Plant Circular RNA Database

Detail information of AT3G20720_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G20720_circ_g.1
					
						ID in PlantcircBase
						ath_circ_023004
					
						Alias
						3:7240691-7243400
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 7240691-7243400  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G20720						
					
						Parent gene annotation
						
							Amino-terminal region of chorein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G20720_circ_g.2 AT3G20720_circ_g.3 AT3G20720_circ_g.4 AT3G20720_circ_g.5 AT3G20720_circ_g.6 AT3G20720_circ_g.7 						
					
						Support reads
						3
					
						Tissues
						root
					
						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
						AT3G20720.2:11
AT3G20720.1:11

General Information
CircRNA Name	AT3G20720_circ_g.1
ID in PlantcircBase	ath_circ_023004
Alias	3:7240691-7243400
Organism	Arabidpsis thaliana
Position	chr3: 7240691-7243400 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G20720
Parent gene annotation	Amino-terminal region of chorein
Parent gene strand	+
Alternative splicing	AT3G20720_circ_g.2 AT3G20720_circ_g.3 AT3G20720_circ_g.4 AT3G20720_circ_g.5 AT3G20720_circ_g.6 AT3G20720_circ_g.7
Support reads	3
Tissues	root
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	AT3G20720.2:11 AT3G20720.1:11

			
						 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  
						
							ATCTGACGTGACTAGGCATATTATACTTGCAGGCCTGTGTTTCAGACGGAGAATCAGCTAACTA
TTTAACTAAGATTTTGATTGGTGGGCTATTTTTAAGcttccgtatgtcagtaatgtacaaacag
aacccatagttgtgcaaatcgataaacttgatcttgttcttgaagaaaatcctgatgccgatgt
gacaaagg

									
								

					

						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: 911
Transcript exons: 7240691-7240800,7240895-7240949,7241249-7241337,7241585-
7241651,7241727-7241789,7241999-7242166,7242282-7242375,
7242460-7242539,7242630-7242702,7242808-7242851,7243333-
7243400
CTTCCGTATGTCAGTAATGTACAAACAGAACCCATAGTTGTGCAAATCGATAAACTTGATCTTG
TTCTTGAAGAAAATCCTGATGCCGATGTGACAAAGGGTCCAAGCAGTAGTCAGTCTCCAACCGC
CTCTGCAAAAAGTAATGGTTATGGATTCGCCGACAAGATTGCAGATGGAATGACTTTACAAGTT
AAGGTGGTCAATCTTCTTCTTGAAACTGGAGGTGGTGCCAACCGTGAAGGAGGGGCAGCCTGGG
CTGCTCCGCTGGCATCTATTACAATTCGTAACCTTGTTCTGTACACCACTAATGAGAGTTGGAA
GGTTGTAAATCTGAAAGAAGCAAGGGACTTCTCTACTAACACAGGATTTATTTATTTGTTTAAG
AAACTTGAATGGGAAGCTTTATCAATTGATCTTCTACCACATCCTGATATGTTCACTGAAGCTA
ATTTAGCCCGGTCTGAAGAAGCAAATCTCAGAGATGAGGATGGTGCAAAACGAGTATTCTTTGG
CGGAGAACGCTTTTTAGAAGGAATTTCTGGCCAAGCATATATCACGGTTCAGAGAACAGCACTA
AACAGTCCACTTGGGCTTGAAGTCCAGTTGCACATTCCAGAAGCTGTTTGTCCAGCCTTAAGTG
AACCAGGGTTGCGTGCTCTTCTCCGCTTTCTAACTGGAATGTACTTATGCCTAAACCGAGGAGA
TGTGGATCCAAAATCTCAGCAGTCTGCTGAAGCAGCTGGACGTTCTCTTGTCTCCGTTCTTGTG
GATCATGTATTTCTTTGCATTAAAGATGCTGAATTCCAACTGGAACTGCTGATGCAATCACTCC
TTTTTTCTCGGGCCTGTGTTTCAGACGGAGAATCAGCTAACTATTTAACTAAGATTTTGATTGG
TGGGCTATTTTTAAG
						
					

