCAGCGCAAAGTCATGGTAATTTGACG
CTTCTATTGCTTCCCAAACTCTGGAATAATGTTTTTGGATTATAAAACAAAATTATTAGTGGTT
TCTTGTTGCAGGAAGATGTTTCTGCTATTTTTAGCAAAGCAGACAAAGACAAGTCTGGGACACT
GACTCTCAAAGAGTTCCAAGAAGCAATGGATGACATTTGTGTTAGATACCCTCAAGTGGAGCTC
TACTTGAAGAGTAAACGTATGCGTGGCATTGCAGATCTTCTTAAAGAAGCCGAAACTGATGATG
TATCTAAGAATAACATTGAACTGAAGATCGAAGAGTTCAAATCGGCTCTATCTCAGGTTGACTC
ACAAGTGAAGTTTCTTCCAGCTACTGCACAGGTAATTCGGTGGAAGTTTAGGAATTTAAGTCTT
CGTTCATCTTCAATAAATCTCATTTTTGCTGGATTCTTATCAATTAGTTATATGTGGATTTTTA
AGGTTGCTGCGCAGCAAGGTGCTTACCTAGCTAAATGCTTTGACCGTATGGAAGAGTGTGAGAA
GAGTCCAGAAGGTCCCATTAGGATGAGAGGAGAAGGTCGTCACCGTTTCCGCCCCTTCAG
						
					

			
		

Sequences
Splice junction sequence	ACCTAGCTAAATGCTTTGACCGTATGGAAGAGTGTGAGAAGAGTCCAGAAGGTCCCATTAGGAT GAGAGGAGAAGGTCGTCACCGTTTCCGCCCCTTCAGtggtggtggacttatagcgtattctgag gcaaacgcatcttatggagcaaatggtggtgctgttgttgaaactggaaccaagaagaagaagg tggtgctg
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	TGGTGGTGGACTTATAGCGTATTCTGAGGCAAACGCATCTTATGGAGCAAATGGTGGTGCTGTT GTTGAAACTGGAACCAAGAAGAAGAAGGTGGTGCTGCTCGGAACTGGATGGGCTGGAACTAGTT TCTTGAAGAATTTGAACAATTCTCAATATGAGGTTCAGATTATATCGCCTCGGAACTACTTTGC TTTCACTCCTTTACTACCTAGTGTTACTTGTGGAACTGTTGAAGCTCGTAGTGTTGTTGAGCCT ATTCGAAACATTGGAAGAAAGGTAATTCTGCTGTAAATATGGCTAACTCTAAATGGAAATTTTG GTTGAAAAAATAGCTAATGCACATTCGTTTTCCTGCCTTGACAAATAGAAGAATGTTGATACTT CTTACTTGGAGGCAGAATGTTTCAAAATTGATCCAGCTAGCAAGAAGGTTTACTGCCGATCCAA ACAAGGCCTTAGTTCAAATGGAAAGAAAGAATTTTCTGTTGACTATGACTACCTTGTAATTGCT ACTGGAGCTCAGTCTAACACCTTTAACATACCCGGAGTGGAGGAGAACTGTCATTTTCTGAAAG TATGTTCTCTTGGCTCTTAATTCCTTTTCCTGCTCTACTTGGTATGCATTGATAGTTTAAAGCT GAAAAGCATGTGAAAGTAGAGTGATCATTTGTAGGATGTTAACTTTCTGTGGCTTTAATTGGTT TCATTATGTGCTTATAGGAGGTTGAAGATGCTCAGAGAATCCGTAAAACTGTAATTGATTCCTT TGAGAAGGCAAGTCTACCAGAACTAAGCGATGAAGAGAGAAAGAGAATCCTGCATTTTGTGGTT GTTGGTGGTGGGCCAACAGGTGTTGAGTTTGCCGCTGAGCTACATGATTTTGTTACTGAGGATC TAGTCAGTCTCTATCCTAGAGCCAAGGGTTCAGTGCGAATCACGCTTCTGGAGGCCGCAGACCA CATCCTGACCATGTGAAATTTCTTTACTCTAAAATTTTTGATCAATCGTCTCCCTATAATTTTT GGTCAGACGATTAGAAGTTTCAGGTTTCCATAAAAACCTCGTTACTAATTCATGGAAAGCTTTT CTTTCACAGGTTTGACAAGAGAATCACTGAGTTTGCCGAAGAAAAGTTTAGCAGAGATGGAATT GATGTGAAACTTGGCTCGATGGTAACTAAAGTGAATGAGAAAGATATATCTGCTAAAACCAAAG GAGGAGAGGTTTCCTCGATTCCTTATGGAATGATTGTCTGGTCAACTGGTATTGGAACTCGTCC TGTGATAAAAGATTTTATGAAACAAATTGGTCAGGTAAAGTAATGCGCTTTAGATTTAAACTCA CACTTTACAATTTTCAACATCTCCTAGCAAACAAATTTCAACAACTCGCTCTAAGAAATTGTCT TTGTAATTTCAGGGTAATAGACGAGCTCTGGCAACTGATGAATGGCTTCGCGTAGAAGGAACTG ATAATATATATGCCCTTGGTGATTGCGCAACCATTAACCAGCGCAAAGTCATGGTAATTTGACG CTTCTATTGCTTCCCAAACTCTGGAATAATGTTTTTGGATTATAAAACAAAATTATTAGTGGTT TCTTGTTGCAGGAAGATGTTTCTGCTATTTTTAGCAAAGCAGACAAAGACAAGTCTGGGACACT GACTCTCAAAGAGTTCCAAGAAGCAATGGATGACATTTGTGTTAGATACCCTCAAGTGGAGCTC TACTTGAAGAGTAAACGTATGCGTGGCATTGCAGATCTTCTTAAAGAAGCCGAAACTGATGATG TATCTAAGAATAACATTGAACTGAAGATCGAAGAGTTCAAATCGGCTCTATCTCAGGTTGACTC ACAAGTGAAGTTTCTTCCAGCTACTGCACAGGTAATTCGGTGGAAGTTTAGGAATTTAAGTCTT CGTTCATCTTCAATAAATCTCATTTTTGCTGGATTCTTATCAATTAGTTATATGTGGATTTTTA AGGTTGCTGCGCAGCAAGGTGCTTACCTAGCTAAATGCTTTGACCGTATGGAAGAGTGTGAGAA GAGTCCAGAAGGTCCCATTAGGATGAGAGGAGAAGGTCGTCACCGTTTCCGCCCCTTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.178164215