						Genomic sequence
						
							CTTCCGTATGTCAGTAATGTACAAACAGAACCCATAGTTGTGCAAATCGATAAACTTGATCTTG
TTCTTGAAGAAAATCCTGATGCCGATGTGACAAAGGGTCCAAGCAGGTACTGAGACCTTACTTC
CATCTCTTTTGCTTCTACCCAGTCTTGCTTAACTTCCCAGATTATTTATTGAGTCTTTCATTTT
TTTCCCCTTCAGTAGTCAGTCTCCAACCGCCTCTGCAAAAAGTAATGGTTATGGATTCGCCGAC
AAGGTGAGATATCTCAGCTACTTCGTCAATATTTCAAAAAATTATTCCATAAAGCACTGAGGCA
TCAGTAGGTTTCTACTTAGTGGTTCAAATGGTCTAGCCTACTCTAGTTAGGTAGGTTGTTTTGA
GCTTGGTTCATTATTGGTCTTTCTTACACATGTGGTTGAAGACTAGCTAAGTATATAATCCTTT
TCTTTTGTCGAAGCAATGATGTGAATTTGCCACCTTTCTTTTGATTCATATAGTTATATTCATT
CTGGTATTGAGGTACTTGTTGAATTATATTTTATCACGTTGATCAGATTGCAGATGGAATGACT
TTACAAGTTAAGGTGGTCAATCTTCTTCTTGAAACTGGAGGTGGTGCCAACCGTGAAGGAGGGG
CAGCCTGGTAAGTTACTTTTACTGCATACATTGTCTAGATATATGGGATTTAGCTTCATCTCTA
TGGGGTGTTGGAATCTCGTTACGTAGGGTTCTTTGATACATATTACTGATTAGATTATAATTTA
TGTCTTTCACACTCCTACCTGACTGTAATTTCATTTTCGTTGTCCTCTACTCGGGGATTAAATC
TAAATGCCTTGGATTGTTACTTATGTATATAGTATATCTAAGCTTTTATACTTTGTATCTAGGG
CTGCTCCGCTGGCATCTATTACAATTCGTAACCTTGTTCTGTACACCACTAATGAGAGTTGGAA
GGTGAGATTTGCGAGCATGATGTAAGAAAATTGTTTTCTGGAAGAATTAGTACTCTGAATGAAT
TTTCATTTACAGGTTGTAAATCTGAAAGAAGCAAGGGACTTCTCTACTAACACAGGATTTATTT
ATTTGTTTAAGGTATTGATGCCACTCTTTAGCTAGTTTTCCTTGATACATATTCTTGATGGATT
AAGCATTCCATCTTAGCGAAAACAGTGCCATATATCTATCTATTTCCATGGCGCTTGCTTTTAA
AAGTTCTTTATTCCTACCTGATAATCTTCTTTGAAGATAATATTCTTGATGTGATTTTTTTCTA
CATGTGATGCATATCCTTTCGTTATCAGAAACTTGAATGGGAAGCTTTATCAATTGATCTTCTA
CCACATCCTGATATGTTCACTGAAGCTAATTTAGCCCGGTCTGAAGAAGCAAATCTCAGAGATG
AGGATGGTGCAAAACGAGTATTCTTTGGCGGAGAACGCTTTTTAGAAGGAATTTCTGGCCAAGC
ATATGTAAACATTTGTTTTCGTTTCTCTTTTACTTGTACATATGATATTAAAGCGGGATGTAAT
GCATTAGATGTTTTGGTACCTAATTCATTAGCCTTGATGGTGGCCTCTTGTTCAGATCACGGTT
CAGAGAACAGCACTAAACAGTCCACTTGGGCTTGAAGTCCAGTTGCACATTCCAGAAGCTGTTT
GTCCAGCCTTAAGTGAACCAGGTTTTTCAGATATATTCTCTTAGTTTTCAGATAGCAGGTTGAT
GCAGATGGATAACTAAGACTACTCGTTATTCTTTGGAATAGGGTTGCGTGCTCTTCTCCGCTTT
CTAACTGGAATGTACTTATGCCTAAACCGAGGAGATGTGGATCCAAAATCTCAGCAGGTCTTAT
ATTTCTCACTCACAGTTGATCTTGTTAAAGGAACGGTTTACATGAATTTTTGTTCTCACTCTTT
CATGGTATGCCTATACCAGTCTGCTGAAGCAGCTGGACGTTCTCTTGTCTCCGTTCTTGTGGAT
CATGTATTTCTTTGCATTAAAGATGCTGGTTAGTTAATTTGACTCACCACATGTTAGCTAAAGA
GTGCAGTCTTGCATGGAACCATTACTCTTGTATCCTGGGTTTAACATTTACGGCCTTTCTACGT
TTCAGAATTCCAACTGGAACTGCTGATGCAATCACTCCTTTTTTCTCGGGTATGTTCTCACTGA
TTCTTAAATTTCGATATAGAAACAATTCTTGCATTCACATCTGCACCATGGAACTTTCTTAGTT
CTGGGAAATCGTAAACCAAATTTCAGGAACTCTAGTTCGTATGATTTAGTTCTAAGTGTGTATA
AGTTTAGTACGAGTTGGAACAAGACGCACACATTATCTATAATAAAATCGGATCTCGGGCAATG
TGAGGAATTCATAAAGAAATTAGGGATTTGGACCAGATTTTCTCCCTCGTGAAAATGGTTAATA
AACCACTCTAATATAATGAATGCATATAATGGGTTTGACCACTCACTTGGTTGTCTCAAGCTCT
ATATATCTCTTCCCAGTCATGTTATGTTCACTAGAAAGTTGTTTGCCCTCAGATGATTTAATGC
ACTTCAGTACGCCAAGCATCTTGAATAAAATCTAGTTGTATGGTGCTGAAATCTGACGTGACTA
GGCATATTATACTTGCAGGCCTGTGTTTCAGACGGAGAATCAGCTAACTATTTAACTAAGATTT
TGATTGGTGGGCTATTTTTAAG
						
					

			
		

Sequences
Splice junction sequence	ATCTGACGTGACTAGGCATATTATACTTGCAGGCCTGTGTTTCAGACGGAGAATCAGCTAACTA TTTAACTAAGATTTTGATTGGTGGGCTATTTTTAAGcttccgtatgtcagtaatgtacaaacag aacccatagttgtgcaaatcgataaacttgatcttgttcttgaagaaaatcctgatgccgatgt gacaaagg
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: 911 Transcript exons: 7240691-7240800,7240895-7240949,7241249-7241337,7241585- 7241651,7241727-7241789,7241999-7242166,7242282-7242375, 7242460-7242539,7242630-7242702,7242808-7242851,7243333- 7243400 CTTCCGTATGTCAGTAATGTACAAACAGAACCCATAGTTGTGCAAATCGATAAACTTGATCTTG TTCTTGAAGAAAATCCTGATGCCGATGTGACAAAGGGTCCAAGCAGTAGTCAGTCTCCAACCGC CTCTGCAAAAAGTAATGGTTATGGATTCGCCGACAAGATTGCAGATGGAATGACTTTACAAGTT AAGGTGGTCAATCTTCTTCTTGAAACTGGAGGTGGTGCCAACCGTGAAGGAGGGGCAGCCTGGG CTGCTCCGCTGGCATCTATTACAATTCGTAACCTTGTTCTGTACACCACTAATGAGAGTTGGAA GGTTGTAAATCTGAAAGAAGCAAGGGACTTCTCTACTAACACAGGATTTATTTATTTGTTTAAG AAACTTGAATGGGAAGCTTTATCAATTGATCTTCTACCACATCCTGATATGTTCACTGAAGCTA ATTTAGCCCGGTCTGAAGAAGCAAATCTCAGAGATGAGGATGGTGCAAAACGAGTATTCTTTGG CGGAGAACGCTTTTTAGAAGGAATTTCTGGCCAAGCATATATCACGGTTCAGAGAACAGCACTA AACAGTCCACTTGGGCTTGAAGTCCAGTTGCACATTCCAGAAGCTGTTTGTCCAGCCTTAAGTG AACCAGGGTTGCGTGCTCTTCTCCGCTTTCTAACTGGAATGTACTTATGCCTAAACCGAGGAGA TGTGGATCCAAAATCTCAGCAGTCTGCTGAAGCAGCTGGACGTTCTCTTGTCTCCGTTCTTGTG GATCATGTATTTCTTTGCATTAAAGATGCTGAATTCCAACTGGAACTGCTGATGCAATCACTCC TTTTTTCTCGGGCCTGTGTTTCAGACGGAGAATCAGCTAACTATTTAACTAAGATTTTGATTGG TGGGCTATTTTTAAG
Genomic sequence	CTTCCGTATGTCAGTAATGTACAAACAGAACCCATAGTTGTGCAAATCGATAAACTTGATCTTG TTCTTGAAGAAAATCCTGATGCCGATGTGACAAAGGGTCCAAGCAGGTACTGAGACCTTACTTC CATCTCTTTTGCTTCTACCCAGTCTTGCTTAACTTCCCAGATTATTTATTGAGTCTTTCATTTT TTTCCCCTTCAGTAGTCAGTCTCCAACCGCCTCTGCAAAAAGTAATGGTTATGGATTCGCCGAC AAGGTGAGATATCTCAGCTACTTCGTCAATATTTCAAAAAATTATTCCATAAAGCACTGAGGCA TCAGTAGGTTTCTACTTAGTGGTTCAAATGGTCTAGCCTACTCTAGTTAGGTAGGTTGTTTTGA GCTTGGTTCATTATTGGTCTTTCTTACACATGTGGTTGAAGACTAGCTAAGTATATAATCCTTT TCTTTTGTCGAAGCAATGATGTGAATTTGCCACCTTTCTTTTGATTCATATAGTTATATTCATT CTGGTATTGAGGTACTTGTTGAATTATATTTTATCACGTTGATCAGATTGCAGATGGAATGACT TTACAAGTTAAGGTGGTCAATCTTCTTCTTGAAACTGGAGGTGGTGCCAACCGTGAAGGAGGGG CAGCCTGGTAAGTTACTTTTACTGCATACATTGTCTAGATATATGGGATTTAGCTTCATCTCTA TGGGGTGTTGGAATCTCGTTACGTAGGGTTCTTTGATACATATTACTGATTAGATTATAATTTA