Conservation Information
Conserved circRNAs	NA
PMCS	0.178164215

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							2574201-2575335(+)
						
					

						Potential amino acid sequence
						
							MFDKRITEFAEEKFSRDGIDVKLGSMVTKVNEKDISAKTKGGEVSSIPYGMIVWSTGIGTRPVI
KDFMKQIGQGNRRALATDEWLRVEGTDNIYALGDCATINQRKVMEDVSAIFSKADKDKSGTLTL
KEFQEAMDDICVRYPQVELYLKSKRMRGIADLLKEAETDDVSKNNIELKIEEFKSALSQVDSQV
KFLPATAQVAAQQGAYLAKCFDRMEECEKSPEGPIRMRGEGRHRFRPFSGGGLIAYSEANASYG
ANGGAVVETGTKKKKVVLLGTGWAGTSFLKNLNNSQYEVQIISPRNYFAFTPLLPSVTCGTVEA
RSVVEPIRNIGRKNVDTSYLEAECFKIDPASKKVYCRSKQGLSSNGKKEFSVDYDYLVIATGAQ
SNTFNIPGVEENCHFLKEVEDAQRIRKTVIDSFEKASLPELSDEERKRILHFVVVGGGPTGVEF
AAELHDFVTEDLVSLYPRAKGSVRITLLEAADHILTMFDKRITEFAEEKFSRDGIDVKLGSMVT
KVNEKDISAKTKGGEVSSIPYGMIVWSTGIGTRPVIKDFMKQIGQGNRRALATDEWLRVEGTDN
IYALGDCATINQRKVMEDVSAIFSKADKDKSGTLTLKEFQEAMDDICVRYPQVELYLKSKRMRG
IADLLKEAETDDVSKNNIELKIEEFKSALSQVDSQVKFLPATAQVAAQQGAYLAKCFDRMEECE
KSPEGPIRMRGEGRHRFRPFSGGGLIAYSEANASYGANGGAVVETGTKKKKVVLLGTGWAGTSF
LKNLNNSQYEVQIISPRNYFAFTPLLPSVTCGTVEARSVVEPIRNIGRKNVDTSYLEAECFKID
PASKKVYCRSKQGLSSNGKKEFSVDYDYLVIATGAQSNTFNIPGVEENCHFLKEVEDAQRIRKT
VIDSFEKASLPELSDEERKRILHFVVVGGGPTGVEFAAELHDFVTEDLVSLYPRAKGSVRITLL
EAADHILTMFDKRITEFAEEKFSRDGIDVKLGSMVTKVNEKDISAKTKGGEVSSIPYGMIVWST
GIGTRPVIKDFMKQIGQGNRRALATDEWLRVEGTDNIYALGDCATINQRKVMEDVSAIFSKADK
DKSGTLTLKEFQEAMDDICVRYPQVELYLKSKRMRGIADLLKEAETDDVSKNNIELKIEEFKSA
LSQVDSQVKFLPATAQVAAQQGAYLAKCFDRMEECEKSPEGPIRMRGEGRHRFRPFSGGGLIAY
SEANASYGANGGAVVETGTKKKKVVLLGTGWAGTSFLKNLNNSQYEVQIISPRNYFAFTPLLPS
VTCGTVEARSVVEPIRNIGRKNVDTSYLEAECFKIDPASKKVYCRSKQGLSSNGKKEFSVDYDY
LVIATGAQSNTFNIPGVEENCHFLKEVEDAQRIRKTVIDSFEKASLPELSDEERKRILHFVVVG
GGPTGVEFAAELHDFVTEDLVSLYPRAKGSVRITLLEAADHILTMFDKRITEFAEEKFSRDGID
VKLGSMVTKVNEKDISAKTKGGEVSSIPYGMIVWSTGIGTRPVIKDFMKQIGQGNRRALATDEW
LRVEGTDNIYALGDCATINQRKVMEDVSAIFSKADKDKSGTLTLKEFQEAMDDICVRYPQVELY
LKSKRMRGIADLLKEAETDDVSKNNIELKIEEFKSALSQVDSQVKFLPATAQVAAQQGAYLAKC
FDRMEECEKSPEGPIRMRGEGRHRFRPF(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	2574201-2575335(+)
Potential amino acid sequence	MFDKRITEFAEEKFSRDGIDVKLGSMVTKVNEKDISAKTKGGEVSSIPYGMIVWSTGIGTRPVI KDFMKQIGQGNRRALATDEWLRVEGTDNIYALGDCATINQRKVMEDVSAIFSKADKDKSGTLTL KEFQEAMDDICVRYPQVELYLKSKRMRGIADLLKEAETDDVSKNNIELKIEEFKSALSQVDSQV KFLPATAQVAAQQGAYLAKCFDRMEECEKSPEGPIRMRGEGRHRFRPFSGGGLIAYSEANASYG ANGGAVVETGTKKKKVVLLGTGWAGTSFLKNLNNSQYEVQIISPRNYFAFTPLLPSVTCGTVEA RSVVEPIRNIGRKNVDTSYLEAECFKIDPASKKVYCRSKQGLSSNGKKEFSVDYDYLVIATGAQ SNTFNIPGVEENCHFLKEVEDAQRIRKTVIDSFEKASLPELSDEERKRILHFVVVGGGPTGVEF AAELHDFVTEDLVSLYPRAKGSVRITLLEAADHILTMFDKRITEFAEEKFSRDGIDVKLGSMVT KVNEKDISAKTKGGEVSSIPYGMIVWSTGIGTRPVIKDFMKQIGQGNRRALATDEWLRVEGTDN IYALGDCATINQRKVMEDVSAIFSKADKDKSGTLTLKEFQEAMDDICVRYPQVELYLKSKRMRG IADLLKEAETDDVSKNNIELKIEEFKSALSQVDSQVKFLPATAQVAAQQGAYLAKCFDRMEECE KSPEGPIRMRGEGRHRFRPFSGGGLIAYSEANASYGANGGAVVETGTKKKKVVLLGTGWAGTSF LKNLNNSQYEVQIISPRNYFAFTPLLPSVTCGTVEARSVVEPIRNIGRKNVDTSYLEAECFKID PASKKVYCRSKQGLSSNGKKEFSVDYDYLVIATGAQSNTFNIPGVEENCHFLKEVEDAQRIRKT VIDSFEKASLPELSDEERKRILHFVVVGGGPTGVEFAAELHDFVTEDLVSLYPRAKGSVRITLL EAADHILTMFDKRITEFAEEKFSRDGIDVKLGSMVTKVNEKDISAKTKGGEVSSIPYGMIVWST GIGTRPVIKDFMKQIGQGNRRALATDEWLRVEGTDNIYALGDCATINQRKVMEDVSAIFSKADK DKSGTLTLKEFQEAMDDICVRYPQVELYLKSKRMRGIADLLKEAETDDVSKNNIELKIEEFKSA LSQVDSQVKFLPATAQVAAQQGAYLAKCFDRMEECEKSPEGPIRMRGEGRHRFRPFSGGGLIAY SEANASYGANGGAVVETGTKKKKVVLLGTGWAGTSFLKNLNNSQYEVQIISPRNYFAFTPLLPS VTCGTVEARSVVEPIRNIGRKNVDTSYLEAECFKIDPASKKVYCRSKQGLSSNGKKEFSVDYDY LVIATGAQSNTFNIPGVEENCHFLKEVEDAQRIRKTVIDSFEKASLPELSDEERKRILHFVVVG GGPTGVEFAAELHDFVTEDLVSLYPRAKGSVRITLLEAADHILTMFDKRITEFAEEKFSRDGID VKLGSMVTKVNEKDISAKTKGGEVSSIPYGMIVWSTGIGTRPVIKDFMKQIGQGNRRALATDEW LRVEGTDNIYALGDCATINQRKVMEDVSAIFSKADKDKSGTLTLKEFQEAMDDICVRYPQVELY LKSKRMRGIADLLKEAETDDVSKNNIELKIEEFKSALSQVDSQVKFLPATAQVAAQQGAYLAKC FDRMEECEKSPEGPIRMRGEGRHRFRPF(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT4G05020_circ_g.3

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