TGTCTTTCACACTCCTACCTGACTGTAATTTCATTTTCGTTGTCCTCTACTCGGGGATTAAATC TAAATGCCTTGGATTGTTACTTATGTATATAGTATATCTAAGCTTTTATACTTTGTATCTAGGG CTGCTCCGCTGGCATCTATTACAATTCGTAACCTTGTTCTGTACACCACTAATGAGAGTTGGAA GGTGAGATTTGCGAGCATGATGTAAGAAAATTGTTTTCTGGAAGAATTAGTACTCTGAATGAAT TTTCATTTACAGGTTGTAAATCTGAAAGAAGCAAGGGACTTCTCTACTAACACAGGATTTATTT ATTTGTTTAAGGTATTGATGCCACTCTTTAGCTAGTTTTCCTTGATACATATTCTTGATGGATT AAGCATTCCATCTTAGCGAAAACAGTGCCATATATCTATCTATTTCCATGGCGCTTGCTTTTAA AAGTTCTTTATTCCTACCTGATAATCTTCTTTGAAGATAATATTCTTGATGTGATTTTTTTCTA CATGTGATGCATATCCTTTCGTTATCAGAAACTTGAATGGGAAGCTTTATCAATTGATCTTCTA CCACATCCTGATATGTTCACTGAAGCTAATTTAGCCCGGTCTGAAGAAGCAAATCTCAGAGATG AGGATGGTGCAAAACGAGTATTCTTTGGCGGAGAACGCTTTTTAGAAGGAATTTCTGGCCAAGC ATATGTAAACATTTGTTTTCGTTTCTCTTTTACTTGTACATATGATATTAAAGCGGGATGTAAT GCATTAGATGTTTTGGTACCTAATTCATTAGCCTTGATGGTGGCCTCTTGTTCAGATCACGGTT CAGAGAACAGCACTAAACAGTCCACTTGGGCTTGAAGTCCAGTTGCACATTCCAGAAGCTGTTT GTCCAGCCTTAAGTGAACCAGGTTTTTCAGATATATTCTCTTAGTTTTCAGATAGCAGGTTGAT GCAGATGGATAACTAAGACTACTCGTTATTCTTTGGAATAGGGTTGCGTGCTCTTCTCCGCTTT CTAACTGGAATGTACTTATGCCTAAACCGAGGAGATGTGGATCCAAAATCTCAGCAGGTCTTAT ATTTCTCACTCACAGTTGATCTTGTTAAAGGAACGGTTTACATGAATTTTTGTTCTCACTCTTT CATGGTATGCCTATACCAGTCTGCTGAAGCAGCTGGACGTTCTCTTGTCTCCGTTCTTGTGGAT CATGTATTTCTTTGCATTAAAGATGCTGGTTAGTTAATTTGACTCACCACATGTTAGCTAAAGA GTGCAGTCTTGCATGGAACCATTACTCTTGTATCCTGGGTTTAACATTTACGGCCTTTCTACGT TTCAGAATTCCAACTGGAACTGCTGATGCAATCACTCCTTTTTTCTCGGGTATGTTCTCACTGA TTCTTAAATTTCGATATAGAAACAATTCTTGCATTCACATCTGCACCATGGAACTTTCTTAGTT CTGGGAAATCGTAAACCAAATTTCAGGAACTCTAGTTCGTATGATTTAGTTCTAAGTGTGTATA AGTTTAGTACGAGTTGGAACAAGACGCACACATTATCTATAATAAAATCGGATCTCGGGCAATG TGAGGAATTCATAAAGAAATTAGGGATTTGGACCAGATTTTCTCCCTCGTGAAAATGGTTAATA AACCACTCTAATATAATGAATGCATATAATGGGTTTGACCACTCACTTGGTTGTCTCAAGCTCT ATATATCTCTTCCCAGTCATGTTATGTTCACTAGAAAGTTGTTTGCCCTCAGATGATTTAATGC ACTTCAGTACGCCAAGCATCTTGAATAAAATCTAGTTGTATGGTGCTGAAATCTGACGTGACTA GGCATATTATACTTGCAGGCCTGTGTTTCAGACGGAGAATCAGCTAACTATTTAACTAAGATTT TGATTGGTGGGCTATTTTTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.202317356

Conservation Information
Conserved circRNAs	NA
PMCS	0.202317356

			
						 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 AT3G20720_circ_g.1

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